Document:

EX-10.6

 Exhibit 10.6 

EMPLOYMENT AGREEMENT 

This Employment Agreement (this “Agreement”), dated as of June 12, 2015, is made by and between Seres Therapeutics, Inc., a
Delaware corporation (together with any successor thereto, the “Company”), and Roger J. Pomerantz, M.D. (“Executive”) (collectively referred to as the “Parties” or individually referred to as a
“Party”). 
 RECITALS 
  

	A.	It is the desire of the Company to assure itself of the services of Executive following the Effective Date (as defined below) and thereafter by entering into this Agreement. 

 

	B.	Executive and the Company mutually desire that Executive provide services to the Company on the terms herein provided. 

AGREEMENT 
 NOW,
THEREFORE, in consideration of the foregoing and of the respective covenants and agreements set forth below, the Parties hereto agree as follows: 
 1.
Employment. 
 (a) General. Effective on the closing of the Company’s initial public offering of stock pursuant to an
effective registration statement filed under the Securities Act of 1933, as amended (the “Effective Date”), the Company shall employ Executive and Executive shall remain in the employ of the Company, for the period and in the
positions set forth in this Section 1, and subject to the other terms and conditions herein provided. 
 (b) At-Will
Employment. The Company and Executive acknowledge that Executive’s employment is and shall continue to be at-will, as defined under applicable law, and that Executive’s employment with the Company may be terminated by either Party at
any time for any or no reason (subject to the notice requirements of Section 3(b)). This “at-will” nature of Executive’s employment shall remain unchanged during Executive’s tenure as an employee and may not be
changed, except in an express writing signed by Executive and a duly authorized officer of the Company. If Executive’s employment terminates for any reason, Executive shall not be entitled to any payments, benefits, damages, award or
compensation other than as provided in this Agreement or otherwise agreed to in writing by the Company or as provided by applicable law. The term of this Agreement (the “Term”) shall commence on the Effective Date and end on the
date this Agreement is terminated under Section 3. 
 (c) Positions and Duties. Executive shall serve as President and
Chief Executive Officer of the Company with such responsibilities, duties and authority normally associated with such positions and as may from time to time be assigned to Executive by the Board of Directors of the Company or an authorized committee
of the Board (in either case, the “Board”). Executive shall devote substantially all of Executive’s working time and efforts to the business and affairs of the Company (which shall include service to its affiliates, if
applicable) and shall not engage in outside business activities (including serving on outside boards or committees) 

 
without the consent of the Board, provided that Executive shall be permitted to (i) manage Executive’s personal, financial and legal affairs, (ii) participate in trade
associations, and (iii) serve on the board of directors of not-for-profit or tax-exempt charitable organizations, in each case, subject to compliance with this Agreement and provided that such activities do not materially interfere with
Executive’s performance of Executive’s duties and responsibilities hereunder. Executive agrees to observe and comply with the rules and policies of the Company as adopted by the Company from time to time, in each case as amended from time
to time, as set forth in writing, and as delivered or made available to Executive (each, a “Policy”). 
 2. Compensation and Related
Matters. 
 (a) Annual Base Salary. During the Term, Executive shall receive a base salary at a rate of $464,100 per annum,
which shall be paid in accordance with the customary payroll practices of the Company and shall be pro-rated for partial years of employment. Such annual base salary shall be reviewed (and may be adjusted) from time to time by the Board (such annual
base salary, as it may be adjusted from time to time, the “Annual Base Salary”). 
 (b) Bonus. During the Term,
Executive will be eligible to participate in an annual incentive program established by the Board. Executive’s annual incentive compensation under such incentive program (the “Annual Bonus”) shall be targeted at 50% of
Executive’s Annual Base Salary. The Annual Bonus payable under the incentive program shall be based on the achievement of performance goals to be determined by the Board. The payment of any Annual Bonus pursuant to the incentive program shall
be subject to Executive’s continued employment with the Company through the date of payment, except as otherwise provided in Section 4(b). 

(c) Benefits. During the Term, Executive shall be eligible to participate in employee benefit plans, programs and arrangements of the
Company (including medical, dental and 401(k) plans), consistent with the terms thereof and as such plans, programs and arrangements may be amended from time to time. In no event shall Executive be eligible to participate in any severance plan or
program of the Company, except as set forth in Section 4 of this Agreement. In addition, until the first anniversary of the Effective Date and at the Company’s option thereafter, the Company will reimburse you for reasonable costs
you incur for (a) travel between your current residence in Pennsylvania and the Company’s headquarters in Cambridge, Massachusetts, and (b) reasonable lodging near Cambridge, Massachusetts when performing services for the Company.

 (d) Vacation. During the Term, Executive shall be entitled to paid personal leave in accordance with the Company’s Policies.
Any vacation shall be taken at the reasonable and mutual convenience of the Company and Executive. 
 (e) Business Expenses. During
the Term, the Company shall reimburse Executive for all reasonable travel and other business expenses incurred by Executive in the performance of Executive’s duties to the Company in accordance with the Company’s expense reimbursement
Policy. 
 (f) Key Person Insurance. At any time during the Term, the Company shall have the right to insure the life of Executive
for the Company’s sole benefit. The Company shall have the 

  
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right to determine the amount of insurance and the type of policy. Executive shall reasonably cooperate with the Company in obtaining such insurance by submitting to physical examinations, by
supplying all information reasonably required by any insurance carrier, and by executing all necessary documents reasonably required by any insurance carrier, provided that any information provided to an insurance company or broker shall not be
provided to the Company without the prior written authorization of Executive. Executive shall incur no financial obligation by executing any required document, and shall have no interest in any such policy. 

3. Termination. 
 Executive’s
employment hereunder may be terminated by the Company or Executive, as applicable, without any breach of this Agreement under the following circumstances: 

(a) Circumstances. 

(i) Death. Executive’s employment hereunder shall terminate upon Executive’s death. 

(ii) Disability. If Executive has incurred a Disability, as defined below, the Company may terminate Executive’s
employment. 
 (iii) Termination for Cause. The Company may terminate Executive’s employment for Cause, as
defined below. 
 (iv) Termination without Cause. The Company may terminate Executive’s employment without Cause.

 (v) Resignation from the Company for Good Reason. Executive may resign Executive’s employment with the Company
for Good Reason, as defined below. 
 (vi) Resignation from the Company Without Good Reason. Executive may resign
Executive’s employment with the Company for any reason other than Good Reason or for no reason. 
 (b) Notice of Termination.
Any termination of Executive’s employment by the Company or by Executive under this Section 3 (other than termination pursuant to paragraph (a)(i)) shall be communicated by a written notice to the other Party hereto
(i) indicating the specific termination provision in this Agreement relied upon, (ii) setting forth in reasonable detail the facts and circumstances claimed to provide a basis for termination of Executive’s employment under the
provision so indicated, if applicable, and (iii) specifying a Date of Termination which, if submitted by Executive, shall be at least forty-five (45) days following the date of such notice (a “Notice of Termination”);
provided, however, that in the event that Executive delivers a Notice of Termination to the Company, the Company may, in its sole discretion, change the Date of Termination to any date that occurs following the date of Company’s receipt
of such Notice of Termination and is prior to the date specified in such Notice of Termination. A Notice of Termination submitted by the Company may provide for a Date of Termination on the date Executive receives the Notice of Termination, or any
date 

  
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thereafter elected by the Company in its sole discretion. The failure by the Company to set forth in the Notice of Termination any fact or circumstance which contributes to a showing of Cause
shall not waive any right of the Company hereunder or preclude the Company from asserting such fact or circumstance in enforcing the Company’s rights hereunder. 

(c) Company Obligations upon Termination. Upon termination of Executive’s employment pursuant to any of the circumstances listed
in this Section 3, Executive (or Executive’s estate) shall be entitled to receive the sum of: (i) the portion of Executive’s Annual Base Salary earned through the Date of Termination, but not yet paid to Executive;
(ii) any expenses owed to Executive pursuant to Section 2(e); and (iii) any amount accrued and arising from Executive’s participation in, or benefits accrued under any employee benefit plans, programs or arrangements,
which amounts shall be payable in accordance with the terms and conditions of such employee benefit plans, programs or arrangements (collectively, the “Company Arrangements”). Except as otherwise expressly required by law
(e.g., COBRA) or as specifically provided herein, all of Executive’s rights to salary, severance, benefits, bonuses and other compensatory amounts hereunder (if any) shall cease upon the termination of Executive’s employment
hereunder. In the event that Executive’s employment is terminated by the Company for any reason, Executive’s sole and exclusive remedy shall be to receive the payments and benefits described in this Section 3(c) or
Section 4, as applicable. 
 (d) Deemed Resignation. Upon termination of Executive’s employment for any reason,
Executive shall be deemed to have resigned from all offices and directorships, if any, then held with the Company or any of its subsidiaries. 
 4.
Severance Payments. 
 (a) Termination for Cause, or Termination Upon Death, Disability or Resignation from the Company
Without Good Reason. If Executive’s employment shall terminate as a result of Executive’s death pursuant to Section 3(a)(i) or Disability pursuant to Section 3(a)(ii), pursuant to Section 3(a)(iii)
for Cause, or pursuant to Section 3(a)(vi) for Executive’s resignation from the Company without Good Reason, then Executive shall not be entitled to any severance payments or benefits, except as provided in Section 3(c).

 (b) Termination without Cause, or Resignation from the Company for Good Reason. If Executive’s employment terminates without
Cause pursuant to Section 3(a)(iv), or pursuant to Section 3(a)(v) due to Executive’s resignation for Good Reason, then, subject to Executive signing on or before the
21st day following Executive’s Separation from Service (as defined below), and not revoking, a release of claims substantially in the form attached as Exhibit A to this Agreement (the
“Release”), and Executive’s continued compliance with Section 5, Executive shall receive, in addition to payments and benefits set forth in Section 3(c), the following: 

(i) an amount in cash equal to the Annual Base Salary, payable in the form of salary continuation in regular installments over
the 12-month period following the date of Executive’s Separation from Service (the “Severance Period”) in accordance with the Company’s normal payroll practices; 

  
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 (ii) to the extent unpaid as of the Date of Termination, an amount of cash equal
to any Annual Bonus earned by Executive for the Company’s fiscal year prior to the fiscal year in which the Date of Termination occurs, as determined by the Board in its discretion based upon actual performance achieved, which Annual Bonus, if
any, shall be paid to Executive in the fiscal year in which the Date of Termination occurs when bonuses for such prior fiscal year are paid in the ordinary course to actively employed senior executives of the Company; and 

(iii) if Executive elects to receive continued medical, dental or vision coverage under one or more of the Company’s group
healthcare plans pursuant to the Consolidated Omnibus Budget Reconciliation Act of 1985, as amended (“COBRA”), the Company shall directly pay, or reimburse Executive for, the COBRA premiums for Executive and Executive’s covered
dependents under such plans during the period commencing on Executive’s Separation from Service and ending upon the earliest of (X) the last day of the Severance Period, (Y) the date that Executive and/or Executive’s covered
dependents become no longer eligible for COBRA or (Z) the date Executive becomes eligible to receive healthcare coverage from a subsequent employer (and Executive agrees to promptly notify the Company of such eligibility). Notwithstanding the
foregoing, if the Company determines in its sole discretion that it cannot provide the foregoing benefit without potentially violating applicable law (including, without limitation, Section 2716 of the Public Health Service Act) or incurring an
excise tax, the Company shall in lieu thereof provide to Executive a taxable monthly payment in an amount equal to the monthly COBRA premium that Executive would be required to pay to continue Executive’s and Executive’s covered
dependents’ group health coverage in effect on the Date of Termination (which amount shall be based on the premium for the first month of COBRA coverage), less the amount Executive would have had to pay to receive group health coverage for
Executive and his or her covered dependents based on the cost sharing levels in effect on the Date of Termination, which payments shall be made regardless of whether Executive elects COBRA continuation coverage and shall commence in the month
following the month in which the Date of Termination occurs and shall end on the earlier of (X) the last day of the Severance Period, (Y) the date that Executive and/or Executive’s covered dependents become no longer eligible for
COBRA or (Z) the date Executive becomes eligible to receive healthcare coverage from a subsequent employer (and Executive agrees to promptly notify the Company of such eligibility). 

(c) Change in Control. Notwithstanding anything to the contrary in Section 4(b), in the event Executive’s employment
terminates without Cause pursuant to Section 3(a)(iv), or pursuant to Section 3(a)(v) due to Executive’s resignation for Good Reason, in either case, within 60 days prior to or 12 months following the date of a Change in
Control, subject to Executive signing on or before the 21st day following Executive’s Separation from Service, and not revoking, the Release, all unvested equity or equity-based awards held
by Executive under any Company equity compensation plans that vest solely based on the passage of time shall immediately become 100% vested (for the avoidance of doubt, with any such awards that vest in whole or in part based on the attainment of
performance-vesting conditions being governed by the terms of the applicable award agreement). 
 (d) Survival. Notwithstanding
anything to the contrary in this Agreement, the provisions of Sections 5 through 9 will survive the termination of Executive’s employment and the termination of the Term. 

  
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 5. Restrictive Covenants. As a condition to the effectiveness of this Agreement, Executive will
execute and deliver to the Company contemporaneously herewith the Employee Non-Competition, Non-Solicitation, Confidentiality and Assignment Agreement attached as Exhibit B (the “Proprietary Information Agreement”). Executive
agrees to abide by the terms of the Proprietary Information Agreement, which are hereby incorporated by reference into this Agreement. Executive acknowledges that the provisions of the Proprietary Information Agreement will survive the termination
of Executive’s employment and the termination of the Term for the periods set forth in the Proprietary Information Agreement. 
 6. Assignment
and Successors. 
 The Company may assign its rights and obligations under this Agreement to any of its affiliates or to any
successor to all or substantially all of the business or the assets of the Company (by merger or otherwise), and may assign or encumber this Agreement and its rights hereunder as security for indebtedness of the Company and its affiliates. This
Agreement shall be binding upon and inure to the benefit of the Company, Executive and their respective successors, assigns, personnel and legal representatives, executors, administrators, heirs, distributees, devisees, and legatees, as applicable.
None of Executive’s rights or obligations may be assigned or transferred by Executive, other than Executive’s rights to payments hereunder, which may be transferred only by will or operation of law. Notwithstanding the foregoing, Executive
shall be entitled, to the extent permitted under applicable law and applicable Company Arrangements, to select and change a beneficiary or beneficiaries to receive compensation hereunder following Executive’s death by giving written notice
thereof to the Company. 
 7. Certain Definitions. 

(a) Cause. The Company shall have “Cause” to terminate Executive’s employment hereunder upon: 

(i) Executive’s failure to (A) substantially perform Executive’s duties with the Company (other than any such
failure resulting from Executive’s Disability) or (B) comply with, in any material respect, any of the Company’s Policies; 

(ii) the Board’s determination that Executive failed in any material respect to carry out or comply with any lawful and
reasonable directive of the Board; 
 (iii) Executive’s breach of a material provision of this Agreement; 

(iv) Executive’s conviction, plea of no contest, plea of nolo contendere, or imposition of unadjudicated probation
for any felony or crime involving moral turpitude; 
 (v) Executive’s unlawful use (including being under the influence)
or possession of illegal drugs on the Company’s (or any of its affiliate’s) premises or while performing Executive’s duties and responsibilities under this Agreement; or 

(vi) Executive’s commission of an act of fraud, embezzlement, misappropriation, willful misconduct, or breach of fiduciary
duty against the Company or any of its affiliates. 

  
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 (b) Change in Control. “Change in Control” shall have the meaning set forth in
the version of the Seres Therapeutics, Inc. 2015 Incentive Award Plan in effect on the Effective Date. 
 (c) Code. “Code”
shall mean the Internal Revenue Code of 1986, as amended, and the regulations and guidance promulgated thereunder. 
 (d) Date of
Termination. “Date of Termination” shall mean (i) if Executive’s employment is terminated by Executive’s death, the date of Executive’s death; or (ii) if Executive’s employment is terminated pursuant to
Section 3(a)(ii) – (vi) either the date indicated in the Notice of Termination or the date specified by the Company pursuant to Section 3(b), whichever is earlier. 

(e) Disability. “Disability” shall mean, at any time the Company or any of its affiliates sponsors a long-term disability
plan for the Company’s employees, “disability” as defined in such long-term disability plan for the purpose of determining a participant’s eligibility for benefits, provided, however, if the long-term disability plan
contains multiple definitions of disability, “Disability” shall refer to that definition of disability which, if Executive qualified for such disability benefits, would provide coverage for the longest period of time. The determination of
whether Executive has a Disability shall be made by the person or persons required to make disability determinations under the long-term disability plan. At any time the Company does not sponsor a long-term disability plan for its employees,
“Disability” shall mean Executive’s inability to perform, with or without reasonable accommodation, the essential functions of Executive’s positions hereunder for a total of three months during any six-month period as a result of
incapacity due to mental or physical illness as determined by a physician selected by the Company or its insurers and acceptable to Executive or Executive’s legal representative, with such agreement as to acceptability not to be unreasonably
withheld or delayed. Any refusal by Executive to submit to a medical examination for the purpose of determining Disability shall be deemed to constitute conclusive evidence of Executive’s Disability. 

(f) Good Reason. For the sole purpose of determining Executive’s right to severance payments and benefits as described above,
Executive’s resignation will be for “Good Reason” if Executive resigns within ninety days after any of the following events, unless Executive consents to the applicable event: (i) a decrease in Executive’s Annual Base
Salary, other than a reduction in Annual Base Salary of less than 10% that is implemented in connection with a contemporaneous reduction in annual base salaries affecting other senior executives of the Company, (ii) a material decrease in
Executive’s authority or areas of responsibility as are commensurate with Executive’s title or positions, or (iii) the relocation of Executive’s primary office to a location more than 50 miles from the Boston metropolitan area.
Notwithstanding the 

  
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foregoing, no Good Reason will have occurred unless and until Executive has: (a) provided the Company, within 60 days of Executive’s knowledge of the occurrence of the facts and
circumstances underlying the Good Reason event, written-notice stating with specificity the applicable facts and circumstances underlying such finding of Good Reason; and (b) provided the Company with an opportunity to cure the same within 30
days after the receipt of such notice. 
 8. Parachute Payments. 

(a) Notwithstanding any other provisions of this Agreement, in the event that any payment or benefit by the Company or otherwise to or for the
benefit of Executive, whether paid or payable or distributed or distributable pursuant to the terms of this Agreement or otherwise (all such payments and benefits, including the payments and benefits under Section 4(b) and
Section 4(c) hereof, being hereinafter referred to as the “Total Payments”), would be subject (in whole or in part) to the excise tax imposed by Section 4999 of the Code (the “Excise Tax”), then the
Total Payments shall be reduced (in the order provided in Section 8(b)) to the minimum extent necessary to avoid the imposition of the Excise Tax on the Total Payments, but only if (i) the net amount of such Total Payments, as so
reduced (and after subtracting the net amount of federal, state and local income and employment taxes on such reduced Total Payments and after taking into account the phase out of itemized deductions and personal exemptions attributable to such
reduced Total Payments), is greater than or equal to (ii) the net amount of such Total Payments without such reduction (but after subtracting the net amount of federal, state and local income and employment taxes on such Total Payments and the
amount of the Excise Tax to which Executive would be subject in respect of such unreduced Total Payments and after taking into account the phase out of itemized deductions and personal exemptions attributable to such unreduced Total Payments). 

(b) The Total Payments shall be reduced in the following order: (i) reduction on a pro-rata basis of any cash severance payments that are
exempt from Section 409A of the Code (“Section 409A”), (ii) reduction on a pro-rata basis any non-cash severance payments or benefits that are exempt from Section 409A, (iii) reduction on a pro-rata basis of any
other payments or benefits that are exempt from Section 409A, and (iv) reduction of any payments or benefits otherwise payable to Executive on a pro-rata basis or such other manner that complies with Section 409A; provided, in case of
clauses (ii), (iii) and (iv), that reduction of any payments attributable to the acceleration of vesting of Company equity awards shall be first applied to Company equity awards that would otherwise vest last in time. 

(c) All determinations regarding the application of this Section 8 shall be made by an accounting firm or consulting group with
experience in performing calculations regarding the applicability of Section 280G of the Code and the Excise Tax selected by the Company (the “Independent Advisors”). For purposes of determinations, no portion of the Total
Payments shall be taken into account which, in the opinion of the Independent Advisors, (i) does not constitute a “parachute payment” within the meaning of Section 280G(b)(2) of the Code (including by reason of
Section 280G(b)(4)(A) of the Code) or (ii) constitutes reasonable compensation for services actually rendered, within the meaning of Section 280G(b)(4)(B) of the Code, in excess of the “base amount” (as defined in
Section 280G(b)(3) of the Code) allocable to 

  
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such reasonable compensation. The costs of obtaining such determination and all related fees and expenses (including related fees and expenses incurred in any later audit) shall be borne by the
Company. 
 (d) In the event it is later determined that a greater reduction in the Total Payments should have been made to implement the
objective and intent of this Section 8, the excess amount shall be returned immediately by Executive to the Company. 
 9. Miscellaneous
Provisions. 
 (a) Governing Law. This Agreement shall be governed, construed, interpreted and enforced in accordance
with its express terms, and otherwise in accordance with the substantive laws of the Commonwealth of Massachusetts without reference to the principles of conflicts of law of the Commonwealth of Massachusetts or any other jurisdiction, and where
applicable, the laws of the United States. 
 (b) Validity. The invalidity or unenforceability of any provision or
provisions of this Agreement shall not affect the validity or enforceability of any other provision of this Agreement, which shall remain in full force and effect.  

(c) Notices. Any notice, request, claim, demand, document and other communication hereunder to any Party shall be effective upon
receipt (or refusal of receipt) and shall be in writing and delivered personally or sent by facsimile or certified or registered mail, postage prepaid, as follows: 

(i) If to the Company, the Chief Financial Officer at its headquarters, 

(ii) If to Executive, at the last address that the Company has in its personnel records for Executive, or 

(iii) at any other address as any Party shall have specified by notice in writing to the other Party. 

(d) Counterparts. This Agreement may be executed in several counterparts, each of which shall be deemed to be an original, but all of
which together will constitute one and the same Agreement. Signatures delivered by facsimile shall be deemed effective for all purposes. 

(e) Entire Agreement. The terms of this Agreement, and the Proprietary Information Agreement incorporated herein by reference as set
forth in Section 5, are intended by the Parties to be the final expression of their agreement with respect to the subject matter hereof and supersede all prior understandings and agreements, whether written or oral, including the
employment offer letter agreement between Executive and the Company, dated as of April 28, 2014. The Parties further intend that this Agreement shall constitute the complete and exclusive statement of their terms and that no extrinsic evidence
whatsoever may be introduced in any judicial, administrative, or other legal proceeding to vary the terms of this Agreement. 

  
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 (f) Amendments; Waivers. This Agreement may not be modified, amended, or terminated except
by an instrument in writing, signed by Executive and a duly authorized officer of Company. By an instrument in writing similarly executed, Executive or a duly authorized officer of the Company may waive compliance by the other Party with any
specifically identified provision of this Agreement that such other Party was or is obligated to comply with or perform; provided, however, that such waiver shall not operate as a waiver of, or estoppel with respect to, any other or
subsequent failure. No failure to exercise and no delay in exercising any right, remedy, or power hereunder preclude any other or further exercise of any other right, remedy, or power provided herein or by law or in equity. 

(g) No Inconsistent Actions. The Parties hereto shall not voluntarily undertake or fail to undertake any action or course of action
inconsistent with the provisions or essential intent of this Agreement. Furthermore, it is the intent of the Parties hereto to act in a fair and reasonable manner with respect to the interpretation and application of the provisions of this
Agreement. 
 (h) Construction. This Agreement shall be deemed drafted equally by both the Parties. Its language shall be construed
as a whole and according to its fair meaning. Any presumption or principle that the language is to be construed against any Party shall not apply. The headings in this Agreement are only for convenience and are not intended to affect construction or
interpretation. Any references to paragraphs, subparagraphs, sections or subsections are to those parts of this Agreement, unless the context clearly indicates to the contrary. Also, unless the context clearly indicates to the contrary, (i) the
plural includes the singular and the singular includes the plural; (ii) “and” and “or” are each used both conjunctively and disjunctively; (iii) “any,” “all,” “each,” or “every”
means “any and all,” and “each and every”; (iv) “includes” and “including” are each “without limitation”; (v) “herein,” “hereof,” “hereunder” and other similar
compounds of the word “here” refer to the entire Agreement and not to any particular paragraph, subparagraph, section or subsection; and (vi) all pronouns and any variations thereof shall be deemed to refer to the masculine, feminine,
neuter, singular or plural as the identity of the entities or persons referred to may require. 
 (i) Arbitration. Any controversy,
claim or dispute arising out of or relating to this Agreement, shall be settled solely and exclusively by a binding arbitration process administered by JAMS/Endispute in Boston, Massachusetts. Such arbitration shall be conducted in accordance with
the then-existing JAMS/Endispute Rules of Practice and Procedure, with the following exceptions if in conflict: (i) one arbitrator who is a retired judge shall be chosen by JAMS/Endispute; (ii) each Party to the arbitration will pay
one-half of the expenses and fees of the arbitrator, together with other expenses of the arbitration incurred or approved by the arbitrator; and (iii) arbitration may proceed in the absence of any Party if written notice (pursuant to the
JAMS/Endispute rules and regulations) of the proceedings has been given to such Party. Each Party shall bear its own attorney’s fees and expenses; provided that the arbitrator may assess the prevailing Party’s fees and costs against the
non-prevailing Party as part of the arbitrator’s award. The Parties agree to abide by all decisions and awards rendered in such proceedings. Such decisions and awards rendered by the arbitrator shall be final and conclusive. All such
controversies, claims or disputes shall be settled in this manner in lieu of any action at law or equity; provided, however, that nothing in this subsection shall be construed as precluding the bringing of an action for injunctive relief or
specific performance as provided in this 

  
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Agreement. This dispute resolution process and any arbitration hereunder shall be confidential and neither any Party nor the neutral arbitrator shall disclose the existence, contents or results
of such process without the prior written consent of all Parties, except where necessary or compelled in a Court to enforce this arbitration provision or an Award from such arbitration or otherwise in a legal proceeding. If JAMS/Endispute no longer
exists or is otherwise unavailable, the Parties agree that the American Arbitration Association (“AAA’) shall administer the arbitration in accordance with its then-existing rules as modified by this subsection. In such event, all
references herein to JAMS/Endispute shall mean AAA. Notwithstanding the foregoing, Executive and the Company each have the right to resolve any issue or dispute over intellectual property rights by Court action instead of arbitration. 

(j) Enforcement. If any provision of this Agreement is held to be illegal, invalid or unenforceable under present or future laws
effective during the Term, such provision shall be fully severable; this Agreement shall be construed and enforced as if such illegal, invalid or unenforceable provision had never comprised a portion of this Agreement; and the remaining provisions
of this Agreement shall remain in full force and effect and shall not be affected by the illegal, invalid or unenforceable provision or by its severance from this Agreement. Furthermore, in lieu of such illegal, invalid or unenforceable provision
there shall be added automatically as part of this Agreement a provision as similar in terms to such illegal, invalid or unenforceable provision as may be possible and be legal, valid and enforceable. 

(k) Withholding. The Company shall be entitled to withhold from any amounts payable under this Agreement any federal, state, local or
foreign withholding or other taxes or charges which the Company is required to withhold. The Company shall be entitled to rely on an opinion of counsel if any questions as to the amount or requirement of withholding shall arise. 

(l) Section 409A. 

(i) General. The intent of the Parties is that the payments and benefits under this Agreement comply with or be exempt
from Section 409A and, accordingly, to the maximum extent permitted, this Agreement shall be interpreted to be in compliance therewith. 

(ii) Separation from Service. Notwithstanding anything in this Agreement to the contrary, any compensation or benefits
payable under this Agreement that is considered nonqualified deferred compensation under Section 409A and is designated under this Agreement as payable upon Executive’s termination of employment shall be payable only upon Executive’s
“separation from service” with the Company within the meaning of Section 409A (a “Separation from Service”) and, except as provided below, any such compensation or benefits described in Section 4 shall not
be paid, or, in the case of installments, shall not commence payment, until the thirtieth (30th) day following Executive’s Separation from Service (the “First Payment Date”). Any installment payments that would have been
made to Executive during the thirty (30) day period immediately following Executive’s Separation from Service but for the preceding sentence shall be paid to Executive on the First Payment Date and the remaining payments shall be made as
provided in this Agreement. 

  
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 (iii) Specified Employee. Notwithstanding anything in this Agreement to
the contrary, if Executive is deemed by the Company at the time of Executive’s Separation from Service to be a “specified employee” for purposes of Section 409A, to the extent delayed commencement of any portion of the benefits
to which Executive is entitled under this Agreement is required in order to avoid a prohibited distribution under Section 409A, such portion of Executive’s benefits shall not be provided to Executive prior to the earlier of (i) the
expiration of the six-month period measured from the date of Executive’s Separation from Service with the Company or (ii) the date of Executive’s death. Upon the first business day following the expiration of the applicable
Section 409A period, all payments deferred pursuant to the preceding sentence shall be paid in a lump sum to Executive (or Executive’s estate or beneficiaries), and any remaining payments due to Executive under this Agreement shall be paid
as otherwise provided herein. 
 (iv) Expense Reimbursements. To the extent that any reimbursements under this
Agreement are subject to Section 409A, any such reimbursements payable to Executive shall be paid to Executive no later than December 31 of the year following the year in which the expense was incurred; provided, that Executive submits
Executive’s reimbursement request promptly following the date the expense is incurred, the amount of expenses reimbursed in one year shall not affect the amount eligible for reimbursement in any subsequent year, other than medical expenses
referred to in Section 105(b) of the Code, and Executive’s right to reimbursement under this Agreement will not be subject to liquidation or exchange for another benefit. 

(v) Installments. Executive’s right to receive any installment payments under this Agreement, including without
limitation any continuation salary payments that are payable on Company payroll dates, shall be treated as a right to receive a series of separate payments and, accordingly, each such installment payment shall at all times be considered a separate
and distinct payment as permitted under Section 409A. Except as otherwise permitted under Section 409A, no payment hereunder shall be accelerated or deferred unless such acceleration or deferral would not result in additional tax or
interest pursuant to Section 409A. 
 10. Executive Acknowledgement. 

Executive acknowledges that Executive has read and understands this Agreement, is fully aware of its legal effect, has not acted in reliance
upon any representations or promises made by the Company other than those contained in writing herein, and has entered into this Agreement freely based on Executive’s own judgment. 

[Signature Page Follows] 

  
 12 

 IN WITNESS WHEREOF, the Parties have executed this Agreement on the date and year first above
written. 
  

					
	SERES THERAPEUTICS, INC.
		
	By:		 /s/ Eric D. Shaff

			Name:		Eric D. Shaff
			Title:		Chief Financial Officer
					
	
	 /s/ Roger J. Pomerantz

	Roger J. Pomerantz, M.D.

 EXHIBIT A 

Separation Agreement and Release 

This Separation Agreement and Release (“Agreement”) is made by and between Roger J. Pomerantz, M.D.
(“Executive”) and Seres Therapeutics, Inc. (the “Company”) (collectively referred to as the “Parties” or individually referred to as a “Party”). Capitalized terms used but not defined in this Agreement shall
have the meanings set forth in the Employment Agreement (as defined below). 
 WHEREAS, the Parties have previously entered into that
certain Employment Agreement, dated as of June 12, 2015 (the “Employment Agreement”); and 
 WHEREAS, in connection with
Executive’s termination of employment with the Company or a subsidiary or affiliate of the Company effective             , 20    , the Parties wish to resolve any
and all disputes, claims, complaints, grievances, charges, actions, petitions, and demands that Executive may have against the Company and any of the Releasees as defined below, including, but not limited to, any and all claims arising out of or in
any way related to Executive’s employment with or separation from the Company or its subsidiaries or affiliates but, for the avoidance of doubt, nothing herein will be deemed to release any rights or remedies in connection with Executive’s
ownership of vested equity securities of the Company or Executive’s right to indemnification by the Company or any of its affiliates pursuant to contract or applicable law (collectively, the “Retained Claims”). 

NOW, THEREFORE, in consideration of the severance payments and benefits described in Section 4 of the Employment Agreement, which,
pursuant to the Employment Agreement, are conditioned on Executive’s execution and non-revocation of this Agreement, and in consideration of the mutual promises made herein, the Company and Executive hereby agree as follows: 

1. Severance Payments; Salary and Benefits. The Company agrees to provide Executive with the severance payments and benefits described
in Section 4(b) and/or Section 4(c) of the Employment Agreement, payable at the times set forth in, and subject to the terms and conditions of, the Employment Agreement. In addition, to the extent not already paid, and subject to the terms
and conditions of the Employment Agreement, the Company shall pay or provide to Executive all other payments or benefits described in Section 3(c) of the Employment Agreement, subject to and in accordance with the terms thereof. 

2. Release of Claims. Executive agrees that, other than with respect to the Retained Claims, the foregoing consideration represents
settlement in full of all outstanding obligations owed to Executive by the Company, any of its direct or indirect subsidiaries and affiliates, and any of their current and former officers, directors, equity holders, managers, employees, agents,
investors, attorneys, shareholders, administrators, affiliates, benefit plans, plan administrators, insurers, trustees, divisions, and subsidiaries and predecessor and successor corporations and assigns (collectively, the “Releasees”).
Executive, on Executive’s own behalf and on behalf of any of Executive’s affiliated companies or entities and any of their respective heirs, family members, executors, agents, and assigns, other than with respect to the Retained Claims,
hereby and forever releases the Releasees from, and agrees not to sue concerning, or in any manner to 

 
institute, prosecute, or pursue, any claim, complaint, charge, duty, obligation, or cause of action relating to any matters of any kind, whether presently known or unknown, suspected or
unsuspected, that Executive may possess against any of the Releasees arising from any omissions, acts, facts, or damages that have occurred up until and including the Effective Date of this Agreement (as defined in Section 7 below), including,
without limitation: 
 (a) any and all claims relating to or arising from Executive’s employment or service relationship with the
Company or any of its direct or indirect subsidiaries or affiliates and the termination of that relationship; 
 (b) any and all claims
relating to, or arising from, Executive’s right to purchase, or actual purchase of any shares of stock or other equity interests of the Company or any of its affiliates, including, without limitation, any claims for fraud, misrepresentation,
breach of fiduciary duty, breach of duty under applicable state corporate law, and securities fraud under any state or federal law; 
 (c)
any and all claims for wrongful discharge of employment; termination in violation of public policy; discrimination; harassment; retaliation; breach of contract, both express and implied; breach of covenant of good faith and fair dealing, both
express and implied; promissory estoppel; negligent or intentional infliction of emotional distress; fraud; negligent or intentional misrepresentation; negligent or intentional interference with contract or prospective economic advantage; unfair
business practices; defamation; libel; slander; negligence; personal injury; assault; battery; invasion of privacy; false imprisonment; conversion; and disability benefits; 

(d) any and all claims for violation of any federal, state, or municipal statute, including, but not limited to, Title VII of the Civil Rights
Act of 1964; the Civil Rights Act of 1991; the Rehabilitation Act of 1973; the Americans with Disabilities Act of 1990; the Equal Pay Act; the Fair Credit Reporting Act; the Age Discrimination in Employment Act of 1967; the Older Workers Benefit
Protection Act; the Employee Retirement Income Security Act of 1974; the Worker Adjustment and Retraining Notification Act; the Family and Medical Leave Act; and the Sarbanes-Oxley Act of 2002; 

(e) any and all claims for violation of the federal or any state constitution; 

(f) any and all claims arising out of any other laws and regulations relating to employment or employment discrimination; 

(g) any claim for any loss, cost, damage, or expense arising out of any dispute over the non-withholding or other tax treatment of any of the
proceeds received by Executive as a result of this Agreement; and 
 (h) any and all claims for attorneys’ fees and costs. 

Executive agrees that the release set forth in this section shall be and remain in effect in all respects as a complete general release as to the matters
released. This release does not release claims that cannot be released as a matter of law, including, but not limited to, Executive’s right 

  
 2 

 
to report possible violations of federal law or regulation to any governmental agency or entity in accordance with the provisions of and rules promulgated under Section 21F of the Securities
Exchange Act of 1934 or Section 806 of the Sarbanes-Oxley Act of 2002, or any other whistleblower protection provisions of state or federal law or regulation, Executive’s right to file a charge with or participate in a charge by the Equal
Employment Opportunity Commission, or any other local, state, or federal administrative body or government agency that is authorized to enforce or administer laws related to employment, against the Company (with the understanding that
Executive’s release of claims herein bars Executive from recovering such monetary relief from the Company or any Releasee), claims for unemployment compensation or any state disability insurance benefits pursuant to the terms of applicable
state law, claims to continued participation in certain of the Company’s group benefit plans pursuant to the terms and conditions of COBRA, claims to any benefit entitlements vested as the date of separation of Executive’s employment,
pursuant to written terms of any employee benefit plan of the Company or its affiliates and Executive’s right under applicable law and any Retained Claims. This release further does not release claims for breach of Section 3(c),
Section 4(b) or Section 4(c) of the Employment Agreement. 
 3. Acknowledgment of Waiver of Claims under ADEA. Executive
understands and acknowledges that Executive is waiving and releasing any rights Executive may have under the Age Discrimination in Employment Act of 1967 (“ADEA”), and that this waiver and release is knowing and voluntary. Executive
understands and agrees that this waiver and release does not apply to any rights or claims that may arise under the ADEA after the Effective Date of this Agreement. Executive understands and acknowledges that the consideration given for this waiver
and release is in addition to anything of value to which Executive was already entitled. Executive further understands and acknowledges that Executive has been advised by this writing that: (a) Executive should consult with an attorney prior to
executing this Agreement; (b) Executive has 21 days within which to consider this Agreement; (c) Executive has 7 days following Executive’s execution of this Agreement to revoke this Agreement pursuant to written notice to the General
Counsel of the Company; (d) this Agreement shall not be effective until after the revocation period has expired; and (e) nothing in this Agreement prevents or precludes Executive from challenging or seeking a determination in good faith of
the validity of this waiver under the ADEA, nor does it impose any condition precedent, penalties, or costs for doing so, unless specifically authorized by federal law. In the event Executive signs this Agreement and returns it to the Company in
less than the 21 day period identified above, Executive hereby acknowledges that Executive has freely and voluntarily chosen to waive the time period allotted for considering this Agreement. 

4. Severability. In the event that any provision or any portion of any provision hereof or any surviving agreement made a part hereof
becomes or is declared by a court of competent jurisdiction or arbitrator to be illegal, unenforceable, or void, this Agreement shall continue in full force and effect without said provision or portion of provision. 

5. No Oral Modification. This Agreement may only be amended in a writing signed by Executive and a duly authorized officer of the
Company. 

  
 3 

 6. Governing Law; Dispute Resolution. This Agreement shall be subject to the provisions of
Sections 9(a), 9(c) and 9(i) of the Employment Agreement. 
 7. Effective Date. If Executive has attained or is over the age of 40 as
of the date of Executive’s termination of employment, then each Party has seven days after that Party signs this Agreement to revoke it and this Agreement will become effective on the eighth day after Executive signed this Agreement, so long as
it has been signed by the Parties and has not been revoked by either Party before that date (the “Effective Date”). If Executive has not attained the age of 40 as of the date of Executive’s termination of employment, then the
“Effective Date” shall be the date on which Executive signs this Agreement. 
 8. Voluntary Execution of Agreement.
Executive understands and agrees that Executive executed this Agreement voluntarily, without any duress or undue influence on the part or behalf of the Company or any third party, with the full intent of releasing all of Executive’s claims
against the Company and any of the other Releasees. Executive acknowledges that: (a) Executive has read this Agreement; (b) Executive has not relied upon any representations or statements made by the Company that are not specifically set
forth in this Agreement; (c) Executive has been represented in the preparation, negotiation, and execution of this Agreement by legal counsel of Executive’s own choice or has elected not to retain legal counsel; (d) Executive
understands the terms and consequences of this Agreement and of the releases it contains; and (e) Executive is fully aware of the legal and binding effect of this Agreement. 

IN WITNESS WHEREOF, the Parties have executed this Agreement on the respective dates set forth below. 

 

									
	Dated:		  
				  

							Roger J. Pomerantz, M.D.
				
							SERES THERAPEUTICS, INC.
					
	Dated:		  
				By:		  

									Name:
									Title:

  
 4 

 EXHIBIT B 

Employee Non-Competition, Non-Solicitation, Confidentiality and Assignment Agreement 

In consideration and as a condition of my employment or continued employment by Seres Therapeutics, Inc. (the “Company”), I
hereby agree as follows: 

 

 1. Proprietary Information. I agree that all information, whether or not in writing, whether or
not disclosed before or after I was first employed by the Company, concerning the Company’s business, technology, business relationships or financial affairs that the Company has not released to the general public (collectively,
“Proprietary Information”), and all tangible embodiments thereof, are and will be the exclusive property of the Company. By way of illustration, Proprietary Information may include information or material that has not been made generally
available to the public, such as: (a) corporate information, including plans, strategies, methods, policies, resolutions, notes, email correspondence, negotiations or litigation; (b) marketing information, including
strategies, methods, customer identities or other information about customers, prospect identities or other information about prospects, or market analyses or projections; (c) financial information, including cost and performance data,
debt arrangements, equity structure, investors and holdings, purchasing and sales data and price lists; and (d) operational and technological information, including plans, specifications, manuals, forms, templates, software, designs,
methods, procedures, formulas, discoveries, inventions, improvements, biological or chemical materials, concepts and ideas; and (e) personnel information, including personnel lists, reporting or organizational structure, resumes,
personnel data, compensation structure, performance evaluations and termination arrangements or documents. Proprietary Information includes, without limitation, (1) information received in confidence by the Company from its customers or
suppliers or other third parties, and (2) all biological or chemical materials and other tangible embodiments of the Proprietary Information. Nothing in this Agreement shall prohibit me from reporting possible violations of federal law or
regulation to any governmental agency or entity in accordance with the provisions of and rules promulgated under Section 21F of the Securities Exchange Act of 1934 or Section 805 of the Sarbanes-Oxley Act of 2002, or any other
whistleblower protection provisions of state or federal law or regulation.

 2. Recognition of Company’s Rights. I will not, at any time, without the Company’s prior
written permission, either during or after my employment, disclose or transfer any Proprietary Information to anyone outside of the Company, or use or permit to be used any Proprietary Information for any purpose other than the performance of my
duties as an employee of the Company. I will cooperate with the Company and use my best efforts to prevent the unauthorized disclosure of all Proprietary Information. I will deliver to the Company all copies and other tangible embodiments of
Proprietary Information in my possession or control upon the earlier of a request by the Company or termination of my employment. 
 3. Rights of
Others. I understand that the Company is now and may hereafter be subject to non-disclosure or confidentiality agreements with third persons which require the Company to protect or refrain from use of proprietary information. I agree to be
bound by the terms of such agreements in the event I have access to such proprietary information. 
 4. Commitment to Company; Avoidance of Conflict
of Interest. While an employee of the Company, I will devote my full-time efforts to the Company’s business and I will not engage in any other business activity that conflicts with my duties to the Company. I will advise the president
of the Company or his or her nominee at such time as any activity of either the Company or another business presents me with a conflict of interest or the appearance of a conflict of interest as an employee of the Company. I will take whatever
action is requested of me by the Company to resolve any conflict or appearance of conflict which it finds to exist. 
 5. Developments. I
hereby assign and transfer and, to the extent any such assignment cannot be made at present, will assign and transfer, to the Company and its successors and assigns, all my right, title and interest in and to all Developments (as defined below)
that: (a) are created, developed, made, conceived or reduced to practice by me (alone or jointly with others) or under my direction

 

 
(collectively, “conceived”) during the period of my employment and six (6) months thereafter and that relate to the business of the Company or to products, methods or services
being researched, developed, manufactured or sold by the Company; or (b) result from tasks assigned to me by the Company; or (c) result from the use of premises, Proprietary Information or personal property (whether tangible or intangible)
owned, licensed or leased by the Company (collectively, “Company-Related Developments”), and all patent rights, trademarks, copyrights and other intellectual property rights in all countries and territories worldwide claiming,
covering or otherwise arising from or pertaining to Company-Related Developments (collectively, “Intellectual Property Rights”). I further agree that “Company-Related Developments” include, without limitation, all
Developments that (i) were conceived by me before my employment, (ii) relate to the business of the Company or to products, methods or services being researched, developed, manufactured or sold by the Company, and (iii) were not
subject to an obligation to assign to another entity when conceived. I will make full and prompt disclosure to the Company of all Company-Related Developments, as well as all other Developments conceived by me during the period of my employment and
six (6) months thereafter. I acknowledge that all work performed by me as an employee of the Company is on a “work for hire” basis. I hereby waive all claims to any moral rights or other special rights which I may have or accrue in
any Company-Related Developments. “Developments” mean inventions, discoveries, designs, developments, methods, modifications, improvements, processes, biological or chemical materials, algorithms, databases, computer programs, formulae,
techniques, trade secrets, graphics or images, audio or visual works, and other works of authorship. 
 To preclude any possible uncertainty, I have set
forth on Appendix A attached hereto a complete list of Developments conceived by me before my employment that are not Company-Related Developments (“Prior Inventions”). I have also listed on Appendix A all patent rights of
which I am an inventor, other than those contained within Intellectual Property Rights (“Other Patent Rights”). If no such disclosure is attached, I represent that there are no Prior Inventions or Other Patent Rights. If, in the course of
my employment with the Company, I incorporate a Prior Invention into a Company product, process or research or development program

 
or other work done for the Company, I hereby grant to the Company a nonexclusive, royalty-free, fully paid-up, irrevocable, perpetual, worldwide license (with the full right to sublicense through
multiple tiers) to make, have made, modify, use, offer for sale, import and sell such Prior Invention. Notwithstanding the foregoing, I will not incorporate, or permit to be incorporated, Prior Inventions in any Company-Related Development without
the Company’s prior written consent. 
 I understand that to the extent this Agreement is required to be construed in accordance with the laws of any
state which precludes a requirement in an employee agreement to assign certain classes of inventions made by an employee, this Section will be interpreted not to apply to any invention which a court rules and/or the Company agrees falls within such
classes. 
 6. Documents and Other Materials. I will keep and maintain adequate and current records of all Proprietary Information and
Company-Related Developments conceived by me, which records will be available to and remain the sole property of the Company at all times. All files, letters, notes, memoranda, reports, records, data, sketches, drawings, notebooks, layouts, charts,
quotations and proposals, specification sheets, program listings, blueprints, models, prototypes, materials or other written, photographic or other tangible material containing or embodying Proprietary Information, whether created by me or others,
which come into my custody or possession, are the exclusive property of the Company to be used by me only in the performance of my duties for the Company. In the event of the termination of my employment for any reason, I will deliver to the Company
all of the foregoing, and all other materials of any nature pertaining to the Proprietary Information of the Company and to my work, and will not take or keep in my possession any of the foregoing or any copies. Any property situated on the
Company’s premises and owned by the Company, including laboratory space, computers, disks and other storage media, filing cabinets or other work areas, is subject to inspection by the Company at any time with or without notice. 

7. Enforcement of Intellectual Property Rights. I will cooperate fully with the Company, both during and after my employment with the Company,
with respect to the procurement, maintenance and enforcement of Intellectual Property Rights, as well as all other patent rights, trademarks, copyrights and

 

  
 2 

 
other intellectual property rights in all countries and territories worldwide owned by or licensed to the Company. I will sign, both during and after the term of this Agreement, all papers,
including copyright applications, patent applications, declarations, oaths, assignments of priority rights, and powers of attorney, which the Company may deem necessary or desirable in order to protect its rights and interests in any Company-Related
Development or Intellectual Property Rights. If the Company is unable, after reasonable effort, to secure my signature on any such papers, I hereby irrevocably designate and appoint each officer of the Company as my agent and attorney-in-fact to
execute any such papers on my behalf, and to take any and all actions as the Company may deem necessary or desirable in order to protect its rights and interests in the same. 

8. Non-Competition and Non-Solicitation. In order to protect the Company’s Proprietary Information and good will, during my employment and
for a period of twelve (12) months following the termination of my employment for any reason (the “Restricted Period”), I will not directly or indirectly, whether as owner, partner, shareholder, director, consultant, agent, employee,
co-venturer or otherwise: 
 (a) Engage, participate or invest in any business that develops, manufactures or markets microbiome
therapeutics, or products or services that the Company has under development or that are the subject of active planning at any time during my employment (collectively, the “Competitive Products”); provided that this will not prohibit any
possible investment in publicly traded stock of a company representing less than one percent of the stock of such company; 
 (b) Directly
or indirectly, in any manner, other than for the benefit of the Company, (i) call upon, solicit, divert or take away any of the customers, business or prospective customers of the Company or any of its suppliers, and/or (ii) solicit,
entice or attempt to persuade any other employee or consultant of the Company to leave the services of the Company for any reason. 
 (c)
I acknowledge and agree that if I violate any of the provisions of this Section, in addition to any other remedies to which the Company may be entitled in law or equity, the running of the Restricted Period will be extended by the time during which
I engage in such violation(s). 

 (d) I acknowledge and agree that the provisions of this agreement shall apply during and
following my employment by the Company, and shall not be affected by any change in my job duties, whether material or immaterial. 
 9. Government
Contracts. I acknowledge that the Company may have from time to time agreements with other persons or with the United States Government or its agencies which impose obligations or restrictions on the Company regarding inventions made during
the course of work under such agreements or regarding the confidential nature of such work. I agree to comply with any such obligations or restrictions upon the direction of the Company. In addition to the rights assigned under Section 5, I
also assign to the Company (or any of its nominees) all rights which I have or acquired in any Developments, full title to which is required to be in the United States under any contract between the Company and the United States or any of its
agencies. 
 10. Prior Agreements. I hereby represent that, except as I have fully disclosed previously in writing to the Company, I am not
bound by the terms of any agreement with any previous employer or other party to refrain from using or disclosing any trade secret or confidential or proprietary information in the course of my employment with the Company or to refrain from
competing, directly or indirectly, with the business of such previous employer or any other party. I further represent that my performance of all the terms of this Agreement as an employee of the Company does not and will not breach any agreement to
keep in confidence proprietary information, knowledge or data acquired by me in confidence or in trust prior to my employment with the Company. I will not disclose to the Company or induce the Company to use any confidential or proprietary
information or material belonging to any previous employer or others. 
 11. Remedies Upon Breach. I understand that the restrictions
contained in this Agreement are necessary for the protection of the business and goodwill of the Company and I consider them to be reasonable for such purpose. Any breach of this Agreement is likely to cause the Company substantial and irrevocable
damage and therefore, in the event of such breach, the Company, in addition to such other remedies which may be available, will be entitled to specific performance and other injunctive relief.

 

  
 3 

 12. Use of Voice, Image and Likeness. I give the Company permission to use my voice, image or
likeness, with or without using my name, for the purposes of advertising and promoting the Company, or for other purposes deemed appropriate by the Company in its reasonable discretion, except to the extent expressly prohibited by law. 

13. Publications and Public Statements. I will obtain the Company’s written approval before publishing or submitting for publication any
material that relates to my work at the Company and/or incorporates any Proprietary Information. To ensure that the Company delivers a consistent message about its products, services and operations to the public, and further in recognition that even
positive statements may have a detrimental effect on the Company in certain securities transactions and other contexts, any statement about the Company which I create, publish or post during my period of employment and for six (6) months
thereafter, on any media accessible by the public, including but not limited to electronic bulletin boards and Internet-based chat rooms, must first be reviewed and approved by an officer of the Company before it is released in the public domain.

 14. No Employment Obligation. I understand that this Agreement does not create an obligation on the Company or any other person to continue
my employment. I acknowledge that, unless otherwise agreed in a formal written employment agreement signed on behalf of the Company by an authorized officer, my employment with the Company is at will and therefore may be terminated by the Company or
me at any time and for any reason. 
 15. Survival and Assignment by the Company. I understand that my obligations under this Agreement will
continue in accordance with its express terms regardless of any changes in my title, position, duties, salary, compensation or benefits or other terms and conditions of employment. I further understand that my obligations under this Agreement will
continue following the termination of my employment regardless of the manner of such termination and will be binding upon my heirs, executors and administrators. The Company will have the right to assign this Agreement to its affiliates, successors
and assigns. I expressly consent to be bound by the provisions of this Agreement for the benefit of the Company or any parent, subsidiary or affiliate to whose employ I may be transferred without the necessity that this Agreement be resigned at the
time of such transfer. 

 16. Disclosure to Future Employers. I will provide a copy of this Agreement to any prospective
employer, partner or co-venturer prior to entering into an employment, partnership or other business relationship with such person or entity. 
 17.
Exit Interview. If and when I depart from the Company, I may be required to attend an exit interview and sign an “Employee Exit Acknowledgement” to reaffirm my acceptance and acknowledgement of the obligations set forth in this
Agreement. During the Restricted Period following termination of my employment, I will notify the Company of any change in my address and of each subsequent employment or business activity, including the name and address of my employer or other
post-Company employment plans and the nature of my activities. 
 18. Severability. In case any provisions (or portions thereof) contained in
this Agreement will, for any reason, be held invalid, illegal or unenforceable in any respect, such invalidity, illegality or unenforceability will not affect the other provisions of this Agreement, and this Agreement will be construed as if such
invalid, illegal or unenforceable provision had never been contained herein. If, moreover, any one or more of the provisions contained in this Agreement will for any reason be held to be excessively broad as to duration, geographical scope, activity
or subject, it will be construed by limiting and reducing it, so as to be enforceable to the extent compatible with the applicable law as it will then appear. 

19. Entire Agreement. This Agreement constitutes the entire and only agreement between the Company and me respecting the subject matter hereof,
and supersedes all prior agreements and understandings, oral or written, between us concerning such subject matter. No modification, amendment, waiver or termination of this Agreement or of any provision hereof will be binding unless made in writing
and signed by an authorized officer of the Company. Failure of the Company to insist upon strict compliance with any of the terms, covenants or conditions hereof will not be deemed a waiver of such terms, covenants or conditions. In the event of any
inconsistency between this Agreement and any other contract between the Company and me, the provisions of this Agreement will prevail. 
 20.
Interpretation. This Agreement will be deemed to be made and entered into in the Commonwealth of Massachusetts, and will in all respects be interpreted,

 

  
 4 

 
enforced and governed under the laws of the Commonwealth of Massachusetts. I hereby agree to consent to personal jurisdiction of the state and federal courts situated within Suffolk County,
Massachusetts for purposes of enforcing this

 
Agreement, and waive any objection that I might have to personal jurisdiction or venue in those courts. As used in this Agreement, “including” means “including but not limited
to”. 

 

  
 BY SIGNING BELOW, I
CERTIFY THAT I HAVE READ THIS AGREEMENT CAREFULLY AND AM SATISFIED THAT I UNDERSTAND IT COMPLETELY. 
 IN WITNESS WHEREOF, the
undersigned has executed this agreement as a sealed instrument as of the date set forth below. 
  

					
	Signed:		  
		
			    (Employee’s full name)		

  

									
	Type or print name:		Roger J. Pomerantz, M.D.						
					
	Last four digits of SSN:		  
				Date:		  

  
 5 

 Appendix A 
  

					
	To:		Seres Therapeutics, Inc.		
			
	From:		Roger J. Pomerantz, M.D.		
			
	Date:		  
		

			
		
	SUBJECT:		Prior Inventions

 The following is a complete list of all inventions or improvements relevant to the subject matter of my
employment by the Company that have been made or conceived or first reduced to practice by me alone or jointly with others prior to my engagement by the Company: 
  

	 	 ̈	No inventions or improvements 

  

	 	 ̈	See below: 

			
	  
		
		
	  
		
		
	  
		
		
	  
		
		
	  
		
		
	  
		
		
	  
		

  

	 	 ̈	Additional sheets attached 

 The following is a list of all patents, patent applications and
other patent rights that I invented: 
  

	 	 ̈	None 

  

	 	 ̈	See below:EX-10.7

 Exhibit 10.7 

EMPLOYMENT AGREEMENT 

This Employment Agreement (this “Agreement”), dated as of June 14, 2015, is made by and between Seres Therapeutics, Inc., a
Delaware corporation (together with any successor thereto, the “Company”), and Eric D. Shaff (“Executive”) (collectively referred to as the “Parties” or individually referred to as a
“Party”). 
 RECITALS 
  

	A.	It is the desire of the Company to assure itself of the services of Executive following the Effective Date (as defined below) and thereafter by entering into this Agreement. 

 

	B.	Executive and the Company mutually desire that Executive provide services to the Company on the terms herein provided. 

AGREEMENT 
 NOW,
THEREFORE, in consideration of the foregoing and of the respective covenants and agreements set forth below, the Parties hereto agree as follows: 
 1.
Employment. 
 (a) General. Effective on the closing of the Company’s initial public offering of stock pursuant to an
effective registration statement filed under the Securities Act of 1933, as amended (the “Effective Date”), the Company shall employ Executive and Executive shall remain in the employ of the Company, for the period and in the
positions set forth in this Section 1, and subject to the other terms and conditions herein provided. 
 (b) At-Will
Employment. The Company and Executive acknowledge that Executive’s employment is and shall continue to be at-will, as defined under applicable law, and that Executive’s employment with the Company may be terminated by either Party at
any time for any or no reason (subject to the notice requirements of Section 3(b)). This “at-will” nature of Executive’s employment shall remain unchanged during Executive’s tenure as an employee and may not be
changed, except in an express writing signed by Executive and a duly authorized officer of the Company. If Executive’s employment terminates for any reason, Executive shall not be entitled to any payments, benefits, damages, award or
compensation other than as provided in this Agreement or otherwise agreed to in writing by the Company or as provided by applicable law. The term of this Agreement (the “Term”) shall commence on the Effective Date and end on the
date this Agreement is terminated under Section 3. 
 (c) Positions and Duties. Executive shall serve as Chief Financial
Officer and Executive Vice President of the Company with such responsibilities, duties and authority normally associated with such positions and as may from time to time be assigned to Executive by the Chief Executive Officer of the Company.
Executive shall devote substantially all of Executive’s working time and efforts to the business and affairs of the Company (which shall include service to its affiliates, if applicable) and shall not engage in outside business activities
(including serving on outside boards or committees) without the consent of the Board (as defined 

 
below), provided that Executive shall be permitted to (i) manage Executive’s personal, financial and legal affairs, (ii) participate in trade associations, and (iii) serve on
the board of directors of not-for-profit or tax-exempt charitable organizations, in each case, subject to compliance with this Agreement and provided that such activities do not materially interfere with Executive’s performance of
Executive’s duties and responsibilities hereunder. Executive agrees to observe and comply with the rules and policies of the Company as adopted by the Company from time to time, in each case as amended from time to time, as set forth in
writing, and as delivered or made available to Executive (each, a “Policy”). 
 2. Compensation and Related Matters. 

(a) Annual Base Salary. During the Term, Executive shall receive a base salary at a rate of $324,500 per annum, which shall be paid in
accordance with the customary payroll practices of the Company and shall be pro-rated for partial years of employment. Such annual base salary shall be reviewed (and may be adjusted) from time to time by the Board of Directors of the Company or an
authorized committee of the Board (in either case, the “Board”) (such annual base salary, as it may be adjusted from time to time, the “Annual Base Salary”). 

(b) Bonus. During the Term, Executive will be eligible to participate in an annual incentive program established by the Board.
Executive’s annual incentive compensation under such incentive program (the “Annual Bonus”) shall be targeted at 35% of Executive’s Annual Base Salary. The Annual Bonus payable under the incentive program shall be based on
the achievement of performance goals to be determined by the Board. The payment of any Annual Bonus pursuant to the incentive program shall be subject to Executive’s continued employment with the Company through the date of payment, except as
otherwise provided in Section 4(b). 
 (c) Benefits. During the Term, Executive shall be eligible to participate in
employee benefit plans, programs and arrangements of the Company (including medical, dental and 401(k) plans), consistent with the terms thereof and as such plans, programs and arrangements may be amended from time to time. In no event shall
Executive be eligible to participate in any severance plan or program of the Company, except as set forth in Section 4 of this Agreement. 

(d) Vacation. During the Term, Executive shall be entitled to paid personal leave in accordance with the Company’s Policies. Any
vacation shall be taken at the reasonable and mutual convenience of the Company and Executive. 
 (e) Business Expenses. During the
Term, the Company shall reimburse Executive for all reasonable travel and other business expenses incurred by Executive in the performance of Executive’s duties to the Company in accordance with the Company’s expense reimbursement Policy.

 (f) Key Person Insurance. At any time during the Term, the Company shall have the right to insure the life of Executive for the
Company’s sole benefit. The Company shall have the right to determine the amount of insurance and the type of policy. Executive shall reasonably cooperate with the Company in obtaining such insurance by submitting to physical examinations, by
supplying all information reasonably required by any insurance carrier, and by executing all necessary documents reasonably required by any insurance carrier, provided that any information 

  
 2 

 
provided to an insurance company or broker shall not be provided to the Company without the prior written authorization of Executive. Executive shall incur no financial obligation by executing
any required document, and shall have no interest in any such policy. 
 3. Termination. 

Executive’s employment hereunder may be terminated by the Company or Executive, as applicable, without any breach of this Agreement under
the following circumstances: 
 (a) Circumstances. 

(i) Death. Executive’s employment hereunder shall terminate upon Executive’s death. 

(ii) Disability. If Executive has incurred a Disability, as defined below, the Company may terminate Executive’s
employment. 
 (iii) Termination for Cause. The Company may terminate Executive’s employment for Cause, as
defined below. 
 (iv) Termination without Cause. The Company may terminate Executive’s employment without Cause.

 (v) Resignation from the Company for Good Reason. Executive may resign Executive’s employment with the Company
for Good Reason, as defined below. 
 (vi) Resignation from the Company Without Good Reason. Executive may resign
Executive’s employment with the Company for any reason other than Good Reason or for no reason. 
 (b) Notice of Termination.
Any termination of Executive’s employment by the Company or by Executive under this Section 3 (other than termination pursuant to paragraph (a)(i)) shall be communicated by a written notice to the other Party hereto
(i) indicating the specific termination provision in this Agreement relied upon, (ii) setting forth in reasonable detail the facts and circumstances claimed to provide a basis for termination of Executive’s employment under the
provision so indicated, if applicable, and (iii) specifying a Date of Termination which, if submitted by Executive, shall be at least forty-five (45) days following the date of such notice (a “Notice of Termination”);
provided, however, that in the event that Executive delivers a Notice of Termination to the Company, the Company may, in its sole discretion, change the Date of Termination to any date that occurs following the date of Company’s receipt
of such Notice of Termination and is prior to the date specified in such Notice of Termination. A Notice of Termination submitted by the Company may provide for a Date of Termination on the date Executive receives the Notice of Termination, or any
date thereafter elected by the Company in its sole discretion. The failure by the Company to set forth in the Notice of Termination any fact or circumstance which contributes to a showing of Cause shall not waive any right of the Company hereunder
or preclude the Company from asserting such fact or circumstance in enforcing the Company’s rights hereunder. 

  
 3 

 (c) Company Obligations upon Termination. Upon termination of Executive’s employment
pursuant to any of the circumstances listed in this Section 3, Executive (or Executive’s estate) shall be entitled to receive the sum of: (i) the portion of Executive’s Annual Base Salary earned through the Date of
Termination, but not yet paid to Executive; (ii) any expenses owed to Executive pursuant to Section 2(e); and (iii) any amount accrued and arising from Executive’s participation in, or benefits accrued under any employee
benefit plans, programs or arrangements, which amounts shall be payable in accordance with the terms and conditions of such employee benefit plans, programs or arrangements (collectively, the “Company Arrangements”). Except as
otherwise expressly required by law (e.g., COBRA) or as specifically provided herein, all of Executive’s rights to salary, severance, benefits, bonuses and other compensatory amounts hereunder (if any) shall cease upon the termination of
Executive’s employment hereunder. In the event that Executive’s employment is terminated by the Company for any reason, Executive’s sole and exclusive remedy shall be to receive the payments and benefits described in this
Section 3(c) or Section 4, as applicable. 
 (d) Deemed Resignation. Upon termination of Executive’s
employment for any reason, Executive shall be deemed to have resigned from all offices and directorships, if any, then held with the Company or any of its subsidiaries. 

4. Severance Payments. 
 (a)
Termination for Cause, or Termination Upon Death, Disability or Resignation from the Company Without Good Reason. If Executive’s employment shall terminate as a result of Executive’s death pursuant to Section 3(a)(i)
or Disability pursuant to Section 3(a)(ii), pursuant to Section 3(a)(iii) for Cause, or pursuant to Section 3(a)(vi) for Executive’s resignation from the Company without Good Reason, then Executive shall not
be entitled to any severance payments or benefits, except as provided in Section 3(c). 
 (b) Termination without Cause, or
Resignation from the Company for Good Reason. If Executive’s employment terminates without Cause pursuant to Section 3(a)(iv), or pursuant to Section 3(a)(v) due to Executive’s resignation for Good Reason, then,
subject to Executive signing on or before the 21st day following Executive’s Separation from Service (as defined below), and not revoking, a release of claims substantially in the form
attached as Exhibit A to this Agreement (the “Release”), and Executive’s continued compliance with Section 5, Executive shall receive, in addition to payments and benefits set forth in
Section 3(c), the following: 
 (i) an amount in cash equal to 0.5 times the Annual Base Salary, payable in the
form of salary continuation in regular installments over the 6-month period following the date of Executive’s Separation from Service (the “Severance Period”) in accordance with the Company’s normal payroll practices; 

(ii) to the extent unpaid as of the Date of Termination, an amount of cash equal to any Annual Bonus earned by Executive for
the Company’s fiscal year prior to the fiscal year in which the Date of Termination occurs, as determined by the Board in its discretion based upon actual performance achieved, which Annual Bonus, if any, shall be

  
 4 

 
paid to Executive in the fiscal year in which the Date of Termination occurs when bonuses for such prior fiscal year are paid in the ordinary course to actively employed senior executives of the
Company; and 
 (iii) if Executive elects to receive continued medical, dental or vision coverage under one or more of the
Company’s group healthcare plans pursuant to the Consolidated Omnibus Budget Reconciliation Act of 1985, as amended (“COBRA”), the Company shall directly pay, or reimburse Executive for, the COBRA premiums for Executive and
Executive’s covered dependents under such plans during the period commencing on Executive’s Separation from Service and ending upon the earliest of (X) the last day of the Severance Period, (Y) the date that Executive and/or
Executive’s covered dependents become no longer eligible for COBRA or (Z) the date Executive becomes eligible to receive healthcare coverage from a subsequent employer (and Executive agrees to promptly notify the Company of such
eligibility). Notwithstanding the foregoing, if the Company determines in its sole discretion that it cannot provide the foregoing benefit without potentially violating applicable law (including, without limitation, Section 2716 of the Public
Health Service Act) or incurring an excise tax, the Company shall in lieu thereof provide to Executive a taxable monthly payment in an amount equal to the monthly COBRA premium that Executive would be required to pay to continue Executive’s and
Executive’s covered dependents’ group health coverage in effect on the Date of Termination (which amount shall be based on the premium for the first month of COBRA coverage), less the amount Executive would have had to pay to receive group
health coverage for Executive and his or her covered dependents based on the cost sharing levels in effect on the Date of Termination, which payments shall be made regardless of whether Executive elects COBRA continuation coverage and shall commence
in the month following the month in which the Date of Termination occurs and shall end on the earlier of (X) the last day of the Severance Period, (Y) the date that Executive and/or Executive’s covered dependents become no longer
eligible for COBRA or (Z) the date Executive becomes eligible to receive healthcare coverage from a subsequent employer (and Executive agrees to promptly notify the Company of such eligibility). 

(c) Change in Control. Notwithstanding anything to the contrary in Section 4(b), in the event Executive’s employment
terminates without Cause pursuant to Section 3(a)(iv), or pursuant to Section 3(a)(v) due to Executive’s resignation for Good Reason, in either case, within 60 days prior to or 12 months following the date of a Change in
Control, subject to Executive signing on or before the 21st day following Executive’s Separation from Service, and not revoking, the Release, all unvested equity or equity-based awards held
by Executive under any Company equity compensation plans that vest solely based on the passage of time shall immediately become 100% vested (for the avoidance of doubt, with any such awards that vest in whole or in part based on the attainment of
performance-vesting conditions being governed by the terms of the applicable award agreement). 
 (d) Survival. Notwithstanding
anything to the contrary in this Agreement, the provisions of Sections 5 through 9 will survive the termination of Executive’s employment and the termination of the Term. 

  
 5 

 5. Restrictive Covenants. As a condition to the effectiveness of this Agreement, Executive will
execute and deliver to the Company contemporaneously herewith the Employee Non-Competition, Non-Solicitation, Confidentiality and Assignment Agreement attached as Exhibit B (the “Proprietary Information Agreement”). Executive
agrees to abide by the terms of the Proprietary Information Agreement, which are hereby incorporated by reference into this Agreement. Executive acknowledges that the provisions of the Proprietary Information Agreement will survive the termination
of Executive’s employment and the termination of the Term for the periods set forth in the Proprietary Information Agreement. 
 6. Assignment
and Successors. 
 The Company may assign its rights and obligations under this Agreement to any of its affiliates or to any
successor to all or substantially all of the business or the assets of the Company (by merger or otherwise), and may assign or encumber this Agreement and its rights hereunder as security for indebtedness of the Company and its affiliates. This
Agreement shall be binding upon and inure to the benefit of the Company, Executive and their respective successors, assigns, personnel and legal representatives, executors, administrators, heirs, distributees, devisees, and legatees, as applicable.
None of Executive’s rights or obligations may be assigned or transferred by Executive, other than Executive’s rights to payments hereunder, which may be transferred only by will or operation of law. Notwithstanding the foregoing, Executive
shall be entitled, to the extent permitted under applicable law and applicable Company Arrangements, to select and change a beneficiary or beneficiaries to receive compensation hereunder following Executive’s death by giving written notice
thereof to the Company. 
 7. Certain Definitions. 

(a) Cause. The Company shall have “Cause” to terminate Executive’s employment hereunder upon: 

(i) Executive’s failure to (A) substantially perform Executive’s duties with the Company (other than any such
failure resulting from Executive’s Disability) or (B) comply with, in any material respect, any of the Company’s Policies; 

(ii) the Board’s determination that Executive failed in any material respect to carry out or comply with any lawful and
reasonable directive of the Board; 
 (iii) Executive’s breach of a material provision of this Agreement; 

(iv) Executive’s conviction, plea of no contest, plea of nolo contendere, or imposition of unadjudicated probation
for any felony or crime involving moral turpitude; 
 (v) Executive’s unlawful use (including being under the influence)
or possession of illegal drugs on the Company’s (or any of its affiliate’s) premises or while performing Executive’s duties and responsibilities under this Agreement; or 

(vi) Executive’s commission of an act of fraud, embezzlement, misappropriation, willful misconduct, or breach of fiduciary
duty against the Company or any of its affiliates. 

  
 6 

 (b) Change in Control. “Change in Control” shall have the meaning set forth in
the version of the Seres Therapeutics, Inc. 2015 Incentive Award Plan in effect on the Effective Date. 
 (c) Code. “Code”
shall mean the Internal Revenue Code of 1986, as amended, and the regulations and guidance promulgated thereunder. 
 (d) Date of
Termination. “Date of Termination” shall mean (i) if Executive’s employment is terminated by Executive’s death, the date of Executive’s death; or (ii) if Executive’s employment is terminated pursuant to
Section 3(a)(ii) – (vi) either the date indicated in the Notice of Termination or the date specified by the Company pursuant to Section 3(b), whichever is earlier. 

(e) Disability. “Disability” shall mean, at any time the Company or any of its affiliates sponsors a long-term disability
plan for the Company’s employees, “disability” as defined in such long-term disability plan for the purpose of determining a participant’s eligibility for benefits, provided, however, if the long-term disability plan
contains multiple definitions of disability, “Disability” shall refer to that definition of disability which, if Executive qualified for such disability benefits, would provide coverage for the longest period of time. The determination of
whether Executive has a Disability shall be made by the person or persons required to make disability determinations under the long-term disability plan. At any time the Company does not sponsor a long-term disability plan for its employees,
“Disability” shall mean Executive’s inability to perform, with or without reasonable accommodation, the essential functions of Executive’s positions hereunder for a total of three months during any six-month period as a result of
incapacity due to mental or physical illness as determined by a physician selected by the Company or its insurers and acceptable to Executive or Executive’s legal representative, with such agreement as to acceptability not to be unreasonably
withheld or delayed. Any refusal by Executive to submit to a medical examination for the purpose of determining Disability shall be deemed to constitute conclusive evidence of Executive’s Disability. 

(f) Good Reason. For the sole purpose of determining Executive’s right to severance payments and benefits as described above,
Executive’s resignation will be for “Good Reason” if Executive resigns within ninety days after any of the following events, unless Executive consents to the applicable event: (i) a decrease in Executive’s Annual Base
Salary, other than a reduction in Annual Base Salary of less than 10% that is implemented in connection with a contemporaneous reduction in annual base salaries affecting other senior executives of the Company, (ii) a material decrease in
Executive’s authority or areas of responsibility as are commensurate with Executive’s title or positions, or (iii) the relocation of Executive’s primary office to a location more than 50 miles from the Boston metropolitan area.
Notwithstanding the foregoing, no Good Reason will have occurred unless and until Executive has: (a) provided the Company, within 60 days of Executive’s knowledge of the occurrence of the facts and circumstances underlying the Good Reason
event, written-notice stating with specificity the applicable facts and circumstances underlying such finding of Good Reason; and (b) provided the Company with an opportunity to cure the same within 30 days after the receipt of such notice.

  
 7 

 8. Parachute Payments. 

(a) Notwithstanding any other provisions of this Agreement, in the event that any payment or benefit by the Company or otherwise to or for the
benefit of Executive, whether paid or payable or distributed or distributable pursuant to the terms of this Agreement or otherwise (all such payments and benefits, including the payments and benefits under Section 4(b) and
Section 4(c) hereof, being hereinafter referred to as the “Total Payments”), would be subject (in whole or in part) to the excise tax imposed by Section 4999 of the Code (the “Excise Tax”), then the
Total Payments shall be reduced (in the order provided in Section 8(b)) to the minimum extent necessary to avoid the imposition of the Excise Tax on the Total Payments, but only if (i) the net amount of such Total Payments, as so
reduced (and after subtracting the net amount of federal, state and local income and employment taxes on such reduced Total Payments and after taking into account the phase out of itemized deductions and personal exemptions attributable to such
reduced Total Payments), is greater than or equal to (ii) the net amount of such Total Payments without such reduction (but after subtracting the net amount of federal, state and local income and employment taxes on such Total Payments and the
amount of the Excise Tax to which Executive would be subject in respect of such unreduced Total Payments and after taking into account the phase out of itemized deductions and personal exemptions attributable to such unreduced Total Payments). 

(b) The Total Payments shall be reduced in the following order: (i) reduction on a pro-rata basis of any cash severance payments that are
exempt from Section 409A of the Code (“Section 409A”), (ii) reduction on a pro-rata basis any non-cash severance payments or benefits that are exempt from Section 409A, (iii) reduction on a pro-rata basis of any
other payments or benefits that are exempt from Section 409A, and (iv) reduction of any payments or benefits otherwise payable to Executive on a pro-rata basis or such other manner that complies with Section 409A; provided, in case of
clauses (ii), (iii) and (iv), that reduction of any payments attributable to the acceleration of vesting of Company equity awards shall be first applied to Company equity awards that would otherwise vest last in time. 

(c) All determinations regarding the application of this Section 8 shall be made by an accounting firm or consulting group with
experience in performing calculations regarding the applicability of Section 280G of the Code and the Excise Tax selected by the Company (the “Independent Advisors”). For purposes of determinations, no portion of the Total
Payments shall be taken into account which, in the opinion of the Independent Advisors, (i) does not constitute a “parachute payment” within the meaning of Section 280G(b)(2) of the Code (including by reason of
Section 280G(b)(4)(A) of the Code) or (ii) constitutes reasonable compensation for services actually rendered, within the meaning of Section 280G(b)(4)(B) of the Code, in excess of the “base amount” (as defined in
Section 280G(b)(3) of the Code) allocable to such reasonable compensation. The costs of obtaining such determination and all related fees and expenses (including related fees and expenses incurred in any later audit) shall be borne by the
Company. 
 (d) In the event it is later determined that a greater reduction in the Total Payments should have been made to implement the
objective and intent of this Section 8, the excess amount shall be returned immediately by Executive to the Company. 

  
 8 

 9. Miscellaneous Provisions. 

(a) Governing Law. This Agreement shall be governed, construed, interpreted and enforced in accordance with its express terms,
and otherwise in accordance with the substantive laws of the Commonwealth of Massachusetts without reference to the principles of conflicts of law of the Commonwealth of Massachusetts or any other jurisdiction, and where applicable, the laws of the
United States. 
 (b) Validity. The invalidity or unenforceability of any provision or provisions of this Agreement
shall not affect the validity or enforceability of any other provision of this Agreement, which shall remain in full force and effect.  

(c) Notices. Any notice, request, claim, demand, document and other communication hereunder to any Party shall be effective upon
receipt (or refusal of receipt) and shall be in writing and delivered personally or sent by facsimile or certified or registered mail, postage prepaid, as follows: 

(i) If to the Company, the Chief Executive Officer at its headquarters, 

(ii) If to Executive, at the last address that the Company has in its personnel records for Executive, or 

(iii) at any other address as any Party shall have specified by notice in writing to the other Party. 

(d) Counterparts. This Agreement may be executed in several counterparts, each of which shall be deemed to be an original, but all of
which together will constitute one and the same Agreement. Signatures delivered by facsimile shall be deemed effective for all purposes. 

(e) Entire Agreement. The terms of this Agreement, and the Proprietary Information Agreement incorporated herein by reference as set
forth in Section 5, are intended by the Parties to be the final expression of their agreement with respect to the subject matter hereof and supersede all prior understandings and agreements, whether written or oral, including the
employment offer letter agreement between Executive and the Company, dated as of October 29, 2014. The Parties further intend that this Agreement shall constitute the complete and exclusive statement of their terms and that no extrinsic
evidence whatsoever may be introduced in any judicial, administrative, or other legal proceeding to vary the terms of this Agreement. 
 (f)
Amendments; Waivers. This Agreement may not be modified, amended, or terminated except by an instrument in writing, signed by Executive and a duly authorized officer of Company. By an instrument in writing similarly executed, Executive or a
duly authorized officer of the Company may waive compliance by the other Party with any specifically identified provision of this Agreement that such other Party was or is obligated to comply with or perform;

  
 9 

 
provided, however, that such waiver shall not operate as a waiver of, or estoppel with respect to, any other or subsequent failure. No failure to exercise and no delay in exercising
any right, remedy, or power hereunder preclude any other or further exercise of any other right, remedy, or power provided herein or by law or in equity. 

(g) No Inconsistent Actions. The Parties hereto shall not voluntarily undertake or fail to undertake any action or course of action
inconsistent with the provisions or essential intent of this Agreement. Furthermore, it is the intent of the Parties hereto to act in a fair and reasonable manner with respect to the interpretation and application of the provisions of this
Agreement. 
 (h) Construction. This Agreement shall be deemed drafted equally by both the Parties. Its language shall be construed
as a whole and according to its fair meaning. Any presumption or principle that the language is to be construed against any Party shall not apply. The headings in this Agreement are only for convenience and are not intended to affect construction or
interpretation. Any references to paragraphs, subparagraphs, sections or subsections are to those parts of this Agreement, unless the context clearly indicates to the contrary. Also, unless the context clearly indicates to the contrary, (i) the
plural includes the singular and the singular includes the plural; (ii) “and” and “or” are each used both conjunctively and disjunctively; (iii) “any,” “all,” “each,” or “every”
means “any and all,” and “each and every”; (iv) “includes” and “including” are each “without limitation”; (v) “herein,” “hereof,” “hereunder” and other similar
compounds of the word “here” refer to the entire Agreement and not to any particular paragraph, subparagraph, section or subsection; and (vi) all pronouns and any variations thereof shall be deemed to refer to the masculine, feminine,
neuter, singular or plural as the identity of the entities or persons referred to may require. 
 (i) Arbitration. Any controversy,
claim or dispute arising out of or relating to this Agreement, shall be settled solely and exclusively by a binding arbitration process administered by JAMS/Endispute in Boston, Massachusetts. Such arbitration shall be conducted in accordance with
the then-existing JAMS/Endispute Rules of Practice and Procedure, with the following exceptions if in conflict: (i) one arbitrator who is a retired judge shall be chosen by JAMS/Endispute; (ii) each Party to the arbitration will pay
one-half of the expenses and fees of the arbitrator, together with other expenses of the arbitration incurred or approved by the arbitrator; and (iii) arbitration may proceed in the absence of any Party if written notice (pursuant to the
JAMS/Endispute rules and regulations) of the proceedings has been given to such Party. Each Party shall bear its own attorney’s fees and expenses; provided that the arbitrator may assess the prevailing Party’s fees and costs against the
non-prevailing Party as part of the arbitrator’s award. The Parties agree to abide by all decisions and awards rendered in such proceedings. Such decisions and awards rendered by the arbitrator shall be final and conclusive. All such
controversies, claims or disputes shall be settled in this manner in lieu of any action at law or equity; provided, however, that nothing in this subsection shall be construed as precluding the bringing of an action for injunctive relief or
specific performance as provided in this Agreement. This dispute resolution process and any arbitration hereunder shall be confidential and neither any Party nor the neutral arbitrator shall disclose the existence, contents or results of such
process without the prior written consent of all Parties, except where necessary or compelled in a Court to enforce this arbitration provision or an Award from such arbitration or otherwise in a legal proceeding. If JAMS/Endispute no longer exists
or is otherwise unavailable, 

  
 10 

 
the Parties agree that the American Arbitration Association (“AAA’) shall administer the arbitration in accordance with its then-existing rules as modified by this subsection. In
such event, all references herein to JAMS/Endispute shall mean AAA. Notwithstanding the foregoing, Executive and the Company each have the right to resolve any issue or dispute over intellectual property rights by Court action instead of
arbitration. 
 (j) Enforcement. If any provision of this Agreement is held to be illegal, invalid or unenforceable under present or
future laws effective during the Term, such provision shall be fully severable; this Agreement shall be construed and enforced as if such illegal, invalid or unenforceable provision had never comprised a portion of this Agreement; and the remaining
provisions of this Agreement shall remain in full force and effect and shall not be affected by the illegal, invalid or unenforceable provision or by its severance from this Agreement. Furthermore, in lieu of such illegal, invalid or unenforceable
provision there shall be added automatically as part of this Agreement a provision as similar in terms to such illegal, invalid or unenforceable provision as may be possible and be legal, valid and enforceable. 

(k) Withholding. The Company shall be entitled to withhold from any amounts payable under this Agreement any federal, state, local or
foreign withholding or other taxes or charges which the Company is required to withhold. The Company shall be entitled to rely on an opinion of counsel if any questions as to the amount or requirement of withholding shall arise. 

(l) Section 409A. 

(i) General. The intent of the Parties is that the payments and benefits under this Agreement comply with or be exempt
from Section 409A and, accordingly, to the maximum extent permitted, this Agreement shall be interpreted to be in compliance therewith. 

(ii) Separation from Service. Notwithstanding anything in this Agreement to the contrary, any compensation or benefits
payable under this Agreement that is considered nonqualified deferred compensation under Section 409A and is designated under this Agreement as payable upon Executive’s termination of employment shall be payable only upon Executive’s
“separation from service” with the Company within the meaning of Section 409A (a “Separation from Service”) and, except as provided below, any such compensation or benefits described in Section 4 shall not
be paid, or, in the case of installments, shall not commence payment, until the thirtieth (30th) day following Executive’s Separation from Service (the “First Payment Date”). Any installment payments that would have been
made to Executive during the thirty (30) day period immediately following Executive’s Separation from Service but for the preceding sentence shall be paid to Executive on the First Payment Date and the remaining payments shall be made as
provided in this Agreement. 
 (iii) Specified Employee. Notwithstanding anything in this Agreement to the contrary,
if Executive is deemed by the Company at the time of Executive’s Separation from Service to be a “specified employee” for purposes of Section 409A, to the extent delayed commencement of any portion of the benefits to which
Executive is entitled 

  
 11 

 
under this Agreement is required in order to avoid a prohibited distribution under Section 409A, such portion of Executive’s benefits shall not be provided to Executive prior to the
earlier of (i) the expiration of the six-month period measured from the date of Executive’s Separation from Service with the Company or (ii) the date of Executive’s death. Upon the first business day following the expiration of
the applicable Section 409A period, all payments deferred pursuant to the preceding sentence shall be paid in a lump sum to Executive (or Executive’s estate or beneficiaries), and any remaining payments due to Executive under this
Agreement shall be paid as otherwise provided herein. 
 (iv) Expense Reimbursements. To the extent that any
reimbursements under this Agreement are subject to Section 409A, any such reimbursements payable to Executive shall be paid to Executive no later than December 31 of the year following the year in which the expense was incurred; provided,
that Executive submits Executive’s reimbursement request promptly following the date the expense is incurred, the amount of expenses reimbursed in one year shall not affect the amount eligible for reimbursement in any subsequent year, other
than medical expenses referred to in Section 105(b) of the Code, and Executive’s right to reimbursement under this Agreement will not be subject to liquidation or exchange for another benefit. 

(v) Installments. Executive’s right to receive any installment payments under this Agreement, including without
limitation any continuation salary payments that are payable on Company payroll dates, shall be treated as a right to receive a series of separate payments and, accordingly, each such installment payment shall at all times be considered a separate
and distinct payment as permitted under Section 409A. Except as otherwise permitted under Section 409A, no payment hereunder shall be accelerated or deferred unless such acceleration or deferral would not result in additional tax or
interest pursuant to Section 409A. 
 10. Executive Acknowledgement. 

Executive acknowledges that Executive has read and understands this Agreement, is fully aware of its legal effect, has not acted in reliance
upon any representations or promises made by the Company other than those contained in writing herein, and has entered into this Agreement freely based on Executive’s own judgment. 

[Signature Page Follows] 

  
 12 

 IN WITNESS WHEREOF, the Parties have executed this Agreement on the date and year first above
written. 
  

					
	SERES THERAPEUTICS, INC.
		
	By:		 /s/ Roger J. Pomerantz

			Name:		Roger J. Pomerantz, M.D.
			Title:		President and Chief Executive Officer
	
	 /s/ Eric D. Shaff

	Eric D. Shaff

 EXHIBIT A 

Separation Agreement and Release 

This Separation Agreement and Release (“Agreement”) is made by and between Eric D. Shaff (“Executive”) and Seres
Therapeutics, Inc. (the “Company”) (collectively referred to as the “Parties” or individually referred to as a “Party”). Capitalized terms used but not defined in this Agreement shall have the meanings set forth in the
Employment Agreement (as defined below). 
 WHEREAS, the Parties have previously entered into that certain Employment Agreement, dated as of
June 14, 2015 (the “Employment Agreement”); and 
 WHEREAS, in connection with Executive’s termination of employment with the
Company or a subsidiary or affiliate of the Company effective             , 20    , the Parties wish to resolve any and all disputes, claims, complaints, grievances,
charges, actions, petitions, and demands that Executive may have against the Company and any of the Releasees as defined below, including, but not limited to, any and all claims arising out of or in any way related to Executive’s employment
with or separation from the Company or its subsidiaries or affiliates but, for the avoidance of doubt, nothing herein will be deemed to release any rights or remedies in connection with Executive’s ownership of vested equity securities of the
Company or Executive’s right to indemnification by the Company or any of its affiliates pursuant to contract or applicable law (collectively, the “Retained Claims”). 

NOW, THEREFORE, in consideration of the severance payments and benefits described in Section 4 of the Employment Agreement, which,
pursuant to the Employment Agreement, are conditioned on Executive’s execution and non-revocation of this Agreement, and in consideration of the mutual promises made herein, the Company and Executive hereby agree as follows: 

1. Severance Payments; Salary and Benefits. The Company agrees to provide Executive with the severance payments and benefits described
in Section 4(b) and/or Section 4(c) of the Employment Agreement, payable at the times set forth in, and subject to the terms and conditions of, the Employment Agreement. In addition, to the extent not already paid, and subject to the terms
and conditions of the Employment Agreement, the Company shall pay or provide to Executive all other payments or benefits described in Section 3(c) of the Employment Agreement, subject to and in accordance with the terms thereof. 

2. Release of Claims. Executive agrees that, other than with respect to the Retained Claims, the foregoing consideration represents
settlement in full of all outstanding obligations owed to Executive by the Company, any of its direct or indirect subsidiaries and affiliates, and any of their current and former officers, directors, equity holders, managers, employees, agents,
investors, attorneys, shareholders, administrators, affiliates, benefit plans, plan administrators, insurers, trustees, divisions, and subsidiaries and predecessor and successor corporations and assigns (collectively, the “Releasees”).
Executive, on Executive’s own behalf and on behalf of any of Executive’s affiliated companies or entities and any of their respective heirs, family members, executors, agents, and assigns, other than with respect to the Retained Claims,
hereby and forever releases the Releasees from, and agrees not to sue concerning, or in any manner to 

 
institute, prosecute, or pursue, any claim, complaint, charge, duty, obligation, or cause of action relating to any matters of any kind, whether presently known or unknown, suspected or
unsuspected, that Executive may possess against any of the Releasees arising from any omissions, acts, facts, or damages that have occurred up until and including the Effective Date of this Agreement (as defined in Section 7 below), including,
without limitation: 
 (a) any and all claims relating to or arising from Executive’s employment or service relationship with the
Company or any of its direct or indirect subsidiaries or affiliates and the termination of that relationship; 
 (b) any and all claims
relating to, or arising from, Executive’s right to purchase, or actual purchase of any shares of stock or other equity interests of the Company or any of its affiliates, including, without limitation, any claims for fraud, misrepresentation,
breach of fiduciary duty, breach of duty under applicable state corporate law, and securities fraud under any state or federal law; 
 (c)
any and all claims for wrongful discharge of employment; termination in violation of public policy; discrimination; harassment; retaliation; breach of contract, both express and implied; breach of covenant of good faith and fair dealing, both
express and implied; promissory estoppel; negligent or intentional infliction of emotional distress; fraud; negligent or intentional misrepresentation; negligent or intentional interference with contract or prospective economic advantage; unfair
business practices; defamation; libel; slander; negligence; personal injury; assault; battery; invasion of privacy; false imprisonment; conversion; and disability benefits; 

(d) any and all claims for violation of any federal, state, or municipal statute, including, but not limited to, Title VII of the Civil Rights
Act of 1964; the Civil Rights Act of 1991; the Rehabilitation Act of 1973; the Americans with Disabilities Act of 1990; the Equal Pay Act; the Fair Credit Reporting Act; the Age Discrimination in Employment Act of 1967; the Older Workers Benefit
Protection Act; the Employee Retirement Income Security Act of 1974; the Worker Adjustment and Retraining Notification Act; the Family and Medical Leave Act; and the Sarbanes-Oxley Act of 2002; 

(e) any and all claims for violation of the federal or any state constitution; 

(f) any and all claims arising out of any other laws and regulations relating to employment or employment discrimination; 

(g) any claim for any loss, cost, damage, or expense arising out of any dispute over the non-withholding or other tax treatment of any of the
proceeds received by Executive as a result of this Agreement; and 
 (h) any and all claims for attorneys’ fees and costs. 

Executive agrees that the release set forth in this section shall be and remain in effect in all respects as a complete general release as to the matters
released. This release does not release claims that cannot be released as a matter of law, including, but not limited to, Executive’s right 

  
 2 

 
to report possible violations of federal law or regulation to any governmental agency or entity in accordance with the provisions of and rules promulgated under Section 21F of the Securities
Exchange Act of 1934 or Section 806 of the Sarbanes-Oxley Act of 2002, or any other whistleblower protection provisions of state or federal law or regulation, Executive’s right to file a charge with or participate in a charge by the Equal
Employment Opportunity Commission, or any other local, state, or federal administrative body or government agency that is authorized to enforce or administer laws related to employment, against the Company (with the understanding that
Executive’s release of claims herein bars Executive from recovering such monetary relief from the Company or any Releasee), claims for unemployment compensation or any state disability insurance benefits pursuant to the terms of applicable
state law, claims to continued participation in certain of the Company’s group benefit plans pursuant to the terms and conditions of COBRA, claims to any benefit entitlements vested as the date of separation of Executive’s employment,
pursuant to written terms of any employee benefit plan of the Company or its affiliates and Executive’s right under applicable law and any Retained Claims. This release further does not release claims for breach of Section 3(c),
Section 4(b) or Section 4(c) of the Employment Agreement. 
 3. Acknowledgment of Waiver of Claims under ADEA. Executive
understands and acknowledges that Executive is waiving and releasing any rights Executive may have under the Age Discrimination in Employment Act of 1967 (“ADEA”), and that this waiver and release is knowing and voluntary. Executive
understands and agrees that this waiver and release does not apply to any rights or claims that may arise under the ADEA after the Effective Date of this Agreement. Executive understands and acknowledges that the consideration given for this waiver
and release is in addition to anything of value to which Executive was already entitled. Executive further understands and acknowledges that Executive has been advised by this writing that: (a) Executive should consult with an attorney prior to
executing this Agreement; (b) Executive has 21 days within which to consider this Agreement; (c) Executive has 7 days following Executive’s execution of this Agreement to revoke this Agreement pursuant to written notice to the General
Counsel of the Company; (d) this Agreement shall not be effective until after the revocation period has expired; and (e) nothing in this Agreement prevents or precludes Executive from challenging or seeking a determination in good faith of
the validity of this waiver under the ADEA, nor does it impose any condition precedent, penalties, or costs for doing so, unless specifically authorized by federal law. In the event Executive signs this Agreement and returns it to the Company in
less than the 21 day period identified above, Executive hereby acknowledges that Executive has freely and voluntarily chosen to waive the time period allotted for considering this Agreement. 

4. Severability. In the event that any provision or any portion of any provision hereof or any surviving agreement made a part hereof
becomes or is declared by a court of competent jurisdiction or arbitrator to be illegal, unenforceable, or void, this Agreement shall continue in full force and effect without said provision or portion of provision. 

5. No Oral Modification. This Agreement may only be amended in a writing signed by Executive and a duly authorized officer of the
Company. 

  
 3 

 6. Governing Law; Dispute Resolution. This Agreement shall be subject to the provisions of
Sections 9(a), 9(c) and 9(i) of the Employment Agreement. 
 7. Effective Date. If Executive has attained or is over the age of 40 as
of the date of Executive’s termination of employment, then each Party has seven days after that Party signs this Agreement to revoke it and this Agreement will become effective on the eighth day after Executive signed this Agreement, so long as
it has been signed by the Parties and has not been revoked by either Party before that date (the “Effective Date”). If Executive has not attained the age of 40 as of the date of Executive’s termination of employment, then the
“Effective Date” shall be the date on which Executive signs this Agreement. 
 8. Voluntary Execution of Agreement.
Executive understands and agrees that Executive executed this Agreement voluntarily, without any duress or undue influence on the part or behalf of the Company or any third party, with the full intent of releasing all of Executive’s claims
against the Company and any of the other Releasees. Executive acknowledges that: (a) Executive has read this Agreement; (b) Executive has not relied upon any representations or statements made by the Company that are not specifically set
forth in this Agreement; (c) Executive has been represented in the preparation, negotiation, and execution of this Agreement by legal counsel of Executive’s own choice or has elected not to retain legal counsel; (d) Executive
understands the terms and consequences of this Agreement and of the releases it contains; and (e) Executive is fully aware of the legal and binding effect of this Agreement. 

IN WITNESS WHEREOF, the Parties have executed this Agreement on the respective dates set forth below. 

 

									
	Dated:		  
				  

							Eric D. Shaff
				
							SERES THERAPEUTICS, INC.
					
	Dated:		  
				By:		  

									Name:
									Title:

  
 4 

 EXHIBIT B 

Employee Non-Competition, Non-Solicitation, Confidentiality and Assignment Agreement 

In consideration and as a condition of my employment or continued employment by Seres Therapeutics, Inc. (the “Company”), I
hereby agree as follows: 

 

 1. Proprietary Information. I agree that all information, whether or not in writing, whether or
not disclosed before or after I was first employed by the Company, concerning the Company’s business, technology, business relationships or financial affairs that the Company has not released to the general public (collectively,
“Proprietary Information”), and all tangible embodiments thereof, are and will be the exclusive property of the Company. By way of illustration, Proprietary Information may include information or material that has not been made generally
available to the public, such as: (a) corporate information, including plans, strategies, methods, policies, resolutions, notes, email correspondence, negotiations or litigation; (b) marketing information, including
strategies, methods, customer identities or other information about customers, prospect identities or other information about prospects, or market analyses or projections; (c) financial information, including cost and performance data,
debt arrangements, equity structure, investors and holdings, purchasing and sales data and price lists; and (d) operational and technological information, including plans, specifications, manuals, forms, templates, software, designs,
methods, procedures, formulas, discoveries, inventions, improvements, biological or chemical materials, concepts and ideas; and (e) personnel information, including personnel lists, reporting or organizational structure, resumes,
personnel data, compensation structure, performance evaluations and termination arrangements or documents. Proprietary Information includes, without limitation, (1) information received in confidence by the Company from its customers or
suppliers or other third parties, and (2) all biological or chemical materials and other tangible embodiments of the Proprietary Information. Nothing in this Agreement shall prohibit me from reporting possible violations of federal law or
regulation to any governmental agency or entity in accordance with the provisions of and rules promulgated under Section 21F of the Securities Exchange Act of 1934 or Section 805 of the Sarbanes-Oxley Act of 2002, or any other
whistleblower protection provisions of state or federal law or regulation.

 2. Recognition of Company’s Rights. I will not, at any time, without the Company’s prior
written permission, either during or after my employment, disclose or transfer any Proprietary Information to anyone outside of the Company, or use or permit to be used any Proprietary Information for any purpose other than the performance of my
duties as an employee of the Company. I will cooperate with the Company and use my best efforts to prevent the unauthorized disclosure of all Proprietary Information. I will deliver to the Company all copies and other tangible embodiments of
Proprietary Information in my possession or control upon the earlier of a request by the Company or termination of my employment. 
 3. Rights of
Others. I understand that the Company is now and may hereafter be subject to non-disclosure or confidentiality agreements with third persons which require the Company to protect or refrain from use of proprietary information. I agree to be
bound by the terms of such agreements in the event I have access to such proprietary information. 
 4. Commitment to Company; Avoidance of Conflict
of Interest. While an employee of the Company, I will devote my full-time efforts to the Company’s business and I will not engage in any other business activity that conflicts with my duties to the Company. I will advise the president
of the Company or his or her nominee at such time as any activity of either the Company or another business presents me with a conflict of interest or the appearance of a conflict of interest as an employee of the Company. I will take whatever
action is requested of me by the Company to resolve any conflict or appearance of conflict which it finds to exist. 
 5. Developments. I
hereby assign and transfer and, to the extent any such assignment cannot be made at present, will assign and transfer, to the Company and its successors and assigns, all my right, title and interest in and to all Developments (as defined below)
that: (a) are created, developed, made, conceived or reduced to practice by me (alone or jointly with others) or under my direction

 

 
(collectively, “conceived”) during the period of my employment and six (6) months thereafter and that relate to the business of the Company or to products, methods or services
being researched, developed, manufactured or sold by the Company; or (b) result from tasks assigned to me by the Company; or (c) result from the use of premises, Proprietary Information or personal property (whether tangible or intangible)
owned, licensed or leased by the Company (collectively, “Company-Related Developments”), and all patent rights, trademarks, copyrights and other intellectual property rights in all countries and territories worldwide claiming,
covering or otherwise arising from or pertaining to Company-Related Developments (collectively, “Intellectual Property Rights”). I further agree that “Company-Related Developments” include, without limitation, all
Developments that (i) were conceived by me before my employment, (ii) relate to the business of the Company or to products, methods or services being researched, developed, manufactured or sold by the Company, and (iii) were not
subject to an obligation to assign to another entity when conceived. I will make full and prompt disclosure to the Company of all Company-Related Developments, as well as all other Developments conceived by me during the period of my employment and
six (6) months thereafter. I acknowledge that all work performed by me as an employee of the Company is on a “work for hire” basis. I hereby waive all claims to any moral rights or other special rights which I may have or accrue in
any Company-Related Developments. “Developments” mean inventions, discoveries, designs, developments, methods, modifications, improvements, processes, biological or chemical materials, algorithms, databases, computer programs, formulae,
techniques, trade secrets, graphics or images, audio or visual works, and other works of authorship. 
 To preclude any possible uncertainty, I have set
forth on Appendix A attached hereto a complete list of Developments conceived by me before my employment that are not Company-Related Developments (“Prior Inventions”). I have also listed on Appendix A all patent rights of
which I am an inventor, other than those contained within Intellectual Property Rights (“Other Patent Rights”). If no such disclosure is attached, I represent that there are no Prior Inventions or Other Patent Rights. If, in the course of
my employment with the Company, I incorporate a Prior Invention into a Company product, process or research or development program

 
or other work done for the Company, I hereby grant to the Company a nonexclusive, royalty-free, fully paid-up, irrevocable, perpetual, worldwide license (with the full right to sublicense through
multiple tiers) to make, have made, modify, use, offer for sale, import and sell such Prior Invention. Notwithstanding the foregoing, I will not incorporate, or permit to be incorporated, Prior Inventions in any Company-Related Development without
the Company’s prior written consent. 
 I understand that to the extent this Agreement is required to be construed in accordance with the laws of any
state which precludes a requirement in an employee agreement to assign certain classes of inventions made by an employee, this Section will be interpreted not to apply to any invention which a court rules and/or the Company agrees falls within such
classes. 
 6. Documents and Other Materials. I will keep and maintain adequate and current records of all Proprietary Information and
Company-Related Developments conceived by me, which records will be available to and remain the sole property of the Company at all times. All files, letters, notes, memoranda, reports, records, data, sketches, drawings, notebooks, layouts, charts,
quotations and proposals, specification sheets, program listings, blueprints, models, prototypes, materials or other written, photographic or other tangible material containing or embodying Proprietary Information, whether created by me or others,
which come into my custody or possession, are the exclusive property of the Company to be used by me only in the performance of my duties for the Company. In the event of the termination of my employment for any reason, I will deliver to the Company
all of the foregoing, and all other materials of any nature pertaining to the Proprietary Information of the Company and to my work, and will not take or keep in my possession any of the foregoing or any copies. Any property situated on the
Company’s premises and owned by the Company, including laboratory space, computers, disks and other storage media, filing cabinets or other work areas, is subject to inspection by the Company at any time with or without notice. 

7. Enforcement of Intellectual Property Rights. I will cooperate fully with the Company, both during and after my employment with the Company,
with respect to the procurement, maintenance and enforcement of Intellectual Property Rights, as well as all other patent rights, trademarks, copyrights and

 

  
 2 

 
other intellectual property rights in all countries and territories worldwide owned by or licensed to the Company. I will sign, both during and after the term of this Agreement, all papers,
including copyright applications, patent applications, declarations, oaths, assignments of priority rights, and powers of attorney, which the Company may deem necessary or desirable in order to protect its rights and interests in any Company-Related
Development or Intellectual Property Rights. If the Company is unable, after reasonable effort, to secure my signature on any such papers, I hereby irrevocably designate and appoint each officer of the Company as my agent and attorney-in-fact to
execute any such papers on my behalf, and to take any and all actions as the Company may deem necessary or desirable in order to protect its rights and interests in the same. 

8. Non-Competition and Non-Solicitation. In order to protect the Company’s Proprietary Information and good will, during my employment and
for a period of twelve (12) months following the termination of my employment for any reason (the “Restricted Period”), I will not directly or indirectly, whether as owner, partner, shareholder, director, consultant, agent, employee,
co-venturer or otherwise: 
 (a) Engage, participate or invest in any business that develops, manufactures or markets microbiome
therapeutics, or products or services that the Company has under development or that are the subject of active planning at any time during my employment (collectively, the “Competitive Products”); provided that this will not prohibit any
possible investment in publicly traded stock of a company representing less than one percent of the stock of such company; 
 (b) Directly
or indirectly, in any manner, other than for the benefit of the Company, (i) call upon, solicit, divert or take away any of the customers, business or prospective customers of the Company or any of its suppliers, and/or (ii) solicit,
entice or attempt to persuade any other employee or consultant of the Company to leave the services of the Company for any reason. 
 (c)
I acknowledge and agree that if I violate any of the provisions of this Section, in addition to any other remedies to which the Company may be entitled in law or equity, the running of the Restricted Period will be extended by the time during which
I engage in such violation(s). 

 (d) I acknowledge and agree that the provisions of this agreement shall apply during and
following my employment by the Company, and shall not be affected by any change in my job duties, whether material or immaterial. 
 9. Government
Contracts. I acknowledge that the Company may have from time to time agreements with other persons or with the United States Government or its agencies which impose obligations or restrictions on the Company regarding inventions made during
the course of work under such agreements or regarding the confidential nature of such work. I agree to comply with any such obligations or restrictions upon the direction of the Company. In addition to the rights assigned under Section 5, I
also assign to the Company (or any of its nominees) all rights which I have or acquired in any Developments, full title to which is required to be in the United States under any contract between the Company and the United States or any of its
agencies. 
 10. Prior Agreements. I hereby represent that, except as I have fully disclosed previously in writing to the Company, I am not
bound by the terms of any agreement with any previous employer or other party to refrain from using or disclosing any trade secret or confidential or proprietary information in the course of my employment with the Company or to refrain from
competing, directly or indirectly, with the business of such previous employer or any other party. I further represent that my performance of all the terms of this Agreement as an employee of the Company does not and will not breach any agreement to
keep in confidence proprietary information, knowledge or data acquired by me in confidence or in trust prior to my employment with the Company. I will not disclose to the Company or induce the Company to use any confidential or proprietary
information or material belonging to any previous employer or others. 
 11. Remedies Upon Breach. I understand that the restrictions
contained in this Agreement are necessary for the protection of the business and goodwill of the Company and I consider them to be reasonable for such purpose. Any breach of this Agreement is likely to cause the Company substantial and irrevocable
damage and therefore, in the event of such breach, the Company, in addition to such other remedies which may be available, will be entitled to specific performance and other injunctive relief.

 

  
 3 

 
 12. Use of Voice, Image and Likeness. I give the Company permission to use my voice, image or
likeness, with or without using my name, for the purposes of advertising and promoting the Company, or for other purposes deemed appropriate by the Company in its reasonable discretion, except to the extent expressly prohibited by law. 

13. Publications and Public Statements. I will obtain the Company’s written approval before publishing or submitting for publication any
material that relates to my work at the Company and/or incorporates any Proprietary Information. To ensure that the Company delivers a consistent message about its products, services and operations to the public, and further in recognition that even
positive statements may have a detrimental effect on the Company in certain securities transactions and other contexts, any statement about the Company which I create, publish or post during my period of employment and for six (6) months
thereafter, on any media accessible by the public, including but not limited to electronic bulletin boards and Internet-based chat rooms, must first be reviewed and approved by an officer of the Company before it is released in the public domain.

 14. No Employment Obligation. I understand that this Agreement does not create an obligation on the Company or any other person to continue
my employment. I acknowledge that, unless otherwise agreed in a formal written employment agreement signed on behalf of the Company by an authorized officer, my employment with the Company is at will and therefore may be terminated by the Company or
me at any time and for any reason. 
 15. Survival and Assignment by the Company. I understand that my obligations under this Agreement will
continue in accordance with its express terms regardless of any changes in my title, position, duties, salary, compensation or benefits or other terms and conditions of employment. I further understand that my obligations under this Agreement will
continue following the termination of my employment regardless of the manner of such termination and will be binding upon my heirs, executors and administrators. The Company will have the right to assign this Agreement to its affiliates, successors
and assigns. I expressly consent to be bound by the provisions of this Agreement for the benefit of the Company or any parent, subsidiary or affiliate to whose employ I may be transferred without the necessity that this Agreement be resigned at the
time of such transfer. 

 16. Disclosure to Future Employers. I will provide a copy of this Agreement to any prospective
employer, partner or co-venturer prior to entering into an employment, partnership or other business relationship with such person or entity. 
 17.
Exit Interview. If and when I depart from the Company, I may be required to attend an exit interview and sign an “Employee Exit Acknowledgement” to reaffirm my acceptance and acknowledgement of the obligations set forth in this
Agreement. During the Restricted Period following termination of my employment, I will notify the Company of any change in my address and of each subsequent employment or business activity, including the name and address of my employer or other
post-Company employment plans and the nature of my activities. 
 18. Severability. In case any provisions (or portions thereof) contained in
this Agreement will, for any reason, be held invalid, illegal or unenforceable in any respect, such invalidity, illegality or unenforceability will not affect the other provisions of this Agreement, and this Agreement will be construed as if such
invalid, illegal or unenforceable provision had never been contained herein. If, moreover, any one or more of the provisions contained in this Agreement will for any reason be held to be excessively broad as to duration, geographical scope, activity
or subject, it will be construed by limiting and reducing it, so as to be enforceable to the extent compatible with the applicable law as it will then appear. 

19. Entire Agreement. This Agreement constitutes the entire and only agreement between the Company and me respecting the subject matter hereof,
and supersedes all prior agreements and understandings, oral or written, between us concerning such subject matter. No modification, amendment, waiver or termination of this Agreement or of any provision hereof will be binding unless made in writing
and signed by an authorized officer of the Company. Failure of the Company to insist upon strict compliance with any of the terms, covenants or conditions hereof will not be deemed a waiver of such terms, covenants or conditions. In the event of any
inconsistency between this Agreement and any other contract between the Company and me, the provisions of this Agreement will prevail. 
 20.
Interpretation. This Agreement will be deemed to be made and entered into in the Commonwealth of Massachusetts, and will in all respects be interpreted,

 

  
 4 

 
enforced and governed under the laws of the Commonwealth of Massachusetts. I hereby agree to consent to personal jurisdiction of the state and federal courts situated within Suffolk County,
Massachusetts for purposes of enforcing this

 
Agreement, and waive any objection that I might have to personal jurisdiction or venue in those courts. As used in this Agreement, “including” means “including but not limited
to”. 

 

  
 BY SIGNING BELOW, I
CERTIFY THAT I HAVE READ THIS AGREEMENT CAREFULLY AND AM SATISFIED THAT I UNDERSTAND IT COMPLETELY. 
 IN WITNESS WHEREOF, the
undersigned has executed this agreement as a sealed instrument as of the date set forth below. 
  

					
	Signed:		  
		
			    (Employee’s full name)		

  

									
	Type or print name:		Eric D. Shaff						
					
	Last four digits of SSN:		  
				Date:		  

  
 5 

 Appendix A 
  

					
	To:		Seres Therapeutics, Inc.		
			
	From:		Eric D. Shaff		
			
	Date:		  
		

					
			
	SUBJECT:		Prior Inventions		

 The following is a complete list of all inventions or improvements relevant to the subject matter of my
employment by the Company that have been made or conceived or first reduced to practice by me alone or jointly with others prior to my engagement by the Company: 
  

	 	 ̈	No inventions or improvements 

  

	 	 ̈	See below: 

			
	  
		
		
	  
		
		
	  
		
		
	  
		
		
	  
		
		
	  
		
		
	  
		

  

	 	 ̈	Additional sheets attached 

 The following is a list of all patents, patent applications and
other patent rights that I invented: 
  

	 	 ̈	None 

  

	 	 ̈	See below:

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