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;

 

2

--------------------------------------------------------------------------------

(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)

 

3

--------------------------------------------------------------------------------

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

 

4

--------------------------------------------------------------------------------

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]

 

5

--------------------------------------------------------------------------------

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