Exhibit 10.1

FIRST AMENDMENT

TO

EMPLOYMENT AGREEMENT

This First Amendment (the “First Amendment”) to that certain Employment
Agreement between Seres Therapeutics, Inc., a Delaware corporation (together
with any successor thereto, the “Company”), and Roger J. Pomerantz, M.D. (the
“Executive”) dated as of June 12, 2015 (the “Employment Agreement”) is made as
of February 3, 2016 (the “Amendment Date”), by and among the Company and the
Executive.

WHEREAS, the Company and the Executive desire to amend the terms of the
Employment Agreement as set forth herein.

NOW, THEREFORE, for good and valuable consideration, the receipt and sufficiency
of which are hereby acknowledged, the Company and the Executive hereby agree to
the following:

1. Amendment to the Employment Agreement. Effective as of the Amendment Date,
the Employment Agreement is hereby amended as follows:

(a) Section 4(b) of the Employment Agreement is hereby amended by inserting the
words “Subject to Section 4(c)” at the beginning of the first sentence of such
section and recapitalizing such sentence accordingly.

(b) Section 4(c) of the Employment Agreement is hereby amended and restated in
its entirety to read as follows:

“(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, and Executive’s continued compliance with Section 5,
Executive shall be entitled to receive, (i) without duplication, the payments
and benefits described in Section 4(b), provided that the Severance Period for
purposes of Section 4(b)(i) and Section 4(b)(iii) shall be increased to 18
months following the date of Executive’s Separation from Service and the amount
payable under Section 4(b)(i) shall be 150% of the Annual Base Salary, payable
in regular installments in accordance with the Company’s normal payroll
practices over the Severance Period (as increased hereby); and (ii) immediate
vesting of 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 (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).”

2. References. The references to “this Agreement” in the Employment Agreement
shall mean the Employment Agreement, as amended by this First Amendment.

3. No Other Amendment. Except as expressly set forth in this First Amendment,
the Employment Agreement shall remain unchanged and shall continue in full force
and effect according to its terms.

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4. Counterparts. This First Amendment may be executed in several counterparts,
each of which shall be deemed an original and all of which together shall
constitute one document.

5. Governing Law. This First Amendment shall be governed by and construed in
accordance with the laws of the Commonwealth of Massachusetts (without giving
effect to any choice or conflict of laws provision or rule that would cause the
application of the laws of any other jurisdiction).

6. Headings. The headings in this First Amendment are for reference purposes
only and will not in any way affect the meaning or interpretation of this First
Amendment.

7. Entire Agreement. This First Amendment constitutes the entire agreement among
the parties concerning the subject matter hereof and supersedes any prior
representations, understandings or agreements.

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IN WITNESS WHEREOF, the parties have executed this First Amendment as of the
Amendment Date.

 

SERES THERAPEUTICS, INC. By:  

/s/ Eric D. Shaff

Name:   Eric D. Shaff Title:   Executive Vice President and Chief Financial
Officer EXECUTIVE

/s/ Roger J. Pomerantz

Roger J. Pomerantz, M.D.

 

 

[Signature Page to First Amendment to Employment Agreement]