<?xml version="1.0" encoding="US-ASCII"?>
<!-- DFIN New ActiveDisclosure (SM) XBRL Linkbase Document - http://www.dfinsolutions.com/ -->
<!-- Creation Date :2023-03-06T20:44:54.3045+00:00 -->
<!-- Copyright (c) 2023 Donnelly Financial Solutions, Inc. All Rights Reserved. -->
<link:linkbase xsi:schemaLocation="http://www.xbrl.org/2003/linkbase http://www.xbrl.org/2003/xbrl-linkbase-2003-12-31.xsd" xmlns:link="http://www.xbrl.org/2003/linkbase" xmlns:xbrldt="http://xbrl.org/2005/xbrldt" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/all" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#all" xlink:type="simple"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-default" xlink:type="simple"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#dimension-domain" xlink:type="simple"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/domain-member" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#domain-member" xlink:type="simple"/>
  <link:arcroleRef arcroleURI="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:href="http://www.xbrl.org/2005/xbrldt-2005.xsd#hypercube-dimension" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_StatementConsolidatedStatementsOfStockholdersEquityDeficit" xlink:href="mcrb-20221231.xsd#Role_StatementConsolidatedStatementsOfStockholdersEquityDeficit" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/StatementCondensedConsolidatedStatementOfStockholdersEquityDeficitParenthetical" xlink:href="mcrb-20221231.xsd#StatementCondensedConsolidatedStatementOfStockholdersEquityDeficitParenthetical" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsTables" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwardsTables" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureNatureOfBusinessAndBasisOfPresentationAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureNatureOfBusinessAndBasisOfPresentationAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesScheduleOfPropertyAndEquipmentEstimatedUsefulLifeDetails" xlink:href="mcrb-20221231.xsd#DisclosureSummaryOfSignificantAccountingPoliciesScheduleOfPropertyAndEquipmentEstimatedUsefulLifeDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureFairValueOfFinancialAssetsAndLiabilitiesSummaryOfFairValueHierarchyForAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasisDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureFairValueOfFinancialAssetsAndLiabilitiesSummaryOfFairValueHierarchyForAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasisDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureInvestmentsScheduleOfInvestmentsBySecurityTypeDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureInvestmentsScheduleOfInvestmentsBySecurityTypeDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureLeasesAdditionalInformationDetails" xlink:href="mcrb-20221231.xsd#DisclosureLeasesAdditionalInformationDetails" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureRestructuringAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureRestructuringAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureNotesPayableAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureNotesPayableAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwardsAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwards2012StockIncentivePlanAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwards2012StockIncentivePlanAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwards2015IncentiveAwardPlanAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwards2015IncentiveAwardPlanAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwards2015EmployeeStockPurchasePlanAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwards2015EmployeeStockPurchasePlanAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwards2022EmploymentInducementAwardPlanAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwards2022EmploymentInducementAwardPlanAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsStockOptionsAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwardsStockOptionsAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsSummaryOfRestrictedStockActivityDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwardsSummaryOfRestrictedStockActivityDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsRestrictedStockUnitsAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwardsRestrictedStockUnitsAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsSummaryOfEstimatedFairValueOfEmployeeStockOptionsDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwardsSummaryOfEstimatedFairValueOfEmployeeStockOptionsDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsSummaryOfStockBasedCompensationExpenseDetail" xlink:href="mcrb-20221231.xsd#DisclosureCommonStockAndStockbasedAwardsSummaryOfStockBasedCompensationExpenseDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureCollaborationRevenueAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureCollaborationRevenueAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureCollaborationRevenueChangesInContractLiabilitiesDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureCollaborationRevenueChangesInContractLiabilitiesDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureNetLossPerShareSummaryOfPotentialCommonSharesExcludedFromCalculationOfDilutedNetLossPerShareDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureNetLossPerShareSummaryOfPotentialCommonSharesExcludedFromCalculationOfDilutedNetLossPerShareDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureIncomeTaxesAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureIncomeTaxesAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail" xlink:href="mcrb-20221231.xsd#Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail" xlink:type="simple"/>
  <link:roleRef roleURI="http://fasb.org/us-gaap/role/eedm/ExtensibleEnumerationLists" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-roles-2022.xsd#eedm" xlink:type="simple"/>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_StatementConsolidatedStatementsOfStockholdersEquityDeficit">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_CumulativeEffectPeriodOfAdoptionAxis" xlink:label="srt_CumulativeEffectPeriodOfAdoptionAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_CumulativeEffectPeriodOfAdoptionDomain" xlink:label="srt_CumulativeEffectPeriodOfAdoptionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_CumulativeEffectPeriodOfAdoptionDomain" xlink:label="srt_CumulativeEffectPeriodOfAdoptionDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_CumulativeEffectPeriodOfAdoptionAdjustmentMember" xlink:label="srt_CumulativeEffectPeriodOfAdoptionAdjustmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockholdersEquity" xlink:label="us-gaap_StockholdersEquity"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockSharesOutstanding" xlink:label="us-gaap_CommonStockSharesOutstanding"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdditionalPaidInCapitalMember" xlink:label="us-gaap_AdditionalPaidInCapitalMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodValueNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodValueNewIssues"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccumulatedOtherComprehensiveIncomeMember" xlink:label="us-gaap_AccumulatedOtherComprehensiveIncomeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RetainedEarningsMember" xlink:label="us-gaap_RetainedEarningsMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_StockIssuedDuringPeriodToRelatedPartyValue" xlink:label="mcrb_StockIssuedDuringPeriodToRelatedPartyValue"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_StockIssuedDuringPeriodToRelatedPartyShares" xlink:label="mcrb_StockIssuedDuringPeriodToRelatedPartyShares"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_StockIssuedDuringPeriodValueAtMarketEquityOfferings" xlink:label="mcrb_StockIssuedDuringPeriodValueAtMarketEquityOfferings"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_StockIssuedDuringPeriodSharesAtMarketEquityOfferings" xlink:label="mcrb_StockIssuedDuringPeriodSharesAtMarketEquityOfferings"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" xlink:label="us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" xlink:label="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedStockValueSharesIssuedNetOfTaxWithholdings" xlink:label="us-gaap_RestrictedStockValueSharesIssuedNetOfTaxWithholdings"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedStockSharesIssuedNetOfSharesForTaxWithholdings" xlink:label="us-gaap_RestrictedStockSharesIssuedNetOfSharesForTaxWithholdings"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_StockRepurchasedDuringPeriodValueEmployeeTaxWithholdings" xlink:label="mcrb_StockRepurchasedDuringPeriodValueEmployeeTaxWithholdings"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_StockRepurchasedDuringPeriodShareEmployeeTaxWithholdings" xlink:label="mcrb_StockRepurchasedDuringPeriodShareEmployeeTaxWithholdings"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan" xlink:label="us-gaap_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" xlink:label="us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" xlink:label="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherComprehensiveIncomeLossAvailableForSaleSecuritiesAdjustmentBeforeReclassificationAdjustmentsNetOfTax" xlink:label="us-gaap_OtherComprehensiveIncomeLossAvailableForSaleSecuritiesAdjustmentBeforeReclassificationAdjustmentsNetOfTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingStandardsUpdateExtensibleList" xlink:label="us-gaap_AccountingStandardsUpdateExtensibleList"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_StatementEquityComponentsAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_CumulativeEffectPeriodOfAdoptionAxis" xlink:to="srt_CumulativeEffectPeriodOfAdoptionDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_CumulativeEffectPeriodOfAdoptionAxis" xlink:to="srt_CumulativeEffectPeriodOfAdoptionDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_CumulativeEffectPeriodOfAdoptionDomain" xlink:to="srt_CumulativeEffectPeriodOfAdoptionAdjustmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockholdersEquity" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="srt_CumulativeEffectPeriodOfAdoptionAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_CommonStockSharesOutstanding" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_AdditionalPaidInCapitalMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueNewIssues" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_AccumulatedOtherComprehensiveIncomeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_RetainedEarningsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="mcrb_StockIssuedDuringPeriodToRelatedPartyValue" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="mcrb_StockIssuedDuringPeriodToRelatedPartyShares" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="mcrb_StockIssuedDuringPeriodValueAtMarketEquityOfferings" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="mcrb_StockIssuedDuringPeriodSharesAtMarketEquityOfferings" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueStockOptionsExercised" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="9" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesStockOptionsExercised" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="10" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_RestrictedStockValueSharesIssuedNetOfTaxWithholdings" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="11" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_RestrictedStockSharesIssuedNetOfSharesForTaxWithholdings" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="12" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="mcrb_StockRepurchasedDuringPeriodValueEmployeeTaxWithholdings" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="13" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="mcrb_StockRepurchasedDuringPeriodShareEmployeeTaxWithholdings" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="14" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodValueEmployeeStockPurchasePlan" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="15" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="16" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AdjustmentsToAdditionalPaidInCapitalSharebasedCompensationRequisiteServicePeriodRecognitionValue" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="17" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_OtherComprehensiveIncomeLossAvailableForSaleSecuritiesAdjustmentBeforeReclassificationAdjustmentsNetOfTax" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="18" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_NetIncomeLoss" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="20" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_AccountingStandardsUpdateExtensibleList" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/StatementCondensedConsolidatedStatementOfStockholdersEquityDeficitParenthetical">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementLineItems" xlink:label="us-gaap_StatementLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementTable" xlink:label="us-gaap_StatementTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransactionTypeAxis" xlink:label="us-gaap_TransactionTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IPOMember" xlink:label="us-gaap_IPOMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransactionDomain" xlink:label="us-gaap_TransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransactionDomain" xlink:label="us-gaap_TransactionDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SecuritiesPurchaseAgreementMember" xlink:label="mcrb_SecuritiesPurchaseAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsOfStockIssuanceCosts" xlink:label="us-gaap_PaymentsOfStockIssuanceCosts"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MarketEquityOfferingMember" xlink:label="mcrb_MarketEquityOfferingMember"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_StatementTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_TransactionTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_IPOMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TransactionTypeAxis" xlink:to="us-gaap_TransactionDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_TransactionTypeAxis" xlink:to="us-gaap_TransactionDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransactionDomain" xlink:to="mcrb_SecuritiesPurchaseAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_StatementLineItems" xlink:to="us-gaap_PaymentsOfStockIssuanceCosts" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_StatementTable" xlink:to="us-gaap_SubsidiarySaleOfStockAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="mcrb_MarketEquityOfferingMember" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsTables">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockLineItems" xlink:label="us-gaap_SubsidiarySaleOfStockLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiaryOrEquityMethodInvesteeSaleOfStockBySubsidiaryOrEquityInvesteeTable" xlink:label="us-gaap_SubsidiaryOrEquityMethodInvesteeSaleOfStockBySubsidiaryOrEquityInvesteeTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OptionIndexedToIssuersEquityTypeAxis" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockMember" xlink:label="us-gaap_EmployeeStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OptionIndexedToIssuersEquityTypeDomain" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OptionIndexedToIssuersEquityTypeDomain" xlink:label="us-gaap_OptionIndexedToIssuersEquityTypeDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" xlink:label="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockOptionMember" xlink:label="us-gaap_EmployeeStockOptionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfSharebasedCompensationRestrictedStockAndRestrictedStockUnitsActivityTableTextBlock" xlink:label="us-gaap_ScheduleOfSharebasedCompensationRestrictedStockAndRestrictedStockUnitsActivityTableTextBlock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock" xlink:label="us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_SubsidiarySaleOfStockLineItems" xlink:to="us-gaap_SubsidiaryOrEquityMethodInvesteeSaleOfStockBySubsidiaryOrEquityInvesteeTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_SubsidiaryOrEquityMethodInvesteeSaleOfStockBySubsidiaryOrEquityInvesteeTable" xlink:to="us-gaap_OptionIndexedToIssuersEquityTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_EmployeeStockMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_OptionIndexedToIssuersEquityTypeAxis" xlink:to="us-gaap_OptionIndexedToIssuersEquityTypeDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_OptionIndexedToIssuersEquityTypeAxis" xlink:to="us-gaap_OptionIndexedToIssuersEquityTypeDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SubsidiarySaleOfStockLineItems" xlink:to="us-gaap_DisclosureOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTextBlock" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OptionIndexedToIssuersEquityTypeDomain" xlink:to="us-gaap_EmployeeStockOptionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_SubsidiaryOrEquityMethodInvesteeSaleOfStockBySubsidiaryOrEquityInvesteeTable" xlink:to="us-gaap_SubsidiarySaleOfStockAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SubsidiarySaleOfStockLineItems" xlink:to="us-gaap_ScheduleOfSharebasedCompensationRestrictedStockAndRestrictedStockUnitsActivityTableTextBlock" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SubsidiarySaleOfStockLineItems" xlink:to="us-gaap_ScheduleOfShareBasedPaymentAwardStockOptionsValuationAssumptionsTableTextBlock" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SubsidiarySaleOfStockLineItems" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTextBlock" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureNatureOfBusinessAndBasisOfPresentationAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:label="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NatureOfBusinessAndBasisOfPresentationTable" xlink:label="mcrb_NatureOfBusinessAndBasisOfPresentationTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsequentEventTypeDomain" xlink:label="us-gaap_SubsequentEventTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsequentEventMember" xlink:label="us-gaap_SubsequentEventMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfArrangementAxis" xlink:label="us-gaap_TypeOfArrangementAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsequentEventTypeAxis" xlink:label="us-gaap_SubsequentEventTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwentyTwentyOneLicenseAgreementMember" xlink:label="mcrb_TwentyTwentyOneLicenseAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_EntityIncorporationMonthAndYearOfIncorporation" xlink:label="mcrb_EntityIncorporationMonthAndYearOfIncorporation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsequentEventTypeDomain" xlink:label="us-gaap_SubsequentEventTypeDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/dei/2022/dei-2022.xsd#dei_EntityIncorporationStateCountryCode" xlink:label="dei_EntityIncorporationStateCountryCode"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RetainedEarningsAccumulatedDeficit" xlink:label="us-gaap_RetainedEarningsAccumulatedDeficit"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CashCashEquivalentsAndShortAndLongTermInvestments" xlink:label="mcrb_CashCashEquivalentsAndShortAndLongTermInvestments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromNotesPayable" xlink:label="us-gaap_ProceedsFromNotesPayable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetIncomeLoss" xlink:label="us-gaap_NetIncomeLoss"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_NetCashProvidedByUsedInOperatingActivities" xlink:label="us-gaap_NetCashProvidedByUsedInOperatingActivities"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MilestonesPayments" xlink:label="mcrb_MilestonesPayments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LineOfCreditFacilityCurrentBorrowingCapacity" xlink:label="us-gaap_LineOfCreditFacilityCurrentBorrowingCapacity"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="mcrb_NatureOfBusinessAndBasisOfPresentationTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SubsequentEventTypeDomain" xlink:to="us-gaap_SubsequentEventMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationTable" xlink:to="us-gaap_SubsequentEventTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="mcrb_TwentyTwentyOneLicenseAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="mcrb_EntityIncorporationMonthAndYearOfIncorporation" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_SubsequentEventTypeAxis" xlink:to="us-gaap_SubsequentEventTypeDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_SubsequentEventTypeAxis" xlink:to="us-gaap_SubsequentEventTypeDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationTable" xlink:to="us-gaap_TypeOfArrangementAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="dei_EntityIncorporationStateCountryCode" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="us-gaap_RetainedEarningsAccumulatedDeficit" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="mcrb_CashCashEquivalentsAndShortAndLongTermInvestments" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="us-gaap_ProceedsFromNotesPayable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="us-gaap_NetIncomeLoss" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="us-gaap_NetCashProvidedByUsedInOperatingActivities" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="mcrb_MilestonesPayments" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_NatureOfBusinessAndBasisOfPresentationLineItems" xlink:to="us-gaap_LineOfCreditFacilityCurrentBorrowingCapacity" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureSummaryOfSignificantAccountingPoliciesAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AccountingPoliciesLineItems" xlink:label="mcrb_AccountingPoliciesLineItems"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AccountingPoliciesTable" xlink:label="mcrb_AccountingPoliciesTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RestatementAxis" xlink:label="srt_RestatementAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RestatementDomain" xlink:label="srt_RestatementDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RestatementDomain" xlink:label="srt_RestatementDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CashEquivalentsOriginalMaturityMaximumPeriod" xlink:label="mcrb_CashEquivalentsOriginalMaturityMaximumPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfAdoptionMember" xlink:label="us-gaap_TypeOfAdoptionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingStandardsUpdate201409Member" xlink:label="us-gaap_AccountingStandardsUpdate201409Member"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RevisionOfPriorPeriodAccountingStandardsUpdateAdjustmentMember" xlink:label="srt_RevisionOfPriorPeriodAccountingStandardsUpdateAdjustmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:label="us-gaap_PropertyPlantAndEquipmentByTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:label="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfAdoptionMember" xlink:label="us-gaap_TypeOfAdoptionMember_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:label="us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:label="us-gaap_PropertyPlantAndEquipmentTypeDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LaboratoryEquipmentMember" xlink:label="mcrb_LaboratoryEquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedInvestmentsNoncurrent" xlink:label="us-gaap_RestrictedInvestmentsNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingStandardsUpdate201602Member" xlink:label="us-gaap_AccountingStandardsUpdate201602Member"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_FurnitureAndOfficeEquipmentMember" xlink:label="mcrb_FurnitureAndOfficeEquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedCashNoncurrent" xlink:label="us-gaap_RestrictedCashNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingStandardsUpdate201818Member" xlink:label="us-gaap_AccountingStandardsUpdate201818Member"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherThanTemporaryImpairmentLossDebtSecuritiesAvailableForSale" xlink:label="us-gaap_OtherThanTemporaryImpairmentLossDebtSecuritiesAvailableForSale"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ImpairmentOfLongLivedAssetsHeldForUse" xlink:label="us-gaap_ImpairmentOfLongLivedAssetsHeldForUse"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_RevenueRecognizedRelatedToSalesBasedRoyalties" xlink:label="mcrb_RevenueRecognizedRelatedToSalesBasedRoyalties"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MinimumPercentageOfLikelihoodOfTaxBenefitBeingRealizedUponSettlement" xlink:label="mcrb_MinimumPercentageOfLikelihoodOfTaxBenefitBeingRealizedUponSettlement"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="mcrb_AccountingPoliciesLineItems" xlink:to="mcrb_AccountingPoliciesTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RestatementAxis" xlink:to="srt_RestatementDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_RestatementAxis" xlink:to="srt_RestatementDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_AccountingPoliciesLineItems" xlink:to="mcrb_CashEquivalentsOriginalMaturityMaximumPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfAdoptionMember" xlink:to="us-gaap_AccountingStandardsUpdate201409Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RestatementDomain" xlink:to="srt_RevisionOfPriorPeriodAccountingStandardsUpdateAdjustmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_AccountingPoliciesTable" xlink:to="us-gaap_PropertyPlantAndEquipmentByTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:to="us-gaap_TypeOfAdoptionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:to="us-gaap_TypeOfAdoptionMember_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:to="us-gaap_PropertyPlantAndEquipmentTypeDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:to="us-gaap_PropertyPlantAndEquipmentTypeDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="mcrb_LaboratoryEquipmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_AccountingPoliciesLineItems" xlink:to="us-gaap_RestrictedInvestmentsNoncurrent" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfAdoptionMember" xlink:to="us-gaap_AccountingStandardsUpdate201602Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_AccountingPoliciesTable" xlink:to="srt_RestatementAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="mcrb_FurnitureAndOfficeEquipmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_AccountingPoliciesLineItems" xlink:to="us-gaap_RestrictedCashNoncurrent" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfAdoptionMember" xlink:to="us-gaap_AccountingStandardsUpdate201818Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_AccountingPoliciesTable" xlink:to="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_AccountingPoliciesLineItems" xlink:to="us-gaap_OtherThanTemporaryImpairmentLossDebtSecuritiesAvailableForSale" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_AccountingPoliciesLineItems" xlink:to="us-gaap_ImpairmentOfLongLivedAssetsHeldForUse" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_AccountingPoliciesLineItems" xlink:to="mcrb_RevenueRecognizedRelatedToSalesBasedRoyalties" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_AccountingPoliciesLineItems" xlink:to="mcrb_MinimumPercentageOfLikelihoodOfTaxBenefitBeingRealizedUponSettlement" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureSummaryOfSignificantAccountingPoliciesScheduleOfPropertyAndEquipmentEstimatedUsefulLifeDetails">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentLineItems" xlink:label="us-gaap_PropertyPlantAndEquipmentLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" xlink:label="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentUsefulLife" xlink:label="us-gaap_PropertyPlantAndEquipmentUsefulLife"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:label="us-gaap_PropertyPlantAndEquipmentByTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:label="us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LaboratoryEquipmentMember" xlink:label="mcrb_LaboratoryEquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentEstimatedUsefulLives" xlink:label="us-gaap_PropertyPlantAndEquipmentEstimatedUsefulLives"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_FurnitureAndOfficeEquipmentMember" xlink:label="mcrb_FurnitureAndOfficeEquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LeaseholdImprovementsMember" xlink:label="us-gaap_LeaseholdImprovementsMember"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_PropertyPlantAndEquipmentUsefulLife" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" xlink:to="us-gaap_PropertyPlantAndEquipmentByTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:to="us-gaap_PropertyPlantAndEquipmentTypeDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="mcrb_LaboratoryEquipmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_PropertyPlantAndEquipmentEstimatedUsefulLives" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="mcrb_FurnitureAndOfficeEquipmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_LeaseholdImprovementsMember" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureFairValueOfFinancialAssetsAndLiabilitiesSummaryOfFairValueHierarchyForAssetsAndLiabilitiesMeasuredAtFairValueOnRecurringBasisDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:label="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_MoneyMarketFundsMember" xlink:label="us-gaap_MoneyMarketFundsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashAndCashEquivalentsAbstract" xlink:label="us-gaap_CashAndCashEquivalentsAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashAndCashEquivalentsFairValueDisclosure" xlink:label="us-gaap_CashAndCashEquivalentsFairValueDisclosure"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommercialPaperMember" xlink:label="us-gaap_CommercialPaperMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:label="us-gaap_FairValueByFairValueHierarchyLevelAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:label="us-gaap_FairValueMeasurementsFairValueHierarchyDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CashAndCashEquivalentsAxis" xlink:label="us-gaap_CashAndCashEquivalentsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:label="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueByMeasurementFrequencyAxis" xlink:label="us-gaap_FairValueByMeasurementFrequencyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueMeasurementFrequencyDomain" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueMeasurementFrequencyDomain" xlink:label="us-gaap_FairValueMeasurementFrequencyDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentsFairValueDisclosureAbstract" xlink:label="us-gaap_InvestmentsFairValueDisclosureAbstract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FinancialInstrumentAxis" xlink:label="us-gaap_FinancialInstrumentAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueInputsLevel1Member" xlink:label="us-gaap_FairValueInputsLevel1Member"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueMeasurementsRecurringMember" xlink:label="us-gaap_FairValueMeasurementsRecurringMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CorporateBondSecuritiesMember" xlink:label="us-gaap_CorporateBondSecuritiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueInputsLevel2Member" xlink:label="us-gaap_FairValueInputsLevel2Member"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_USGovernmentAgenciesDebtSecuritiesMember" xlink:label="us-gaap_USGovernmentAgenciesDebtSecuritiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AssetsFairValueDisclosure" xlink:label="us-gaap_AssetsFairValueDisclosure"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FairValueInputsLevel3Member" xlink:label="us-gaap_FairValueInputsLevel3Member"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" xlink:to="us-gaap_MoneyMarketFundsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CashAndCashEquivalentsAbstract" xlink:to="us-gaap_CashAndCashEquivalentsFairValueDisclosure" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_CommercialPaperMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FairValueByFairValueHierarchyLevelAxis" xlink:to="us-gaap_FairValueMeasurementsFairValueHierarchyDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_CashAndCashEquivalentsAbstract" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByFairValueHierarchyLevelAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_CashAndCashEquivalentsAxis" xlink:to="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_CashAndCashEquivalentsAxis" xlink:to="us-gaap_RestrictedCashAndCashEquivalentsCashAndCashEquivalentsMember_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementFrequencyDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FairValueByMeasurementFrequencyAxis" xlink:to="us-gaap_FairValueMeasurementFrequencyDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentsFairValueDisclosureAbstract" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecurities" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel1Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementFrequencyDomain" xlink:to="us-gaap_FairValueMeasurementsRecurringMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_CorporateBondSecuritiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_InvestmentsFairValueDisclosureAbstract" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FinancialInstrumentAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel2Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisLineItems" xlink:to="us-gaap_AssetsFairValueDisclosure" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_FairValueByMeasurementFrequencyAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_FairValueMeasurementsFairValueHierarchyDomain" xlink:to="us-gaap_FairValueInputsLevel3Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_FairValueAssetsAndLiabilitiesMeasuredOnRecurringAndNonrecurringBasisTable" xlink:to="us-gaap_CashAndCashEquivalentsAxis" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureInvestmentsScheduleOfInvestmentsBySecurityTypeDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:label="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:label="us-gaap_DebtSecuritiesAvailableForSaleTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:label="us-gaap_InvestmentTypeCategorizationMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CertificatesOfDepositMember" xlink:label="us-gaap_CertificatesOfDepositMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentTypeAxis" xlink:label="us-gaap_InvestmentTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InvestmentTypeCategorizationMember" xlink:label="us-gaap_InvestmentTypeCategorizationMember_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:label="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommercialPaperMember" xlink:label="us-gaap_CommercialPaperMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_FinancialInstrumentAxis" xlink:label="us-gaap_FinancialInstrumentAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CorporateBondSecuritiesMember" xlink:label="us-gaap_CorporateBondSecuritiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_USGovernmentAgenciesDebtSecuritiesMember" xlink:label="us-gaap_USGovernmentAgenciesDebtSecuritiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" xlink:label="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AvailableForSaleSecuritiesDebtSecurities" xlink:label="us-gaap_AvailableForSaleSecuritiesDebtSecurities"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_DebtSecuritiesAvailableForSaleTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_InvestmentTypeCategorizationMember" xlink:to="us-gaap_CertificatesOfDepositMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_InvestmentTypeAxis" xlink:to="us-gaap_InvestmentTypeCategorizationMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_InvestmentTypeAxis" xlink:to="us-gaap_InvestmentTypeCategorizationMember_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_CommercialPaperMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_InvestmentTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAmortizedCostBasis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_FinancialInstrumentAxis" xlink:to="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_CorporateBondSecuritiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtSecuritiesAvailableForSaleTable" xlink:to="us-gaap_FinancialInstrumentAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedGainBeforeTax" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransfersAndServicingOfFinancialInstrumentsTypesOfFinancialInstrumentsDomain" xlink:to="us-gaap_USGovernmentAgenciesDebtSecuritiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleDebtSecuritiesAccumulatedGrossUnrealizedLossBeforeTax" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ScheduleOfAvailableForSaleSecuritiesLineItems" xlink:to="us-gaap_AvailableForSaleSecuritiesDebtSecurities" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosurePropertyAndEquipmentNetScheduleOfPropertyAndEquipmentNetDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentLineItems" xlink:label="us-gaap_PropertyPlantAndEquipmentLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" xlink:label="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentGross" xlink:label="us-gaap_PropertyPlantAndEquipmentGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:label="us-gaap_PropertyPlantAndEquipmentByTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:label="us-gaap_PropertyPlantAndEquipmentTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LaboratoryEquipmentMember" xlink:label="mcrb_LaboratoryEquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" xlink:label="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ComputerEquipmentMember" xlink:label="us-gaap_ComputerEquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PropertyPlantAndEquipmentNet" xlink:label="us-gaap_PropertyPlantAndEquipmentNet"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_FurnitureAndOfficeEquipmentMember" xlink:label="mcrb_FurnitureAndOfficeEquipmentMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LeaseholdImprovementsMember" xlink:label="us-gaap_LeaseholdImprovementsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ConstructionInProgressMember" xlink:label="us-gaap_ConstructionInProgressMember"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_PropertyPlantAndEquipmentGross" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfPropertyPlantAndEquipmentTable" xlink:to="us-gaap_PropertyPlantAndEquipmentByTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PropertyPlantAndEquipmentByTypeAxis" xlink:to="us-gaap_PropertyPlantAndEquipmentTypeDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="mcrb_LaboratoryEquipmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_AccumulatedDepreciationDepletionAndAmortizationPropertyPlantAndEquipment" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_ComputerEquipmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentLineItems" xlink:to="us-gaap_PropertyPlantAndEquipmentNet" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="mcrb_FurnitureAndOfficeEquipmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_LeaseholdImprovementsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PropertyPlantAndEquipmentTypeDomain" xlink:to="us-gaap_ConstructionInProgressMember" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureLeasesAdditionalInformationDetails">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeasedAssetsLineItems" xlink:label="us-gaap_OperatingLeasedAssetsLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfOperatingLeasedAssetsTable" xlink:label="us-gaap_ScheduleOfOperatingLeasedAssetsTable"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LesseeOperatingLeaseRemainingTermOfContract" xlink:label="mcrb_LesseeOperatingLeaseRemainingTermOfContract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfArrangementAxis" xlink:label="us-gaap_TypeOfArrangementAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LeaseContractualTermDomain" xlink:label="us-gaap_LeaseContractualTermDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_October2021Member" xlink:label="mcrb_October2021Member"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MortgageLoansOnRealEstateNamePropertyTypeDomain" xlink:label="srt_MortgageLoansOnRealEstateNamePropertyTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_OfficeBuildingMember" xlink:label="srt_OfficeBuildingMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeAxis" xlink:label="srt_RangeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeMember" xlink:label="srt_RangeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeMember" xlink:label="srt_RangeMember_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MortgageLoansOnRealEstateDescriptionTypeOfPropertyAxis" xlink:label="srt_MortgageLoansOnRealEstateDescriptionTypeOfPropertyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MortgageLoansOnRealEstateNamePropertyTypeDomain" xlink:label="srt_MortgageLoansOnRealEstateNamePropertyTypeDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_SegmentGeographicalDomain" xlink:label="srt_SegmentGeographicalDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SpringHousePennsylvaniaMember" xlink:label="mcrb_SpringHousePennsylvaniaMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MaximumMember" xlink:label="srt_MaximumMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfAdoptionMember" xlink:label="us-gaap_TypeOfAdoptionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingStandardsUpdate201602Member" xlink:label="us-gaap_AccountingStandardsUpdate201602Member"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SubleaseAgreementMember" xlink:label="mcrb_SubleaseAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_StatementGeographicalAxis" xlink:label="srt_StatementGeographicalAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_SegmentGeographicalDomain" xlink:label="srt_SegmentGeographicalDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:label="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LeaseContractualTermAxis" xlink:label="us-gaap_LeaseContractualTermAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LeaseContractualTermDomain" xlink:label="us-gaap_LeaseContractualTermDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend" xlink:label="us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_March2022Member" xlink:label="mcrb_March2022Member"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LaboratorySpaceMember" xlink:label="mcrb_LaboratorySpaceMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MinimumMember" xlink:label="srt_MinimumMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseOptionToExtend" xlink:label="us-gaap_LesseeOperatingLeaseOptionToExtend"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LeaseAmendmentMember" xlink:label="mcrb_LeaseAmendmentMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OfficeAndLaboratorySpaceMember" xlink:label="mcrb_OfficeAndLaboratorySpaceMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseRenewalTerm" xlink:label="us-gaap_LesseeOperatingLeaseRenewalTerm"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingLeaseTermOfContract" xlink:label="us-gaap_LesseeOperatingLeaseTermOfContract"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseRightOfUseAsset" xlink:label="us-gaap_OperatingLeaseRightOfUseAsset"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsForTenantImprovements" xlink:label="us-gaap_PaymentsForTenantImprovements"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseLiability" xlink:label="us-gaap_OperatingLeaseLiability"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LeaseholdImprovementsGross" xlink:label="us-gaap_LeaseholdImprovementsGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeasePayments" xlink:label="us-gaap_OperatingLeasePayments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AssetRetirementObligation" xlink:label="us-gaap_AssetRetirementObligation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseWeightedAverageRemainingLeaseTerm1" xlink:label="us-gaap_OperatingLeaseWeightedAverageRemainingLeaseTerm1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLeaseWeightedAverageDiscountRatePercent" xlink:label="us-gaap_OperatingLeaseWeightedAverageDiscountRatePercent"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_ScheduleOfOperatingLeasedAssetsTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="mcrb_LesseeOperatingLeaseRemainingTermOfContract" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LeaseContractualTermDomain" xlink:to="mcrb_October2021Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_MortgageLoansOnRealEstateNamePropertyTypeDomain" xlink:to="srt_OfficeBuildingMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_MortgageLoansOnRealEstateDescriptionTypeOfPropertyAxis" xlink:to="srt_MortgageLoansOnRealEstateNamePropertyTypeDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_MortgageLoansOnRealEstateDescriptionTypeOfPropertyAxis" xlink:to="srt_MortgageLoansOnRealEstateNamePropertyTypeDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_SegmentGeographicalDomain" xlink:to="mcrb_SpringHousePennsylvaniaMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfAdoptionMember" xlink:to="us-gaap_AccountingStandardsUpdate201602Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="mcrb_SubleaseAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_StatementGeographicalAxis" xlink:to="srt_SegmentGeographicalDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_StatementGeographicalAxis" xlink:to="srt_SegmentGeographicalDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:to="us-gaap_TypeOfAdoptionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_LeaseContractualTermAxis" xlink:to="us-gaap_LeaseContractualTermDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_LeaseContractualTermAxis" xlink:to="us-gaap_LeaseContractualTermDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfOperatingLeasedAssetsTable" xlink:to="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_LesseeOperatingLeaseExistenceOfOptionToExtend" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LeaseContractualTermDomain" xlink:to="mcrb_March2022Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_MortgageLoansOnRealEstateNamePropertyTypeDomain" xlink:to="mcrb_LaboratorySpaceMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfOperatingLeasedAssetsTable" xlink:to="srt_RangeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_LesseeOperatingLeaseOptionToExtend" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LeaseContractualTermDomain" xlink:to="mcrb_LeaseAmendmentMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_MortgageLoansOnRealEstateNamePropertyTypeDomain" xlink:to="mcrb_OfficeAndLaboratorySpaceMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfOperatingLeasedAssetsTable" xlink:to="srt_MortgageLoansOnRealEstateDescriptionTypeOfPropertyAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_LesseeOperatingLeaseRenewalTerm" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfOperatingLeasedAssetsTable" xlink:to="srt_StatementGeographicalAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_LesseeOperatingLeaseTermOfContract" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfOperatingLeasedAssetsTable" xlink:to="us-gaap_LeaseContractualTermAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_OperatingLeaseRightOfUseAsset" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfOperatingLeasedAssetsTable" xlink:to="us-gaap_TypeOfArrangementAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_PaymentsForTenantImprovements" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_OperatingLeaseLiability" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_LeaseholdImprovementsGross" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="9" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_OperatingLeasePayments" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="10" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_AssetRetirementObligation" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="11" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_OperatingLeaseWeightedAverageRemainingLeaseTerm1" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="12" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OperatingLeasedAssetsLineItems" xlink:to="us-gaap_OperatingLeaseWeightedAverageDiscountRatePercent" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureRestructuringAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestructuringCostAndReserveLineItems" xlink:label="us-gaap_RestructuringCostAndReserveLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfRestructuringAndRelatedCostsTable" xlink:label="us-gaap_ScheduleOfRestructuringAndRelatedCostsTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationDomain" xlink:label="us-gaap_BalanceSheetLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember" xlink:label="mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestructuringAndRelatedCostNumberOfPositionsEliminatedPeriodPercent" xlink:label="us-gaap_RestructuringAndRelatedCostNumberOfPositionsEliminatedPeriodPercent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestructuringCostAndReserveAxis" xlink:label="us-gaap_RestructuringCostAndReserveAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfRestructuringDomain" xlink:label="us-gaap_TypeOfRestructuringDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfRestructuringDomain" xlink:label="us-gaap_TypeOfRestructuringDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SeveranceAndOtherTerminationBenefitsMember" xlink:label="mcrb_SeveranceAndOtherTerminationBenefitsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationAxis" xlink:label="us-gaap_BalanceSheetLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationDomain" xlink:label="us-gaap_BalanceSheetLocationDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestructuringCharges" xlink:label="us-gaap_RestructuringCharges"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_EmployeeSeveranceAndOtherBenefitsMember" xlink:label="mcrb_EmployeeSeveranceAndOtherBenefitsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsForRestructuring" xlink:label="us-gaap_PaymentsForRestructuring"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestructuringReserveCurrent" xlink:label="us-gaap_RestructuringReserveCurrent"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_RestructuringCostAndReserveLineItems" xlink:to="us-gaap_ScheduleOfRestructuringAndRelatedCostsTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestructuringCostAndReserveLineItems" xlink:to="us-gaap_RestructuringAndRelatedCostNumberOfPositionsEliminatedPeriodPercent" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RestructuringCostAndReserveAxis" xlink:to="us-gaap_TypeOfRestructuringDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RestructuringCostAndReserveAxis" xlink:to="us-gaap_TypeOfRestructuringDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfRestructuringAndRelatedCostsTable" xlink:to="us-gaap_RestructuringCostAndReserveAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfRestructuringDomain" xlink:to="mcrb_SeveranceAndOtherTerminationBenefitsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BalanceSheetLocationAxis" xlink:to="us-gaap_BalanceSheetLocationDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_BalanceSheetLocationAxis" xlink:to="us-gaap_BalanceSheetLocationDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestructuringCostAndReserveLineItems" xlink:to="us-gaap_RestructuringCharges" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfRestructuringAndRelatedCostsTable" xlink:to="us-gaap_BalanceSheetLocationAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfRestructuringDomain" xlink:to="mcrb_EmployeeSeveranceAndOtherBenefitsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestructuringCostAndReserveLineItems" xlink:to="us-gaap_PaymentsForRestructuring" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RestructuringCostAndReserveLineItems" xlink:to="us-gaap_RestructuringReserveCurrent" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureNotesPayableAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentLineItems" xlink:label="us-gaap_DebtInstrumentLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentTable" xlink:label="us-gaap_DebtInstrumentTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentAxis" xlink:label="us-gaap_DebtInstrumentAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LineOfCreditFacilityLenderDomain" xlink:label="us-gaap_LineOfCreditFacilityLenderDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LendersMember" xlink:label="mcrb_LendersMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_VariableRateAxis" xlink:label="us-gaap_VariableRateAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_VariableRateDomain" xlink:label="us-gaap_VariableRateDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_VariableRateDomain" xlink:label="us-gaap_VariableRateDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LongtermDebtTypeAxis" xlink:label="us-gaap_LongtermDebtTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LongtermDebtTypeDomain" xlink:label="us-gaap_LongtermDebtTypeDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LongtermDebtTypeDomain" xlink:label="us-gaap_LongtermDebtTypeDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CreditFacilityDomain" xlink:label="us-gaap_CreditFacilityDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SecondAmendmentToLoanAndSecurityAgreementMember" xlink:label="mcrb_SecondAmendmentToLoanAndSecurityAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CreditFacilityAxis" xlink:label="us-gaap_CreditFacilityAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CreditFacilityDomain" xlink:label="us-gaap_CreditFacilityDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationDomain" xlink:label="us-gaap_BalanceSheetLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CurrentLiabilityMember" xlink:label="mcrb_CurrentLiabilityMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PrimeRateMember" xlink:label="us-gaap_PrimeRateMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentNameDomain" xlink:label="us-gaap_DebtInstrumentNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentNameDomain" xlink:label="us-gaap_DebtInstrumentNameDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LineOfCreditFacilityAxis" xlink:label="us-gaap_LineOfCreditFacilityAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LineOfCreditFacilityLenderDomain" xlink:label="us-gaap_LineOfCreditFacilityLenderDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DebtInstrumentTrancheOneMember" xlink:label="mcrb_DebtInstrumentTrancheOneMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationAxis" xlink:label="us-gaap_BalanceSheetLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity" xlink:label="us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OriginalCreditFacilityMember" xlink:label="mcrb_OriginalCreditFacilityMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_HerculesCapitalIncMember" xlink:label="mcrb_HerculesCapitalIncMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LoanAndSecurityAgreementMember" xlink:label="mcrb_LoanAndSecurityAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NonCurrentLiabilityMember" xlink:label="mcrb_NonCurrentLiabilityMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DebtInstrumentTrancheTwoMember" xlink:label="mcrb_DebtInstrumentTrancheTwoMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ProceedsFromIssuanceOfLongTermDebtGross" xlink:label="mcrb_ProceedsFromIssuanceOfLongTermDebtGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ConvertibleDebtMember" xlink:label="us-gaap_ConvertibleDebtMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DebtInstrumentTrancheThreeMember" xlink:label="mcrb_DebtInstrumentTrancheThreeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentBasisSpreadOnVariableRate1" xlink:label="us-gaap_DebtInstrumentBasisSpreadOnVariableRate1"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NewCreditFacilityMember" xlink:label="mcrb_NewCreditFacilityMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DebtInstrumentTrancheFourMember" xlink:label="mcrb_DebtInstrumentTrancheFourMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LineOfCreditFacilityInterestRateDuringPeriod" xlink:label="us-gaap_LineOfCreditFacilityInterestRateDuringPeriod"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TermLoanFacilityMember" xlink:label="mcrb_TermLoanFacilityMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DebtInstrumentTrancheFiveMember" xlink:label="mcrb_DebtInstrumentTrancheFiveMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LineOfCreditFacilityFrequencyOfPaymentAndPaymentTerms" xlink:label="us-gaap_LineOfCreditFacilityFrequencyOfPaymentAndPaymentTerms"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NotesPayableInterestOnlyPeriod" xlink:label="mcrb_NotesPayableInterestOnlyPeriod"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NotesPayablePrincipalPaymentsEqualMonthlyInstallments" xlink:label="mcrb_NotesPayablePrincipalPaymentsEqualMonthlyInstallments"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RepaymentsOfDebt" xlink:label="us-gaap_RepaymentsOfDebt"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PercentageOfPrepaymentAmountDuringFirstYearFollowingClosingDate" xlink:label="mcrb_PercentageOfPrepaymentAmountDuringFirstYearFollowingClosingDate"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PercentageOfPrepaymentAmountDuringSecondYearFollowingClosingDate" xlink:label="mcrb_PercentageOfPrepaymentAmountDuringSecondYearFollowingClosingDate"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PercentageOfPrepaymentAmountDuringThirdYearFollowingClosingDate" xlink:label="mcrb_PercentageOfPrepaymentAmountDuringThirdYearFollowingClosingDate"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DebtInstrumentsPrepaymentPercentage" xlink:label="mcrb_DebtInstrumentsPrepaymentPercentage"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentFaceAmount" xlink:label="us-gaap_DebtInstrumentFaceAmount"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DebtInstrumentPrepaymentCharges" xlink:label="mcrb_DebtInstrumentPrepaymentCharges"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DebtInstrumentAdditionalAdvancePrepaymentsPercentage" xlink:label="mcrb_DebtInstrumentAdditionalAdvancePrepaymentsPercentage"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentCarryingAmount" xlink:label="us-gaap_DebtInstrumentCarryingAmount"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentInterestRateEffectivePercentage" xlink:label="us-gaap_DebtInstrumentInterestRateEffectivePercentage"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DebtInstrumentRepurchaseAmount" xlink:label="us-gaap_DebtInstrumentRepurchaseAmount"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_InterestExpenseDebt" xlink:label="us-gaap_InterestExpenseDebt"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_DebtInstrumentAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LineOfCreditFacilityLenderDomain" xlink:to="mcrb_LendersMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_VariableRateAxis" xlink:to="us-gaap_VariableRateDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_VariableRateAxis" xlink:to="us-gaap_VariableRateDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_LongtermDebtTypeAxis" xlink:to="us-gaap_LongtermDebtTypeDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_LongtermDebtTypeAxis" xlink:to="us-gaap_LongtermDebtTypeDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CreditFacilityDomain" xlink:to="mcrb_SecondAmendmentToLoanAndSecurityAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_CreditFacilityAxis" xlink:to="us-gaap_CreditFacilityDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_CreditFacilityAxis" xlink:to="us-gaap_CreditFacilityDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="mcrb_CurrentLiabilityMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_VariableRateDomain" xlink:to="us-gaap_PrimeRateMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="us-gaap_DebtInstrumentNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_DebtInstrumentAxis" xlink:to="us-gaap_DebtInstrumentNameDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_LineOfCreditFacilityAxis" xlink:to="us-gaap_LineOfCreditFacilityLenderDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_LineOfCreditFacilityAxis" xlink:to="us-gaap_LineOfCreditFacilityLenderDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentNameDomain" xlink:to="mcrb_DebtInstrumentTrancheOneMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BalanceSheetLocationAxis" xlink:to="us-gaap_BalanceSheetLocationDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_LineOfCreditFacilityMaximumBorrowingCapacity" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongtermDebtTypeDomain" xlink:to="mcrb_OriginalCreditFacilityMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_LineOfCreditFacilityAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LineOfCreditFacilityLenderDomain" xlink:to="mcrb_HerculesCapitalIncMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CreditFacilityDomain" xlink:to="mcrb_LoanAndSecurityAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="mcrb_NonCurrentLiabilityMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentNameDomain" xlink:to="mcrb_DebtInstrumentTrancheTwoMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_ProceedsFromIssuanceOfLongTermDebtGross" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongtermDebtTypeDomain" xlink:to="us-gaap_ConvertibleDebtMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_CreditFacilityAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentNameDomain" xlink:to="mcrb_DebtInstrumentTrancheThreeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentBasisSpreadOnVariableRate1" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongtermDebtTypeDomain" xlink:to="mcrb_NewCreditFacilityMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_LongtermDebtTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentNameDomain" xlink:to="mcrb_DebtInstrumentTrancheFourMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_LineOfCreditFacilityInterestRateDuringPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LongtermDebtTypeDomain" xlink:to="mcrb_TermLoanFacilityMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_VariableRateAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentNameDomain" xlink:to="mcrb_DebtInstrumentTrancheFiveMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_LineOfCreditFacilityFrequencyOfPaymentAndPaymentTerms" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_DebtInstrumentTable" xlink:to="us-gaap_BalanceSheetLocationAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_NotesPayableInterestOnlyPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_NotesPayablePrincipalPaymentsEqualMonthlyInstallments" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_RepaymentsOfDebt" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_PercentageOfPrepaymentAmountDuringFirstYearFollowingClosingDate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="9" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_PercentageOfPrepaymentAmountDuringSecondYearFollowingClosingDate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="10" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_PercentageOfPrepaymentAmountDuringThirdYearFollowingClosingDate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="11" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_DebtInstrumentsPrepaymentPercentage" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="12" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentFaceAmount" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="13" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_DebtInstrumentPrepaymentCharges" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="14" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="mcrb_DebtInstrumentAdditionalAdvancePrepaymentsPercentage" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="15" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentCarryingAmount" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="16" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentInterestRateEffectivePercentage" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="17" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_DebtInstrumentRepurchaseAmount" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="18" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_DebtInstrumentLineItems" xlink:to="us-gaap_InterestExpenseDebt" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IPOMember" xlink:label="us-gaap_IPOMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeAxis" xlink:label="srt_RangeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeMember" xlink:label="srt_RangeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MaximumMember" xlink:label="srt_MaximumMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransactionTypeAxis" xlink:label="us-gaap_TransactionTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TransactionDomain" xlink:label="us-gaap_TransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CowenAndCompanyLimitedLiabilityCompanyMember" xlink:label="mcrb_CowenAndCompanyLimitedLiabilityCompanyMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StatementEquityComponentsAxis" xlink:label="us-gaap_StatementEquityComponentsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EquityComponentDomain" xlink:label="us-gaap_EquityComponentDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwoThousandNineteenSalesAgreementMember" xlink:label="mcrb_TwoThousandNineteenSalesAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockMember" xlink:label="us-gaap_CommonStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockSharesAuthorized" xlink:label="us-gaap_CommonStockSharesAuthorized"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_UnderwrittenPublicOfferingMember" xlink:label="mcrb_UnderwrittenPublicOfferingMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MinimumMember" xlink:label="srt_MinimumMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CowenAndCompanyLLCAndPiperSandlerCoMember" xlink:label="mcrb_CowenAndCompanyLLCAndPiperSandlerCoMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwoThousandNineteenAndTwoThousandTwentySalesAgreementMember" xlink:label="mcrb_TwoThousandNineteenAndTwoThousandTwentySalesAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockParOrStatedValuePerShare" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AtTheMarketEquityOfferingProgramMember" xlink:label="mcrb_AtTheMarketEquityOfferingProgramMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SocieteDesProduitsNestleMember" xlink:label="mcrb_SocieteDesProduitsNestleMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SalesAgreementMember" xlink:label="mcrb_SalesAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ConcurrentPlacementMember" xlink:label="mcrb_ConcurrentPlacementMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_FlagshipPioneeringMember" xlink:label="mcrb_FlagshipPioneeringMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_UnderwritingAgreementMember" xlink:label="mcrb_UnderwritingAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharePrice" xlink:label="us-gaap_SharePrice"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SecuritiesPurchaseAgreementMember" xlink:label="mcrb_SecuritiesPurchaseAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwoThousandTwentyAndTwoThousandTwentyOneSalesAgreementMember" xlink:label="mcrb_TwoThousandTwentyAndTwoThousandTwentyOneSalesAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockSharesIssued" xlink:label="us-gaap_CommonStockSharesIssued"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwoThousandTwentyOneSalesAgreementMember" xlink:label="mcrb_TwoThousandTwentyOneSalesAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OptionToPurchaseAdditionalSharesOfCommonStock" xlink:label="mcrb_OptionToPurchaseAdditionalSharesOfCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromIssuanceInitialPublicOffering" xlink:label="us-gaap_ProceedsFromIssuanceInitialPublicOffering"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_GrossProceedsFromIssuanceOfCommonStock" xlink:label="mcrb_GrossProceedsFromIssuanceOfCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PercentageOfCommissionOnSaleOfCommonStock" xlink:label="mcrb_PercentageOfCommissionOnSaleOfCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OptionExercisablePeriodForPurchaseAdditionalShares" xlink:label="mcrb_OptionExercisablePeriodForPurchaseAdditionalShares"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_IPOMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TransactionTypeAxis" xlink:to="us-gaap_TransactionDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="mcrb_CowenAndCompanyLimitedLiabilityCompanyMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_StatementEquityComponentsAxis" xlink:to="us-gaap_EquityComponentDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransactionDomain" xlink:to="mcrb_TwoThousandNineteenSalesAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EquityComponentDomain" xlink:to="us-gaap_CommonStockMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_CommonStockSharesAuthorized" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_SubsidiarySaleOfStockAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="mcrb_UnderwrittenPublicOfferingMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="mcrb_CowenAndCompanyLLCAndPiperSandlerCoMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransactionDomain" xlink:to="mcrb_TwoThousandNineteenAndTwoThousandTwentySalesAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_CommonStockParOrStatedValuePerShare" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_StatementEquityComponentsAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="mcrb_AtTheMarketEquityOfferingProgramMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="mcrb_SocieteDesProduitsNestleMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransactionDomain" xlink:to="mcrb_SalesAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="srt_RangeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="mcrb_ConcurrentPlacementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="mcrb_FlagshipPioneeringMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransactionDomain" xlink:to="mcrb_UnderwritingAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharePrice" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_TransactionTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransactionDomain" xlink:to="mcrb_SecuritiesPurchaseAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransactionDomain" xlink:to="mcrb_TwoThousandTwentyAndTwoThousandTwentyOneSalesAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_CommonStockSharesIssued" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TransactionDomain" xlink:to="mcrb_TwoThousandTwentyOneSalesAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_OptionToPurchaseAdditionalSharesOfCommonStock" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ProceedsFromIssuanceInitialPublicOffering" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_GrossProceedsFromIssuanceOfCommonStock" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="9" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_PercentageOfCommissionOnSaleOfCommonStock" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="10" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_OptionExercisablePeriodForPurchaseAdditionalShares" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwards2012StockIncentivePlanAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwoThousandTwelveStockIncentivePlanMember" xlink:label="mcrb_TwoThousandTwelveStockIncentivePlanMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeAxis" xlink:label="srt_RangeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeMember" xlink:label="srt_RangeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MinimumMember" xlink:label="srt_MinimumMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardPurchasePriceOfCommonStockPercent" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardPurchasePriceOfCommonStockPercent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MaximumMember" xlink:label="srt_MaximumMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SharebasedCompensationArrangementByShareBasedPaymentAwardStockOptionsTerm" xlink:label="mcrb_SharebasedCompensationArrangementByShareBasedPaymentAwardStockOptionsTerm"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="mcrb_TwoThousandTwelveStockIncentivePlanMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardPurchasePriceOfCommonStockPercent" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_SharebasedCompensationArrangementByShareBasedPaymentAwardStockOptionsTerm" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="srt_RangeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwards2015IncentiveAwardPlanAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwentyFifteenIncentivePlanMember" xlink:label="mcrb_TwentyFifteenIncentivePlanMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeAxis" xlink:label="srt_RangeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeMember" xlink:label="srt_RangeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MinimumMember" xlink:label="srt_MinimumMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" xlink:label="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MaximumMember" xlink:label="srt_MaximumMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PercentageCommonStockOutstandingShares" xlink:label="mcrb_PercentageCommonStockOutstandingShares"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="mcrb_TwentyFifteenIncentivePlanMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_PercentageCommonStockOutstandingShares" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="srt_RangeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwards2015EmployeeStockPurchasePlanAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwoThousandFifteenEmployeeStockPurchasePlanMember" xlink:label="mcrb_TwoThousandFifteenEmployeeStockPurchasePlanMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DeferredCompensationArrangementWithIndividualCommonStockReservedForFutureIssuance" xlink:label="us-gaap_DeferredCompensationArrangementWithIndividualCommonStockReservedForFutureIssuance"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" xlink:label="us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PercentageCommonStockOutstandingShares" xlink:label="mcrb_PercentageCommonStockOutstandingShares"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DefinedContributionPlanMaximumAnnualContributionsPerEmployeePercent" xlink:label="us-gaap_DefinedContributionPlanMaximumAnnualContributionsPerEmployeePercent"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OfferingPeriodUnderThePlan" xlink:label="mcrb_OfferingPeriodUnderThePlan"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PercentageOfPurchasePriceWithRespectToEachOfferingPeriod" xlink:label="mcrb_PercentageOfPurchasePriceWithRespectToEachOfferingPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="mcrb_TwoThousandFifteenEmployeeStockPurchasePlanMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_DeferredCompensationArrangementWithIndividualCommonStockReservedForFutureIssuance" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesEmployeeStockPurchasePlans" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_PercentageCommonStockOutstandingShares" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_DefinedContributionPlanMaximumAnnualContributionsPerEmployeePercent" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_OfferingPeriodUnderThePlan" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_PercentageOfPurchasePriceWithRespectToEachOfferingPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="9" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="10" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwards2022EmploymentInducementAwardPlanAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameDomain" xlink:label="us-gaap_PlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwoThousandTwentyTwoInducementPlanMember" xlink:label="mcrb_TwoThousandTwentyTwoInducementPlanMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeAxis" xlink:label="srt_RangeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeMember" xlink:label="srt_RangeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MaximumMember" xlink:label="srt_MaximumMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PlanNameAxis" xlink:label="us-gaap_PlanNameAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MinimumMember" xlink:label="srt_MinimumMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" xlink:label="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_PlanNameDomain" xlink:to="mcrb_TwoThousandTwentyTwoInducementPlanMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardDescription" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_PlanNameAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_PlanNameAxis" xlink:to="us-gaap_PlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_CommonStockCapitalSharesReservedForFutureIssuance" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="srt_RangeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardExpirationPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardNumberOfSharesAvailableForGrant" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsStockOptionsAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PerformanceSharesMember" xlink:label="us-gaap_PerformanceSharesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisesInPeriodTotalIntrinsicValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisesInPeriodTotalIntrinsicValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestExercisableNumber" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestExercisableNumber"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_PerformanceSharesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsExercisesInPeriodTotalIntrinsicValue" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsGrantsInPeriodGross" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardOptionsVestedAndExpectedToVestExercisableNumber" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsSummaryOfRestrictedStockActivityDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedStockUnitsRSUMember" xlink:label="us-gaap_RestrictedStockUnitsRSUMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedNumber" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeitedInPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsNonvestedWeightedAverageGrantDateFairValue" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsForfeituresWeightedAverageGrantDateFairValue" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriodWeightedAverageGrantDateFairValue" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsRestrictedStockUnitsAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_VestingAxis" xlink:label="us-gaap_VestingAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_VestingDomain" xlink:label="us-gaap_VestingDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_VestingDomain" xlink:label="us-gaap_VestingDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RestrictedStockUnitsRSUMember" xlink:label="us-gaap_RestrictedStockUnitsRSUMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardEquityInstrumentsOtherThanOptionsAggregateIntrinsicValueVested" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardEquityInstrumentsOtherThanOptionsAggregateIntrinsicValueVested"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationAwardTrancheOneMember" xlink:label="us-gaap_ShareBasedCompensationAwardTrancheOneMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_TitleOfIndividualWithRelationshipToEntityDomain" xlink:label="srt_TitleOfIndividualWithRelationshipToEntityDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_EmployeeOneMember" xlink:label="mcrb_EmployeeOneMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_TitleOfIndividualAxis" xlink:label="srt_TitleOfIndividualAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_TitleOfIndividualWithRelationshipToEntityDomain" xlink:label="srt_TitleOfIndividualWithRelationshipToEntityDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PerformanceSharesMember" xlink:label="us-gaap_PerformanceSharesMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NumberOfEmployeesGranted" xlink:label="mcrb_NumberOfEmployeesGranted"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationAwardTrancheTwoMember" xlink:label="us-gaap_ShareBasedCompensationAwardTrancheTwoMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_EmployeeTwoMember" xlink:label="mcrb_EmployeeTwoMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeBenefitsAndShareBasedCompensation" xlink:label="us-gaap_EmployeeBenefitsAndShareBasedCompensation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_VestingAxis" xlink:to="us-gaap_VestingDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_VestingAxis" xlink:to="us-gaap_VestingDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_RestrictedStockUnitsRSUMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardEquityInstrumentsOtherThanOptionsAggregateIntrinsicValueVested" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_VestingDomain" xlink:to="us-gaap_ShareBasedCompensationAwardTrancheOneMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="mcrb_EmployeeOneMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_TitleOfIndividualAxis" xlink:to="srt_TitleOfIndividualWithRelationshipToEntityDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_TitleOfIndividualAxis" xlink:to="srt_TitleOfIndividualWithRelationshipToEntityDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_PerformanceSharesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="mcrb_NumberOfEmployeesGranted" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="srt_TitleOfIndividualAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_VestingDomain" xlink:to="us-gaap_ShareBasedCompensationAwardTrancheTwoMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_TitleOfIndividualWithRelationshipToEntityDomain" xlink:to="mcrb_EmployeeTwoMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_VestingAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardAwardVestingPeriod1" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardAwardVestingRightsPercentage" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsGrantsInPeriodWeightedAverageGrantDateFairValue" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_EmployeeBenefitsAndShareBasedCompensation" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardEquityInstrumentsOtherThanOptionsVestedInPeriod" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsSummaryOfEstimatedFairValueOfEmployeeStockOptionsDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:label="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SaleOfStockNameOfTransactionDomain" xlink:label="us-gaap_SaleOfStockNameOfTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockMember" xlink:label="us-gaap_EmployeeStockMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubsidiarySaleOfStockAxis" xlink:label="us-gaap_SubsidiarySaleOfStockAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockOptionMember" xlink:label="us-gaap_EmployeeStockOptionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" xlink:label="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" xlink:label="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_SaleOfStockNameOfTransactionDomain" xlink:to="us-gaap_EmployeeStockMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_SubsidiarySaleOfStockAxis" xlink:to="us-gaap_SaleOfStockNameOfTransactionDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsRiskFreeInterestRate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_AwardTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_SharebasedCompensationArrangementBySharebasedPaymentAwardFairValueAssumptionsExpectedTerm1" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfShareBasedCompensationArrangementsByShareBasedPaymentAwardTable" xlink:to="us-gaap_SubsidiarySaleOfStockAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedVolatilityRate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardLineItems" xlink:to="us-gaap_ShareBasedCompensationArrangementByShareBasedPaymentAwardFairValueAssumptionsExpectedDividendRate" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/DisclosureCommonStockAndStockbasedAwardsSummaryOfStockBasedCompensationExpenseDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:label="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:label="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationAxis" xlink:label="us-gaap_IncomeStatementLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationDomain" xlink:label="us-gaap_IncomeStatementLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationDomain" xlink:label="us-gaap_IncomeStatementLocationDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:label="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_StockOptionsAndRestrictedStockUnitsMember" xlink:label="mcrb_StockOptionsAndRestrictedStockUnitsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AwardTypeAxis" xlink:label="us-gaap_AwardTypeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AllocatedShareBasedCompensationExpense" xlink:label="us-gaap_AllocatedShareBasedCompensationExpense"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_GeneralAndAdministrativeExpenseMember" xlink:label="us-gaap_GeneralAndAdministrativeExpenseMember"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_IncomeStatementLocationAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" xlink:to="mcrb_StockOptionsAndRestrictedStockUnitsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AwardTypeAxis" xlink:to="us-gaap_ShareBasedCompensationArrangementsByShareBasedPaymentAwardAwardTypeAndPlanNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_EmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsLineItems" xlink:to="us-gaap_AllocatedShareBasedCompensationExpense" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfEmployeeServiceShareBasedCompensationAllocationOfRecognizedPeriodCostsTable" xlink:to="us-gaap_AwardTypeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_GeneralAndAdministrativeExpenseMember" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureCollaborationRevenueAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_ProductOrServiceAxis" xlink:label="srt_ProductOrServiceAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_ProductsAndServicesDomain" xlink:label="srt_ProductsAndServicesDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_ProductsAndServicesDomain" xlink:label="srt_ProductsAndServicesDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfArrangementAxis" xlink:label="us-gaap_TypeOfArrangementAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RepurchaseAgreementCounterpartyNameDomain" xlink:label="srt_RepurchaseAgreementCounterpartyNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AstraZenecaIncorporatedMember" xlink:label="mcrb_AstraZenecaIncorporatedMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CollaborationProductPercentageOfCommercialProfit" xlink:label="mcrb_CollaborationProductPercentageOfCommercialProfit"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationDomain" xlink:label="us-gaap_BalanceSheetLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TotalLiabilitiesRelatedPartyMember" xlink:label="mcrb_TotalLiabilitiesRelatedPartyMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NestleHealthScienceMember" xlink:label="mcrb_NestleHealthScienceMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationAxis" xlink:label="us-gaap_IncomeStatementLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationDomain" xlink:label="us-gaap_IncomeStatementLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfAdoptionMember" xlink:label="us-gaap_TypeOfAdoptionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingStandardsUpdate201818Member" xlink:label="us-gaap_AccountingStandardsUpdate201818Member"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwentyTwentyOneLicenseAgreementMember" xlink:label="mcrb_TwentyTwentyOneLicenseAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:label="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_CounterpartyNameAxis" xlink:label="srt_CounterpartyNameAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RepurchaseAgreementCounterpartyNameDomain" xlink:label="srt_RepurchaseAgreementCounterpartyNameDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LicenseMember" xlink:label="us-gaap_LicenseMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationAxis" xlink:label="us-gaap_BalanceSheetLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CollaborativeArrangementUpfrontPaymentReceived" xlink:label="mcrb_CollaborativeArrangementUpfrontPaymentReceived"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherNoncurrentLiabilitiesMember" xlink:label="us-gaap_OtherNoncurrentLiabilitiesMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PhaseTwoStudyMember" xlink:label="mcrb_PhaseTwoStudyMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_GeneralAndAdministrativeExpenseMember" xlink:label="us-gaap_GeneralAndAdministrativeExpenseMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ServiceMember" xlink:label="us-gaap_ServiceMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MaximumAmountToBeReceivedOnAchievementOfRegulatoryAndSalesMilestones" xlink:label="mcrb_MaximumAmountToBeReceivedOnAchievementOfRegulatoryAndSalesMilestones"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember" xlink:label="mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PhaseThreeStudyMember" xlink:label="mcrb_PhaseThreeStudyMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MaximumAmountToBeReceivedOnAchievementOfSalesMilestones" xlink:label="mcrb_MaximumAmountToBeReceivedOnAchievementOfSalesMilestones"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PhaseTwoBStudyMember" xlink:label="mcrb_PhaseTwoBStudyMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TransactionPriceAllocatedUnderCollaborativeArrangement" xlink:label="mcrb_TransactionPriceAllocatedUnderCollaborativeArrangement"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ResearchCollaborationAndOptionAgreementMember" xlink:label="mcrb_ResearchCollaborationAndOptionAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CollaborationArrangementCostAssociatedWithPreLaunchActivities" xlink:label="mcrb_CollaborationArrangementCostAssociatedWithPreLaunchActivities"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CollaborativeArrangementSharingOfPreLaunchCostsPercentage" xlink:label="mcrb_CollaborativeArrangementSharingOfPreLaunchCostsPercentage"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ProfitLossFromResearchAgreementRelatedParty" xlink:label="mcrb_ProfitLossFromResearchAgreementRelatedParty"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ContractWithCustomerLiability" xlink:label="us-gaap_ContractWithCustomerLiability"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MaximumDevelopmentMilestonePaymentsToBeReceived" xlink:label="mcrb_MaximumDevelopmentMilestonePaymentsToBeReceived"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MaximumRegulatoryPaymentsToBeReceived" xlink:label="mcrb_MaximumRegulatoryPaymentsToBeReceived"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MaximumAmountToBeReceivedOnAchievementOfCertainCommercialMilestones" xlink:label="mcrb_MaximumAmountToBeReceivedOnAchievementOfCertainCommercialMilestones"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CollaborativeArrangementUpfrontMilestonePaymentReceivable" xlink:label="mcrb_CollaborativeArrangementUpfrontMilestonePaymentReceivable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromCollaborators" xlink:label="us-gaap_ProceedsFromCollaborators"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_CollaborativeArrangementUpfrontLicenseFeeReceived" xlink:label="mcrb_CollaborativeArrangementUpfrontLicenseFeeReceived"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RevenueRemainingPerformanceObligation" xlink:label="us-gaap_RevenueRemainingPerformanceObligation"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DeferredRevenueFromRelatedParty" xlink:label="mcrb_DeferredRevenueFromRelatedParty"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_MinimumExclusivityPeriod" xlink:label="mcrb_MinimumExclusivityPeriod"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NumberOfInstallments" xlink:label="mcrb_NumberOfInstallments"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OptionExercisePeriodFromExclusivityPeriod" xlink:label="mcrb_OptionExercisePeriodFromExclusivityPeriod"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TermsOfDefinitiveLicenseAgreementGoodFaithNegotiationPeriod" xlink:label="mcrb_TermsOfDefinitiveLicenseAgreementGoodFaithNegotiationPeriod"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OtherTermsOfDefinitiveLicenseAgreementPeriod" xlink:label="mcrb_OtherTermsOfDefinitiveLicenseAgreementPeriod"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ResearchAgreementEffectiveTerminationDate" xlink:label="mcrb_ResearchAgreementEffectiveTerminationDate"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NoticePeriodForTerminationOfAgreement" xlink:label="mcrb_NoticePeriodForTerminationOfAgreement"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ResearchAndDevelopmentFixedConsideration" xlink:label="mcrb_ResearchAndDevelopmentFixedConsideration"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ResearchAndDevelopmentEstimatedReimbursementCosts" xlink:label="mcrb_ResearchAndDevelopmentEstimatedReimbursementCosts"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ResearchAndDevelopmentReimbursementCostsIncurred" xlink:label="mcrb_ResearchAndDevelopmentReimbursementCostsIncurred"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_RevenueFromResearchAgreement" xlink:label="mcrb_RevenueFromResearchAgreement"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RepurchaseAgreementCounterpartyNameDomain" xlink:to="mcrb_AstraZenecaIncorporatedMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_CollaborationProductPercentageOfCommercialProfit" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="mcrb_TotalLiabilitiesRelatedPartyMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="mcrb_NestleHealthScienceMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_IncomeStatementLocationAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfAdoptionMember" xlink:to="us-gaap_AccountingStandardsUpdate201818Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="mcrb_TwentyTwentyOneLicenseAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:to="us-gaap_TypeOfAdoptionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_CounterpartyNameAxis" xlink:to="srt_RepurchaseAgreementCounterpartyNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="srt_CounterpartyNameAxis" xlink:to="srt_RepurchaseAgreementCounterpartyNameDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_ProductsAndServicesDomain" xlink:to="us-gaap_LicenseMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BalanceSheetLocationAxis" xlink:to="us-gaap_BalanceSheetLocationDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_CollaborativeArrangementUpfrontPaymentReceived" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="us-gaap_OtherNoncurrentLiabilitiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="mcrb_PhaseTwoStudyMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_GeneralAndAdministrativeExpenseMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_ProductsAndServicesDomain" xlink:to="us-gaap_ServiceMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_MaximumAmountToBeReceivedOnAchievementOfRegulatoryAndSalesMilestones" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_BalanceSheetLocationAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="mcrb_PhaseThreeStudyMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_MaximumAmountToBeReceivedOnAchievementOfSalesMilestones" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="mcrb_PhaseTwoBStudyMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_TransactionPriceAllocatedUnderCollaborativeArrangement" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_TypeOfArrangementAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="mcrb_ResearchCollaborationAndOptionAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_CollaborationArrangementCostAssociatedWithPreLaunchActivities" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_CounterpartyNameAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_CollaborativeArrangementSharingOfPreLaunchCostsPercentage" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="srt_ProductOrServiceAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ProfitLossFromResearchAgreementRelatedParty" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="9" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_MaximumDevelopmentMilestonePaymentsToBeReceived" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="10" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_MaximumRegulatoryPaymentsToBeReceived" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="11" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_MaximumAmountToBeReceivedOnAchievementOfCertainCommercialMilestones" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="12" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_CollaborativeArrangementUpfrontMilestonePaymentReceivable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="13" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ProceedsFromCollaborators" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="14" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_CollaborativeArrangementUpfrontLicenseFeeReceived" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="15" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueRemainingPerformanceObligation" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="16" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="17" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_DeferredRevenueFromRelatedParty" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="18" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_MinimumExclusivityPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="19" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_NumberOfInstallments" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="20" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_OptionExercisePeriodFromExclusivityPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="21" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_TermsOfDefinitiveLicenseAgreementGoodFaithNegotiationPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="22" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_OtherTermsOfDefinitiveLicenseAgreementPeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="23" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ResearchAgreementEffectiveTerminationDate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="24" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_NoticePeriodForTerminationOfAgreement" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="25" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ResearchAndDevelopmentFixedConsideration" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="26" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ResearchAndDevelopmentEstimatedReimbursementCosts" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="27" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ResearchAndDevelopmentReimbursementCostsIncurred" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="28" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_RevenueFromResearchAgreement" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureCollaborationRevenueChangesInContractLiabilitiesDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:label="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:label="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ContractWithCustomerLiabilityWithRelatedParty" xlink:label="mcrb_ContractWithCustomerLiabilityWithRelatedParty"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:label="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfAdoptionMember" xlink:label="us-gaap_TypeOfAdoptionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AccountingStandardsUpdate201409Member" xlink:label="us-gaap_AccountingStandardsUpdate201409Member"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ContractWithCustomerLiabilityAdditionsWithRelatedParties" xlink:label="mcrb_ContractWithCustomerLiabilityAdditionsWithRelatedParties"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ContractWithCustomerLiabilityRevenueRecognizedWithRelatedParty" xlink:label="mcrb_ContractWithCustomerLiabilityRevenueRecognizedWithRelatedParty"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ContractWithCustomerLiability" xlink:label="us-gaap_ContractWithCustomerLiability"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ContractWithCustomerLiabilityAdditions" xlink:label="mcrb_ContractWithCustomerLiabilityAdditions"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ContractWithCustomerLiabilityRevenueRecognized" xlink:label="us-gaap_ContractWithCustomerLiabilityRevenueRecognized"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ContractWithCustomerLiabilityWithRelatedParty" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfCollaborativeArrangementsAndNoncollaborativeArrangementTransactionsTable" xlink:to="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TypeOfAdoptionMember" xlink:to="us-gaap_AccountingStandardsUpdate201409Member" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AdjustmentsForNewAccountingPronouncementsAxis" xlink:to="us-gaap_TypeOfAdoptionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ContractWithCustomerLiabilityAdditionsWithRelatedParties" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ContractWithCustomerLiabilityRevenueRecognizedWithRelatedParty" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="mcrb_ContractWithCustomerLiabilityAdditions" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_CollaborativeArrangementsAndNoncollaborativeArrangementTransactionsLineItems" xlink:to="us-gaap_ContractWithCustomerLiabilityRevenueRecognized" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureNetLossPerShareSummaryOfPotentialCommonSharesExcludedFromCalculationOfDilutedNetLossPerShareDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:label="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesNameDomain" xlink:label="us-gaap_AntidilutiveSecuritiesNameDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" xlink:label="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_EmployeeStockOptionMember" xlink:label="us-gaap_EmployeeStockOptionMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_UnvestedRestrictedStockUnitsMember" xlink:label="mcrb_UnvestedRestrictedStockUnitsMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_EmployeeStockPurchasePlanMember" xlink:label="mcrb_EmployeeStockPurchasePlanMember"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" xlink:to="us-gaap_AntidilutiveSecuritiesNameDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareLineItems" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareAmount" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="us-gaap_EmployeeStockOptionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfAntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareTable" xlink:to="us-gaap_AntidilutiveSecuritiesExcludedFromComputationOfEarningsPerShareByAntidilutiveSecuritiesAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="mcrb_UnvestedRestrictedStockUnitsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_AntidilutiveSecuritiesNameDomain" xlink:to="mcrb_EmployeeStockPurchasePlanMember" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureCommitmentsAndContingenciesAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherCommitmentsLineItems" xlink:label="us-gaap_OtherCommitmentsLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherCommitmentsTable" xlink:label="us-gaap_OtherCommitmentsTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_ProductOrServiceAxis" xlink:label="srt_ProductOrServiceAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_ProductsAndServicesDomain" xlink:label="srt_ProductsAndServicesDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LossContingenciesByNatureOfContingencyAxis" xlink:label="us-gaap_LossContingenciesByNatureOfContingencyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LossContingencyNatureDomain" xlink:label="us-gaap_LossContingencyNatureDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LossContingencyNatureDomain" xlink:label="us-gaap_LossContingencyNatureDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TypeOfArrangementAxis" xlink:label="us-gaap_TypeOfArrangementAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:label="us-gaap_ArrangementsAndNonarrangementTransactionsMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeAxis" xlink:label="srt_RangeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeMember" xlink:label="srt_RangeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MaximumMember" xlink:label="srt_MaximumMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IndemnificationGuaranteeMember" xlink:label="us-gaap_IndemnificationGuaranteeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationAxis" xlink:label="us-gaap_IncomeStatementLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationDomain" xlink:label="us-gaap_IncomeStatementLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_BactheraAgreementMember" xlink:label="mcrb_BactheraAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ResearchAndDevelopmentExpenseMember" xlink:label="us-gaap_ResearchAndDevelopmentExpenseMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ConstructionMember" xlink:label="us-gaap_ConstructionMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ContractualObligation" xlink:label="us-gaap_ContractualObligation"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LegalContingenciesMember" xlink:label="mcrb_LegalContingenciesMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_PaymentsToAcquireProductiveAssets" xlink:label="us-gaap_PaymentsToAcquireProductiveAssets"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ConstructionContractorContractDuration" xlink:label="us-gaap_ConstructionContractorContractDuration"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_ConstructionContractDurationAdditionalTermThereafter" xlink:label="mcrb_ConstructionContractDurationAdditionalTermThereafter"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PaymentsOnLongTermContract" xlink:label="mcrb_PaymentsOnLongTermContract"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PrepaymentsOnLongTermContract" xlink:label="mcrb_PrepaymentsOnLongTermContract"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_OtherCommitmentsTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_ProductOrServiceAxis" xlink:to="srt_ProductsAndServicesDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_LossContingenciesByNatureOfContingencyAxis" xlink:to="us-gaap_LossContingencyNatureDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_LossContingenciesByNatureOfContingencyAxis" xlink:to="us-gaap_LossContingencyNatureDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TypeOfArrangementAxis" xlink:to="us-gaap_ArrangementsAndNonarrangementTransactionsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="us-gaap_LossContingenciesByNatureOfContingencyAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LossContingencyNatureDomain" xlink:to="us-gaap_IndemnificationGuaranteeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_ArrangementsAndNonarrangementTransactionsMember" xlink:to="mcrb_BactheraAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_ResearchAndDevelopmentExpenseMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_ProductsAndServicesDomain" xlink:to="us-gaap_ConstructionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_ContractualObligation" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="us-gaap_TypeOfArrangementAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_LossContingencyNatureDomain" xlink:to="mcrb_LegalContingenciesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_PaymentsToAcquireProductiveAssets" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="us-gaap_IncomeStatementLocationAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="us-gaap_ConstructionContractorContractDuration" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="srt_RangeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="mcrb_ConstructionContractDurationAdditionalTermThereafter" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_OtherCommitmentsTable" xlink:to="srt_ProductOrServiceAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="mcrb_PaymentsOnLongTermContract" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_OtherCommitmentsLineItems" xlink:to="mcrb_PrepaymentsOnLongTermContract" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureIncomeTaxesAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_IncomeTaxDisclosureLineItems" xlink:label="mcrb_IncomeTaxDisclosureLineItems"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_IncomeTaxDisclosureTable" xlink:label="mcrb_IncomeTaxDisclosureTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeTaxAuthorityDomain" xlink:label="us-gaap_IncomeTaxAuthorityDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DomesticCountryMember" xlink:label="us-gaap_DomesticCountryMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TaxPeriodAxis" xlink:label="us-gaap_TaxPeriodAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TaxPeriodDomain" xlink:label="us-gaap_TaxPeriodDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TaxPeriodDomain" xlink:label="us-gaap_TaxPeriodDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeAxis" xlink:label="srt_RangeAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_RangeMember" xlink:label="srt_RangeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeTaxAuthorityAxis" xlink:label="us-gaap_IncomeTaxAuthorityAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_SegmentGeographicalDomain" xlink:label="srt_SegmentGeographicalDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.sec.gov/stpr/2022/stpr-2022.xsd#stpr_MA" xlink:label="stpr_MA"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MaximumMember" xlink:label="srt_MaximumMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_BeforeTwoThousandEighteenMember" xlink:label="mcrb_BeforeTwoThousandEighteenMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_StatementGeographicalAxis" xlink:label="srt_StatementGeographicalAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeTaxExpenseBenefit" xlink:label="us-gaap_IncomeTaxExpenseBenefit"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TaxCreditCarryforwardAxis" xlink:label="us-gaap_TaxCreditCarryforwardAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TaxCreditCarryforwardNameDomain" xlink:label="us-gaap_TaxCreditCarryforwardNameDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TaxCreditCarryforwardNameDomain" xlink:label="us-gaap_TaxCreditCarryforwardNameDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ResearchMember" xlink:label="us-gaap_ResearchMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeTaxAuthorityDomain" xlink:label="us-gaap_IncomeTaxAuthorityDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ForeignCountryMember" xlink:label="us-gaap_ForeignCountryMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_MinimumMember" xlink:label="srt_MinimumMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AfterTwoThousandSeventeenMember" xlink:label="mcrb_AfterTwoThousandSeventeenMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OperatingLossCarryforwards" xlink:label="us-gaap_OperatingLossCarryforwards"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OrphanDrugCreditCarryforwardMember" xlink:label="mcrb_OrphanDrugCreditCarryforwardMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StateAndLocalJurisdictionMember" xlink:label="us-gaap_StateAndLocalJurisdictionMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AfterTwoThousandSeventeenAndBeforeJanuaryOneTwoThousandTwentyOneMember" xlink:label="mcrb_AfterTwoThousandSeventeenAndBeforeJanuaryOneTwoThousandTwentyOneMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DeferredTaxLiabilitiesDeferredExpenseCapitalizedResearchAndDevelopmentCosts" xlink:label="us-gaap_DeferredTaxLiabilitiesDeferredExpenseCapitalizedResearchAndDevelopmentCosts"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AfterJanuaryOneTwoThousandTwentyOneMember" xlink:label="mcrb_AfterJanuaryOneTwoThousandTwentyOneMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_DeferredTaxLiabilitiesDeferredExpenseCapitalizedResearchAndDevelopmentPerformancePeriod" xlink:label="mcrb_DeferredTaxLiabilitiesDeferredExpenseCapitalizedResearchAndDevelopmentPerformancePeriod"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_FutureTaxYearsMember" xlink:label="mcrb_FutureTaxYearsMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_OperatingLossCarryforwardsExpirationYear" xlink:label="mcrb_OperatingLossCarryforwardsExpirationYear"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NetOperatingLossesOnTaxableIncomeThresholdPercentage" xlink:label="mcrb_NetOperatingLossesOnTaxableIncomeThresholdPercentage"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_TaxCreditCarryforwardAmount" xlink:label="us-gaap_TaxCreditCarryforwardAmount"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TaxCreditCarryforwardExpirationYear" xlink:label="mcrb_TaxCreditCarryforwardExpirationYear"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_UnrecognizedTaxBenefits" xlink:label="us-gaap_UnrecognizedTaxBenefits"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="mcrb_IncomeTaxDisclosureTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeTaxAuthorityDomain" xlink:to="us-gaap_DomesticCountryMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TaxPeriodAxis" xlink:to="us-gaap_TaxPeriodDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_TaxPeriodAxis" xlink:to="us-gaap_TaxPeriodDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_RangeAxis" xlink:to="srt_RangeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_IncomeTaxDisclosureTable" xlink:to="us-gaap_IncomeTaxAuthorityAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_SegmentGeographicalDomain" xlink:to="stpr_MA" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MaximumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TaxPeriodDomain" xlink:to="mcrb_BeforeTwoThousandEighteenMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="srt_StatementGeographicalAxis" xlink:to="srt_SegmentGeographicalDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="us-gaap_IncomeTaxExpenseBenefit" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_TaxCreditCarryforwardAxis" xlink:to="us-gaap_TaxCreditCarryforwardNameDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_TaxCreditCarryforwardAxis" xlink:to="us-gaap_TaxCreditCarryforwardNameDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TaxCreditCarryforwardNameDomain" xlink:to="us-gaap_ResearchMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_IncomeTaxAuthorityAxis" xlink:to="us-gaap_IncomeTaxAuthorityDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_IncomeTaxAuthorityAxis" xlink:to="us-gaap_IncomeTaxAuthorityDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeTaxAuthorityDomain" xlink:to="us-gaap_ForeignCountryMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_IncomeTaxDisclosureTable" xlink:to="us-gaap_TaxCreditCarryforwardAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_RangeMember" xlink:to="srt_MinimumMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TaxPeriodDomain" xlink:to="mcrb_AfterTwoThousandSeventeenMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="us-gaap_OperatingLossCarryforwards" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TaxCreditCarryforwardNameDomain" xlink:to="mcrb_OrphanDrugCreditCarryforwardMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeTaxAuthorityDomain" xlink:to="us-gaap_StateAndLocalJurisdictionMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_IncomeTaxDisclosureTable" xlink:to="us-gaap_TaxPeriodAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TaxPeriodDomain" xlink:to="mcrb_AfterTwoThousandSeventeenAndBeforeJanuaryOneTwoThousandTwentyOneMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="us-gaap_DeferredTaxLiabilitiesDeferredExpenseCapitalizedResearchAndDevelopmentCosts" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_IncomeTaxDisclosureTable" xlink:to="srt_StatementGeographicalAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TaxPeriodDomain" xlink:to="mcrb_AfterJanuaryOneTwoThousandTwentyOneMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="mcrb_DeferredTaxLiabilitiesDeferredExpenseCapitalizedResearchAndDevelopmentPerformancePeriod" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="mcrb_IncomeTaxDisclosureTable" xlink:to="srt_RangeAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_TaxPeriodDomain" xlink:to="mcrb_FutureTaxYearsMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="mcrb_OperatingLossCarryforwardsExpirationYear" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="mcrb_NetOperatingLossesOnTaxableIncomeThresholdPercentage" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="us-gaap_TaxCreditCarryforwardAmount" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="mcrb_TaxCreditCarryforwardExpirationYear" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="mcrb_IncomeTaxDisclosureLineItems" xlink:to="us-gaap_UnrecognizedTaxBenefits" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://serestherapeutics.com/20221231/taxonomy/role/Role_DisclosureRelatedPartyTransactionsAdditionalInformationDetail">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionLineItems" xlink:label="us-gaap_RelatedPartyTransactionLineItems"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:label="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:label="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyDomain" xlink:label="us-gaap_RelatedPartyDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationDomain" xlink:label="us-gaap_BalanceSheetLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember" xlink:label="mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_NestleHealthScienceMember" xlink:label="mcrb_NestleHealthScienceMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationAxis" xlink:label="us-gaap_IncomeStatementLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_IncomeStatementLocationDomain" xlink:label="us-gaap_IncomeStatementLocationDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionAxis" xlink:label="us-gaap_RelatedPartyTransactionAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionDomain" xlink:label="us-gaap_RelatedPartyTransactionDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionDomain" xlink:label="us-gaap_RelatedPartyTransactionDomain_default"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SubleaseAgreementMember" xlink:label="mcrb_SubleaseAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherIncomeMember" xlink:label="us-gaap_OtherIncomeMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" xlink:label="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_BalanceSheetLocationAxis" xlink:label="us-gaap_BalanceSheetLocationAxis"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_OtherNoncurrentLiabilitiesMember" xlink:label="us-gaap_OtherNoncurrentLiabilitiesMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_FlagshipPioneeringMember" xlink:label="mcrb_FlagshipPioneeringMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TwentyTwentyOneLicenseAgreementMember" xlink:label="mcrb_TwentyTwentyOneLicenseAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ContractWithCustomerLiability" xlink:label="us-gaap_ContractWithCustomerLiability"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_PledgeAndUtilizationAgreementMember" xlink:label="mcrb_PledgeAndUtilizationAgreementMember"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_TransactionPriceAllocatedUnderCollaborativeArrangement" xlink:label="mcrb_TransactionPriceAllocatedUnderCollaborativeArrangement"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionSellingGeneralAndAdministrativeExpensesFromTransactionsWithRelatedParty" xlink:label="us-gaap_RelatedPartyTransactionSellingGeneralAndAdministrativeExpensesFromTransactionsWithRelatedParty"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DueFromRelatedPartiesCurrent" xlink:label="us-gaap_DueFromRelatedPartiesCurrent"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_StockIssuedDuringPeriodSharesNewIssues" xlink:label="us-gaap_StockIssuedDuringPeriodSharesNewIssues"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_CommonStockParOrStatedValuePerShare" xlink:label="us-gaap_CommonStockParOrStatedValuePerShare"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_ProceedsFromIssuanceOfCommonStock" xlink:label="us-gaap_ProceedsFromIssuanceOfCommonStock"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_DueToRelatedPartiesNoncurrent" xlink:label="us-gaap_DueToRelatedPartiesNoncurrent"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_LesseeTermOfOperatingSubleaseDescription" xlink:label="mcrb_LesseeTermOfOperatingSubleaseDescription"/>
    <link:loc xlink:type="locator" xlink:href="mcrb-20221231.xsd#mcrb_SubLeaseCommencementDate" xlink:label="mcrb_SubLeaseCommencementDate"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LesseeOperatingSubleaseExistenceOfOptionToExtend" xlink:label="us-gaap_LesseeOperatingSubleaseExistenceOfOptionToExtend"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_SubleaseIncome" xlink:label="us-gaap_SubleaseIncome"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_RelatedPartyTransactionOtherRevenuesFromTransactionsWithRelatedParty" xlink:label="us-gaap_RelatedPartyTransactionOtherRevenuesFromTransactionsWithRelatedParty"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="true" xbrldt:contextElement="segment" xlink:arcrole="http://xbrl.org/int/dim/arcrole/all" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" xlink:to="us-gaap_RelatedPartyDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="mcrb_AccruedExpensesAndOtherCurrentLiabilitiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="mcrb_NestleHealthScienceMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_IncomeStatementLocationAxis" xlink:to="us-gaap_IncomeStatementLocationDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_RelatedPartyTransactionAxis" xlink:to="us-gaap_RelatedPartyTransactionDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-default" xlink:from="us-gaap_RelatedPartyTransactionAxis" xlink:to="us-gaap_RelatedPartyTransactionDomain_default" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionDomain" xlink:to="mcrb_SubleaseAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_IncomeStatementLocationDomain" xlink:to="us-gaap_OtherIncomeMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_RevenueFromContractWithCustomerExcludingAssessedTax" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/dimension-domain" xlink:from="us-gaap_BalanceSheetLocationAxis" xlink:to="us-gaap_BalanceSheetLocationDomain" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_RelatedPartyTransactionsByRelatedPartyAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_BalanceSheetLocationDomain" xlink:to="us-gaap_OtherNoncurrentLiabilitiesMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyDomain" xlink:to="mcrb_FlagshipPioneeringMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionDomain" xlink:to="mcrb_TwentyTwentyOneLicenseAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_ContractWithCustomerLiability" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="1" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_RelatedPartyTransactionAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionDomain" xlink:to="mcrb_PledgeAndUtilizationAgreementMember" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="mcrb_TransactionPriceAllocatedUnderCollaborativeArrangement" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="2" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_IncomeStatementLocationAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_RelatedPartyTransactionSellingGeneralAndAdministrativeExpensesFromTransactionsWithRelatedParty" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="3" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/hypercube-dimension" xlink:from="us-gaap_ScheduleOfRelatedPartyTransactionsByRelatedPartyTable" xlink:to="us-gaap_BalanceSheetLocationAxis" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="4" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_DueFromRelatedPartiesCurrent" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="5" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_StockIssuedDuringPeriodSharesNewIssues" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="6" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_CommonStockParOrStatedValuePerShare" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="7" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_ProceedsFromIssuanceOfCommonStock" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="8" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_DueToRelatedPartiesNoncurrent" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="9" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="mcrb_LesseeTermOfOperatingSubleaseDescription" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="10" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="mcrb_SubLeaseCommencementDate" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="11" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_LesseeOperatingSubleaseExistenceOfOptionToExtend" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="12" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_SubleaseIncome" priority="2" use="optional"/>
    <link:definitionArc xlink:type="arc" order="13" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="us-gaap_RelatedPartyTransactionLineItems" xlink:to="us-gaap_RelatedPartyTransactionOtherRevenuesFromTransactionsWithRelatedParty" priority="2" use="optional"/>
  </link:definitionLink>
  <link:definitionLink xlink:type="extended" xlink:role="http://fasb.org/us-gaap/role/eedm/ExtensibleEnumerationLists">
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/srt/2022/elts/srt-2022.xsd#srt_ProductsAndServicesDomain" xlink:label="srt_ProductsAndServicesDomain"/>
    <link:loc xlink:type="locator" xlink:href="https://xbrl.fasb.org/us-gaap/2022/elts/us-gaap-2022.xsd#us-gaap_LicenseAndServiceMember" xlink:label="us-gaap_LicenseAndServiceMember"/>
    <link:definitionArc xlink:type="arc" order="0" xbrldt:closed="false" xlink:arcrole="http://xbrl.org/int/dim/arcrole/domain-member" xlink:from="srt_ProductsAndServicesDomain" xlink:to="us-gaap_LicenseAndServiceMember" priority="2" use="optional"/>
  </link:definitionLink>
</link:linkbase>
