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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2019-06-18</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001400240</rptOwnerCik>
            <rptOwnerName>Flagship Pioneering Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>55 CAMBRIDGE PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001724957</rptOwnerCik>
            <rptOwnerName>Flagship Pioneering Fund VI General Partner LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>55 CAMBRIDGE PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001716926</rptOwnerCik>
            <rptOwnerName>Flagship Pioneering Fund VI, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>55 CAMBRIDGE PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001780951</rptOwnerCik>
            <rptOwnerName>Nutritional Health LTP Fund General Partner LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>55 CAMBRIDGE PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001780956</rptOwnerCik>
            <rptOwnerName>Nutritional Health LTP Fund, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>55 CAMBRIDGE PARKWAY</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>CAMBRIDGE</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02142</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4444444</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4444444</value>
                    <footnoteId id="F3"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">On June 18, 2019, Flagship Pioneering Fund VI, L.P. (&quot;Flagship Fund VI&quot;) acquired 4,444,444 shares pursuant to an underwritten public offering of common stock by the issuer (the &quot;Offering&quot;).</footnote>
        <footnote id="F2">The shares are held by Flagship Fund VI.  Flagship Pioneering Fund VI General Partner LLC (&quot;Fund VI GP&quot;) is the general partner of Flagship Fund VI.  Flagship Pioneering, Inc. (&quot;Flagship Pioneering&quot;) is the manager of Fund VI GP.  Noubar B. Afeyan Ph.D. is the CEO and sole shareholder of Flagship Pioneering and may be deemed to have sole voting and investment power with respect to all shares held by Flagship Fund VI.  Each of the reporting persons disclaims beneficial ownership of such shares except to the extent of its pecuniary interest therein.</footnote>
        <footnote id="F3">On June 18, 2019, Nutritional Health LTP Fund, L.P. (&quot;Nutritional LTP&quot;) acquired 4,444,444 shares pursuant to the Offering.</footnote>
        <footnote id="F4">The shares are held by Nutritional LTP.  Nutritional Health LTP Fund General Partner LLC (&quot;Nutritional LTP GP&quot;) is the general partner of Nutritional LTP.  Noubar B. Afeyan Ph.D. is the sole member and manager of Nutritional LTP GP and may be deemed to have sole voting and investment power with respect to all shares held by Nutritional LTP.  Each of the reporting persons disclaims beneficial ownership of such shares except to the extent of its pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Flagship Pioneering, Inc., By: /s/ Noubar B. Afeyan, Name: Noubar B. Afeyan, Ph.D., Title: CEO</signatureName>
        <signatureDate>2019-06-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Flagship Pioneering Fund VI General Partner LLC, By: Flagship Pioneering, Inc., its manager, By: /s/ Noubar B. Afeyan, Name: Noubar B. Afeyan, Ph.D., Title: CEO</signatureName>
        <signatureDate>2019-06-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Flagship Pioneering Fund VI, L.P., By: Flagship Pioneering Fund VI General Partner LLC, its general partner, By: Flagship Pioneering, Inc., its manager, By: /s/ Noubar B. Afeyan, Name: Noubar B. Afeyan, Ph.D., Title: CEO</signatureName>
        <signatureDate>2019-06-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Nutritional Health LTP Fund General Partner LLC, By: /s/ Noubar B. Afeyan, Name: Noubar B. Afeyan, Ph.D., Title: Manager</signatureName>
        <signatureDate>2019-06-28</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Nutritional Health LTP Fund, L.P., By: Nutritional Health LTP Fund General Partner LLC, its general partner, By: /s/ Noubar B. Afeyan, Name: Noubar B. Afeyan, Ph.D., Title: Manager</signatureName>
        <signatureDate>2019-06-28</signatureDate>
    </ownerSignature>
</ownershipDocument>
