EX-10.1





 Exhibit 10.1 

Separation Agreement and Release 

This Separation Agreement and Release (“Agreement”) is made by and between Michele Trucksis, Ph.D., 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 13, 2015, as amended by that certain First Amendment to Employment Agreement, dated August 7, 2015, and that certain Second Amendment to Employment Agreement,
dated March 7, 2018, by and between the Parties (the “Employment Agreement”); 
 WHEREAS, Executive’s employment
with the Company and its subsidiaries terminated without Cause (as defined in the Employment Agreement) effective November 16, 2018 (the “Termination Date”); 

WHEREAS, the Company and Executive have entered into a Consulting Agreement pursuant to which Executive will perform transitional consulting
services following the Termination Date (the “Consulting Agreement”), subject to and in accordance with the terms thereof; and 

WHEREAS, in connection with Executive’s termination of employment, 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, Executive’s right to indemnification by the Company or any of its affiliates pursuant to contract or applicable law or Executive’s rights under the Consulting Agreement (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. Executive shall also be entitled to reimbursement of reasonable attorney’s fees incurred by Executive in connection with the amicable negotiation of this Agreement and
Executive’s Consulting Agreement up to $3,000, less any taxes that the Company reasonably determines it is required to withhold. 












 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 date Executive signs this Agreement, 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; 

  
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 (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; 

(h)    any and all claims arising out of the wage and hour and wage payments laws and regulations of the state or states
in which Executive has provided service to the Company or any of its affiliates (including without limitation the Massachusetts Payment of Wages Law); and 

(i)    any and all claims for attorneys’ fees and costs (except reimbursement of attorneys’ fees as contemplated
in Section 1). 
 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 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 (including Executive’s right to receive an award for information provided to any such government agencies), 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 monetary or other individual relief from the Company or any Releasee in connection with any charge, investigation or proceeding, or any related complaint or lawsuit, filed by Executive or by anyone
else on Executive’s behalf before the federal Equal Employment Opportunity Commission or a comparable state or local agency), 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, or for claims arising under the Consulting 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 date Executive signs 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) 

  
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Executive should consult with an attorney prior to executing this Agreement; (b) Executive has 21 days within which to consider this Agreement, and the Parties expressly agree that such time
period to review this Agreement shall not be extended upon any material or immaterial changes to 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. 
 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.    Trade Secrets; Whistleblower Protections. In accordance with 18 U.S.C. § 1833, notwithstanding anything
to the contrary in the Employment Agreement or the Proprietary Information Agreement: (a) Executive will not be in breach of the Employment Agreement or the Proprietary Information Agreement, and shall not be held criminally or civilly liable
under any federal or state trade secret law (i) for the disclosure of a trade secret that is made in confidence to a federal, state, or local government official or to an attorney solely for the purpose of reporting or investigating a suspected
violation of law, or (ii) for the disclosure of a trade secret that is made in a complaint or other document filed in a lawsuit or other proceeding, if such filing is made under seal; and (b) if Executive files a lawsuit for retaliation by
the Company for reporting a suspected violation of law, Executive may disclose the trade secret to Executive’s attorney, and may use the trade secret information in the court proceeding, if Executive files any document containing the trade
secret under seal, and does not disclose the trade secret, except pursuant to court order. Furthermore, the Parties agree that nothing in the Employment Agreement or the Proprietary Information Agreement, notwithstanding any contrary terms thereof,
prohibits Executive from 

  
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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 806 of the Sarbanes-Oxley Act of 2002, or any other whistleblower protection provisions of state or federal law or regulation (including Executive’s right to receive an award for information provided to any
such government agencies). 
 9.    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. 

[Signature Page Follows] 

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

							
	Dated: November 16, 2018	 		 	/s/ Michele Trucksis
		 		 	Michele Trucksis, Ph.D., M.D.
		 		 		 	
		 		 	SERES THERAPEUTICS, INC.
				
	Dated: November 16, 2018	 		 	By:	 	/s/ Roger J. Pomerantz
		 		 		 	Name: Roger J. Pomerantz, M.D.
		 		 		 	Title: CEO and Chairman