<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0407</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2023-04-27</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001609809</issuerCik>
        <issuerName>Seres Therapeutics, Inc.</issuerName>
        <issuerTradingSymbol>MCRB</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001767321</rptOwnerCik>
            <rptOwnerName>Henn Matthew R.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SERES THERAPEUTICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>200 SIDNEY STREET</rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02139</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>See Remarks</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <aff10b5One>0</aff10b5One>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (Right to Buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.84</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2023-04-27</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>35000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2023-04-27</value>
            </exerciseDate>
            <expirationDate>
                <value>2027-06-18</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>35000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>70000</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">On June 19, 2017, the Reporting Person was granted an option to purchase 70,000 shares of the Issuer's common stock. The option vested and became exercisable in two equal installments upon the satisfaction of certain performance criteria. On April 27, 2023, the Issuer's Board of Directors determined that the performance criteria for the second installment were met, resulting in vesting of the option as to 35,000 shares.</footnote>
    </footnotes>

    <remarks>Chief Scientific Officer and EVP</remarks>

    <ownerSignature>
        <signatureName>/s/ Thomas J. DesRosier, attorney-in-fact for Matthew R. Henn</signatureName>
        <signatureDate>2023-05-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
