Document:

EX-10.3

 Exhibit 10.3 

SERES THERAPEUTICS, INC. 

2015 EMPLOYEE STOCK PURCHASE PLAN 
  

	1.	Purpose. 

 The purposes of this Seres Therapeutics, Inc. 2015 Employee Stock
Purchase Plan (as it may be amended or restated from time to time, the “Plan”) are to assist Eligible Employees of Seres Therapeutics, Inc., a Delaware corporation (the “Company”), and its Designated
Subsidiaries in acquiring a stock ownership interest in the Company pursuant to a plan which is intended to qualify as an “employee stock purchase plan” within the meaning of Section 423(b) of the Code, and to help Eligible Employees
provide for their future security and to encourage them to remain in the employment of the Company and its Designated Subsidiaries. 
  

	2.	Definitions and Construction. 

 Wherever the following terms are used in the Plan
they shall have the meanings specified below, unless the context clearly indicates otherwise. The singular pronoun shall include the plural where the context so indicates. Masculine, feminine and neuter pronouns are used interchangeably and each
comprehends the others. 
 (a) “Administrator” shall mean the entity that conducts the general administration of the
Plan as provided in Section 11. The term “Administrator” shall refer to the Committee unless the Board has assumed the authority for administration of the Plan as provided in Section 11. 

(b) “Applicable Laws” shall mean the requirements relating to the administration of employee stock purchase plans
(within the meaning of Section 423(b) of the Code) under U.S. federal and state securities, tax and other applicable laws, rules and regulations, the applicable rules of any stock exchange or quotation system on which the Common Stock is listed
or quoted and the applicable laws and rules of any foreign country or other jurisdiction where rights under this Plan are granted. 
 (c)
“Board” shall mean the Board of Directors of the Company. 
 (d) “Change in Control” shall
mean and include each of the following: 
 (i) A transaction or series of transactions (other than an offering of Common Stock to the
general public through a registration statement filed with the Securities and Exchange Commission or a transaction or series of transactions that meets the requirements of clauses (A) and (B) of Section 2(d)(iii) below whereby any
“person” or related “group” of “persons” (as such terms are used in Sections 13(d) and 14(d)(2) of the Exchange Act) (other than the Company, any of its Subsidiaries, an employee benefit plan maintained by the Company
or any of its Subsidiaries or a “person” that, prior to such transaction, directly or indirectly controls, is controlled by, or is under common control with, the Company) directly or indirectly acquires beneficial ownership (within the
meaning of Rule 13d-3 under the Exchange Act) of securities of the Company possessing more than 50% of the total combined voting power of the Company’s securities outstanding immediately after such acquisition; or 

(ii) During any period of two consecutive years, individuals who, at the beginning of such period, constitute the Board together with any new
director(s) (other than a director designated by a person who shall have entered into an agreement with the Company to effect a transaction described in Section 2(d)(i) or 2(d)(iii)) whose election by the Board or nomination for election by the
Company’s stockholders was approved by a vote of at least two-thirds of the directors then still in office who either were directors at the beginning of the two-year period or whose election or nomination for election was previously so
approved, cease for any reason to constitute a majority thereof; or 

 (iii) The consummation by the Company (whether directly involving the Company or indirectly
involving the Company through one or more intermediaries) of (x) a merger, consolidation, reorganization, or business combination or (y) a sale or other disposition of all or substantially all of the Company’s assets in any single
transaction or series of related transactions or (z) the acquisition of assets or stock of another entity, in each case other than a transaction: 

(A) which results in the Company’s voting securities outstanding immediately before the transaction continuing to
represent (either by remaining outstanding or by being converted into voting securities of the Company or the person that, as a result of the transaction, controls, directly or indirectly, the Company or owns, directly or indirectly, all or
substantially all of the Company’s assets or otherwise succeeds to the business of the Company (the Company or such person, the “Successor Entity”)) directly or indirectly, at least a majority of the combined voting
power of the Successor Entity’s outstanding voting securities immediately after the transaction, and 
 (B) after which
no person or group beneficially owns voting securities representing 50% or more of the combined voting power of the Successor Entity; provided, however, that no person or group shall be treated for purposes of this
Section 2(d)(iii)(B) as beneficially owning 50% or more of the combined voting power of the Successor Entity solely as a result of the voting power held in the Company prior to the consummation of the transaction. 

The Administrator shall have full and final authority, which shall be exercised in its discretion, to determine conclusively whether a Change
in Control has occurred pursuant to the above definition, the date of the occurrence of such Change in Control and any incidental matters relating thereto. 

(e) “Code” shall mean the Internal Revenue Code of 1986, as amended from time to time, together with the
regulations and official guidance promulgated thereunder. 
 (f) “Common Stock” shall
mean the common stock of the Company and such other securities of the Company that may be substituted therefor pursuant to Section 8.  

(g) “Company” shall mean Seres Therapeutics, Inc., a Delaware corporation. 

(h) “Compensation” of an Eligible Employee shall mean the gross base compensation received by such
Eligible Employee as compensation for services to the Company or any Designated Subsidiary, including overtime payments and excluding sales commissions, incentive compensation, bonuses, expense reimbursements, fringe benefits and other special
payments. 
 (i) “Designated Subsidiary” shall mean any Subsidiary designated by the
Administrator in accordance with Section 11(c)(ii). 
 (j) “Effective Date” shall mean the day
prior to the Public Trading Date. 
 (k) “Eligible Employee” shall mean an Employee: (i) who does
not, immediately after any rights under this Plan are granted, own (directly or through attribution) stock possessing 5% or more of the total combined voting power or value of all classes of Common Stock and other stock of the Company, a Parent or a
Subsidiary (as determined under Section 423(b)(3) of the Code); (ii) whose  

  
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customary employment is for more than twenty hours per week; and (iii) whose customary employment is for more than five months in any calendar year. For purposes of the foregoing clause (i),
the rules of Section 424(d) of the Code with regard to the attribution of stock ownership shall apply in determining the stock ownership of an individual, and stock that an Employee may purchase under outstanding options shall be treated as
stock owned by the Employee; provided, however, that the Administrator may provide in an Offering Document that an Employee shall not be eligible to participate in an Offering Period if: (x) such Employee is a highly compensated
employee within the meaning of Section 423(b)(4)(D) of the Code; and/or (y) such Employee has not met a service requirement designated by the Administrator pursuant to Section 423(b)(4)(A) of the Code (which service requirement may
not exceed two years), and/or (z) such Employee is a citizen or resident of a foreign jurisdiction and the grant of a right to purchase Common Stock under the Plan to such Employee would be prohibited under the laws of such foreign jurisdiction
or the grant of a right to purchase Common Stock under the Plan to such Employee in compliance with the laws of such foreign jurisdiction would cause the Plan to violate the requirements of Section 423 of the Code, as determined by the
Administrator in its sole discretion; provided, further, that any exclusion in clauses (x), (y) or (z) shall be applied in an identical manner under each Offering Period to all Employees, in accordance with Treasury
Regulation Section 1.423-2(e). 
 (l) “Employee” shall mean any officer or other employee (as
defined in accordance with Section 3401(c) of the Code) of the Company or any Designated Subsidiary. “Employee” shall not include any director of the Company or a Designated Subsidiary who does not render services to the Company or a
Designated Subsidiary as an employee within the meaning of Section 3401(c) of the Code. For purposes of the Plan, the employment relationship shall be treated as continuing intact while the individual is on sick leave or other leave of absence
approved by the Company or Designated Subsidiary and meeting the requirements of Treasury Regulation Section 1.421-1(h)(2). Where the period of leave exceeds three (3) months and the individual’s right to reemployment is not
guaranteed either by statute or by contract, the employment relationship shall be deemed to have terminated on the first day immediately following such three (3)-month period. 

(m) “Enrollment Date” shall mean the first Trading Day of each Offering Period. 

(n) “Exchange Act” shall mean the Securities Exchange Act of 1934, as amended from time to time. 

(o) “Fair Market Value” means, as of any date, the value of Common Stock determined as follows:
(i) if the Common Stock is listed on any established stock exchange, its Fair Market Value will be the closing sales price for such Common Stock as quoted on such exchange for such date, or if no sale occurred on such date, the last day
preceding such date during which a sale occurred, as reported in The Wall Street Journal or another source the Administrator deems reliable; (ii) if the Common Stock is not traded on a stock exchange but is quoted on a national market or other
quotation system, the closing sales price on such date, or if no sales occurred on such date, then on the last date preceding such date during which a sale occurred, as reported in The Wall Street Journal or another source the Administrator deems
reliable; or (iii) without an established market for the Common Stock, the Administrator will determine the Fair Market Value in its discretion.  

(p) “Offering Document” shall have the meaning given to such term in Section 4(a). 

(q) “Offering Period” shall have the meaning given to such term in Section 4(a). 

(r) “Parent” shall mean any corporation, other than the Company, in an unbroken chain of corporations
ending with the Company if, at the time of the determination, each of the corporations other than the Company owns stock possessing 50% or more of the total combined voting power of all classes of stock in one of the other corporations in such
chain.  

  
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 (s) “Participant” shall mean any Eligible Employee who has
executed a subscription agreement and been granted rights to purchase Common Stock pursuant to the Plan. 
 (t)
“Plan” shall mean this Seres Therapeutics, Inc. 2015 Employee Stock Purchase Plan, as it may be amended from time to time. 

(u) “Public Trading Date” shall mean the first date upon which Common Stock is listed (or approved for
listing) upon notice of issuance on any securities exchange or designated (or approved for designation) upon notice of issuance as a national market security on an interdealer quotation system. 

(v) “Purchase Date” shall mean the last Trading Day of each Offering Period. 

(w) “Purchase Price” shall mean the purchase price designated by the Administrator in the applicable
Offering Document (which purchase price shall not be less than 85% of the Fair Market Value of a Share on the Enrollment Date or on the Purchase Date, whichever is lower); provided, however, that, in the event no purchase price is
designated by the Administrator in the applicable Offering Document, the purchase price for the Offering Periods covered by such Offering Document shall be 85% of the Fair Market Value of a Share on the Enrollment Date or on the Purchase Date,
whichever is lower; provided, further, that the Purchase Price may be adjusted by the Administrator pursuant to Section 8 and shall not be less than the par value of a Share. 

(x) “Securities Act” shall mean the Securities Act of 1933, as amended from time to time. 

(y) “Share” shall mean a share of Common Stock. 

(z) “Subsidiary” shall mean any corporation, other than the Company, in an unbroken chain of
corporations beginning with the Company if, at the time of the determination, each of the corporations other than the last corporation in an unbroken chain owns stock possessing 50% or more of the total combined voting power of all classes of stock
in one of the other corporations in such chain; provided, however, that a limited liability company or partnership may be treated as a Subsidiary to the extent either (i) such entity is treated as a disregarded entity under
Treasury Regulation Section 301.7701-3(a) by reason of the Company or any other Subsidiary that is a corporation being the sole owner of such entity, or (ii) such entity elects to be classified as a corporation under Treasury Regulation
Section 301.7701-3(a) and such entity would otherwise qualify as a Subsidiary. 
 (aa) “Trading
Day” shall mean a day on which national stock exchanges in the United States are open for trading. 
  

	3.	Shares Subject to the Plan. 

 (a) Number of Shares. Subject to
Section 8, the aggregate number of Shares that may be issued pursuant to rights granted under the Plan shall be [                ] Shares. In addition to the
foregoing, subject to Section 8, on the first day of each calendar year beginning on January 1, 2016 and ending on and including January 1, 2025, the number of Shares available for issuance under the Plan shall be increased by that
number of Shares equal to the least of (i) [                ] Shares, (ii) 1% of the Shares outstanding on the final day of the immediately preceding calendar
year and (iii) such smaller number of Shares as determined by the Board. If any right granted under the Plan shall for any reason terminate without having been exercised, the Common Stock not purchased under such right shall again become
available for issuance under the Plan. 

  
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 (b) Stock Distributed. Any Common Stock distributed pursuant to the Plan may
consist, in whole or in part, of authorized and unissued Common Stock, treasury stock or Common Stock purchased on the open market. 
  

	4.	Offering Periods; Offering Documents. 

 (a)
Offering Periods. The Administrator may from time to time grant or provide for the grant of rights to purchase Common Stock under the Plan to Eligible Employees during one or more periods (each, an
“Offering Period”) selected by the Administrator. The terms and conditions applicable to each Offering Period shall be set forth in an “Offering Document” adopted by the Administrator, which Offering
Document shall be in such form and shall contain such terms and conditions as the Administrator shall deem appropriate and shall be incorporated by reference into and made part of the Plan and shall be attached hereto as part of the Plan. The
provisions of separate Offering Periods under the Plan need not be identical.  
 (b) Offering Documents. Each
Offering Document with respect to an Offering Period shall specify (through incorporation of the provisions of this Plan by reference or otherwise): 

(i) the length of the Offering Period, which period shall not exceed twenty-seven months; 

(ii) the maximum number of Shares that may be purchased by any Eligible Employee during such Offering Period, which, in the absence of a
contrary designation by the Administrator, shall be [750] Shares; 
 (iii) such other provisions as the Administrator determines are
appropriate, subject to the Plan. 
  

	5.	Eligibility and Participation. 

 (a) Eligibility. Any Eligible
Employee who shall be employed by the Company or a Designated Subsidiary on a given Enrollment Date for an Offering Period shall be eligible to participate in the Plan during such Offering Period, subject to the requirements of this Section 5
and the limitations imposed by Section 423(b) of the Code. 
 (b) Enrollment in Plan. 

(i) Except as otherwise set forth in an Offering Document or determined by the Administrator, an Eligible Employee may become a Participant in
the Plan for an Offering Period by delivering a subscription agreement to the Company by such time prior to the Enrollment Date for such Offering Period (or such other date specified in the Offering Document) designated by the Administrator and in
such form as the Company provides. 
 (ii) Each subscription agreement shall designate a whole percentage of such Eligible Employee’s
Compensation to be withheld by the Company or the Designated Subsidiary employing such Eligible Employee on each payday during the Offering Period as payroll deductions under the Plan. An Eligible Employee may designate any whole percentage of
Compensation that is not less than 1% and not more than the maximum percentage specified by the Administrator in the applicable Offering Document 

  
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(which percentage shall be [15]% in the absence of any such designation) as payroll deductions. The payroll deductions made for each Participant shall be credited to an account for such
Participant under the Plan and shall be deposited with the general funds of the Company. 
 (iii) A Participant may increase or decrease the
percentage of Compensation designated in his or her subscription agreement, subject to the limits of this Section 5(b), or may suspend his or her payroll deductions, at any time during an Offering Period; provided, however, that
the Administrator may limit the number of changes a Participant may make to his or her payroll deduction elections during each Offering Period in the applicable Offering Document (and in the absence of any specific designation by the Administrator,
a Participant shall be allowed one change to his or her payroll deduction elections during each Offering Period). Any such change or suspension of payroll deductions shall be effective with the first full payroll period following five business days
after the Company’s receipt of the new subscription agreement (or such shorter or longer period as may be specified by the Administrator in the applicable Offering Document). In the event a Participant suspends his or her payroll deductions,
such Participant’s cumulative payroll deductions prior to the suspension shall remain in his or her account and shall be applied to the purchase of Shares on the next occurring Purchase Date and shall not be paid to such Participant unless he
or she withdraws from participation in the Plan pursuant to Section 7. 
 (iv) Except as otherwise set forth in an Offering Document or
determined by the Administrator, a Participant may participate in the Plan only by means of payroll deduction and may not make contributions by lump sum payment for any Offering Period. 

(c) Payroll Deductions. Except as otherwise provided in the applicable Offering Document, payroll deductions for a Participant
shall commence on the first payroll following the Enrollment Date and shall end on the last payroll in the Offering Period to which the Participant’s authorization is applicable, unless sooner terminated by the Participant as provided in
Section 7 or suspended by the Participant or the Administrator as provided in Section 5(b) and Section 5(f), respectively.  

(d) Effect of Enrollment. A Participant’s completion of a subscription agreement will enroll such Participant in the Plan
for each subsequent Offering Period on the terms contained therein until the Participant either submits a new subscription agreement, withdraws from participation under the Plan as provided in Section 7 (or ceases to be an Eligible Employee).
 
 (e) Limitation on Purchase of Common Stock. An Eligible Employee may be granted rights under the Plan only if such
rights, together with any other rights granted to such Eligible Employee under “employee stock purchase plans” of the Company, any Parent or any Subsidiary, as specified by Section 423(b)(8) of the Code, do not permit such
employee’s rights to purchase stock of the Company or any Parent or Subsidiary to accrue at a rate that exceeds $25,000 of the fair market value of such stock (determined as of the first day of the Offering Period during which such rights are
granted) for each calendar year in which such rights are outstanding at any time. This limitation shall be applied in accordance with Section 423(b)(8) of the Code. 

(f) Suspension of Payroll Deductions. Notwithstanding the foregoing, to the extent necessary to comply with
Section 423(b)(8) of the Code and Section 5(e) or the other limitations set forth in this Plan, a Participant’s payroll deductions may be suspended by the Administrator at any time during an Offering Period. The balance of the amount
credited to the account of each Participant that has not been applied to the purchase of Shares by reason of Section 423(b)(8) of the Code, Section 5(e) or the other limitations set forth in this Plan shall be paid to such Participant in
one lump sum in cash as soon as reasonably practicable after the Purchase Date. 

  
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 (g) Foreign Employees. In order to facilitate participation in the Plan, the
Administrator may provide for such special terms applicable to Participants who are citizens or residents of a foreign jurisdiction, or who are employed by a Designated Subsidiary outside of the United States, as the Administrator may consider
necessary or appropriate to accommodate differences in local law, tax policy or custom. Such special terms may not be more favorable than the terms of rights granted under the Plan to Eligible Employees who are residents of the United States.
Moreover, the Administrator may approve such supplements to, or amendments, restatements or alternative versions of, this Plan as it may consider necessary or appropriate for such purposes without thereby affecting the terms of this Plan as in
effect for any other purpose. No such special terms, supplements, amendments or restatements shall include any provisions that are inconsistent with the terms of this Plan as then in effect unless this Plan could have been amended to eliminate such
inconsistency without further approval by the stockholders of the Company. 
 (h) Leave of Absence. During leaves of
absence approved by the Company meeting the requirements of Treasury Regulation Section 1.421-1(h)(2) under the Code, a Participant may continue participation in the Plan by making cash payments to the Company on his or her normal payday equal
to his or her authorized payroll deduction. 
  

	6.	Grant and Exercise of Rights. 

 (a) Grant of Rights. On the Enrollment Date
of each Offering Period, each Eligible Employee participating in such Offering Period shall be granted a right to purchase the maximum number of Shares specified under Section 4(b), subject to the limits in Section 5(e), and shall have the
right to buy, on each Purchase Date during such Offering Period (at the applicable Purchase Price), such number of whole Shares as is determined by dividing (x) such Participant’s payroll deductions accumulated prior to such Purchase Date
and retained in the Participant’s account as of the Purchase Date, by (y) the applicable Purchase Price (rounded down to the nearest Share). The right shall expire on the last day of the Offering Period. 

(b) Exercise of Rights. On each Purchase Date, each Participant’s accumulated payroll deductions and any other additional
payments specifically provided for in the applicable Offering Document will be applied to the purchase of whole Shares, up to the maximum number of Shares permitted pursuant to the terms of the Plan and the applicable Offering Document, at the
Purchase Price. No fractional Shares shall be issued upon the exercise of rights granted under the Plan, unless the Offering Document specifically provides otherwise. Any cash in lieu of fractional Shares remaining after the purchase of whole Shares
upon exercise of a purchase right will be credited to a Participant’s account and carried forward and applied toward the purchase of whole Shares for the next following Offering Period. Shares issued pursuant to the Plan may be evidenced in
such manner as the Administrator may determine and may be issued in certificated form or issued pursuant to book-entry procedures.  

(c) Pro Rata Allocation of Shares. If the Administrator determines that, on a given Purchase Date, the number of Shares with
respect to which rights are to be exercised may exceed (i) the number of Shares that were available for issuance under the Plan on the Enrollment Date of the applicable Offering Period, or (ii) the number of Shares available for issuance
under the Plan on such Purchase Date, the Administrator may in its sole discretion provide that the Company shall make a pro rata allocation of the Shares available for purchase on such Enrollment Date or Purchase Date, as applicable, in as uniform
a manner as shall be practicable and as it shall determine in its sole discretion to be equitable among all Participants for whom rights to purchase Common Stock are to be exercised pursuant to this Section 6 on such Purchase Date, and shall
either (x) continue all Offering Periods then in effect, or (y) terminate any or all Offering Periods then in effect pursuant to Section 9. The Company may make pro rata allocation of the Shares available on the Enrollment Date of any
applicable Offering Period pursuant to the  

  
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preceding sentence, notwithstanding any authorization of additional Shares for issuance under the Plan by the Company’s stockholders subsequent to such Enrollment Date. The balance of the
amount credited to the account of each Participant that has not been applied to the purchase of Shares shall be paid to such Participant in one lump sum in cash as soon as reasonably practicable after the Purchase Date. 

(d) Withholding. At the time a Participant’s rights under the Plan are exercised, in whole or in part, or at the time some
or all of the Common Stock issued under the Plan is disposed of, the Participant must make adequate provision for the Company’s federal, state, or other tax withholding obligations, if any, that arise upon the exercise of the right or the
disposition of the Common Stock. At any time, the Company may, but shall not be obligated to, withhold from the Participant’s compensation the amount necessary for the Company to meet applicable withholding obligations. 

(e) Conditions to Issuance of Common Stock. The Company shall not be required to issue or deliver any certificate or
certificates for, or make any book entries evidencing, Shares purchased upon the exercise of rights under the Plan prior to fulfillment of all of the following conditions:  

(i) The admission of such Shares to listing on all stock exchanges, if any, on which the Common Stock is then listed; and 

(ii) The completion of any registration or other qualification of such Shares under any state or federal law or under the rulings or
regulations of the Securities and Exchange Commission or any other governmental regulatory body, that the Administrator shall, in its absolute discretion, deem necessary or advisable; and 

(iii) The obtaining of any approval or other clearance from any state or federal governmental agency that the Administrator shall, in its
absolute discretion, determine to be necessary or advisable; and 
 (iv) The payment to the Company of all amounts that it is required to
withhold under federal, state or local law upon exercise of the rights, if any; and 
 (v) The lapse of such reasonable period of time
following the exercise of the rights as the Administrator may from time to time establish for reasons of administrative convenience. 
  

	7.	Withdrawal; Cessation of Eligibility. 

 (a) Withdrawal. A
Participant may withdraw all but not less than all of the payroll deductions credited to his or her account and not yet used to exercise his or her rights under the Plan at any time by giving written notice to the Company in a form acceptable to the
Company no later than one week prior to the end of the Offering Period. All of the Participant’s payroll deductions credited to his or her account during an Offering Period shall be paid to such Participant as soon as reasonably practicable
after receipt of notice of withdrawal and such Participant’s rights for the Offering Period shall be automatically terminated, and no further payroll deductions for the purchase of Shares shall be made for such Offering Period. If a Participant
withdraws from an Offering Period, payroll deductions shall not resume at the beginning of the next Offering Period unless the Participant delivers to the Company a new subscription agreement. 

(b) Future Participation. A Participant’s withdrawal from an Offering Period shall not have any effect upon his or her
eligibility to participate in any similar plan that may hereafter be adopted by the Company or a Designated Subsidiary or in subsequent Offering Periods that commence after the termination of the Offering Period from which the Participant
withdraws. 

  
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 (c) Cessation of Eligibility. Upon a Participant’s ceasing to be an Eligible
Employee for any reason, he or she shall be deemed to have elected to withdraw from the Plan pursuant to this Section 7 and the payroll deductions credited to such Participant’s account during the Offering Period shall be paid to such
Participant or, in the case of his or her death, to the person or persons entitled thereto under Section 12(d), as soon as reasonably practicable, and such Participant’s rights for the Offering Period shall be automatically terminated.

  

	8.	Adjustments Upon Changes in Stock. 

 (a) Changes in Capitalization. Subject
to Section 8(c), in the event that the Administrator determines that any dividend or other distribution (whether in the form of cash, Common Stock, other securities, or other property), Change in Control, reorganization, merger, amalgamation,
consolidation, combination, repurchase, recapitalization, liquidation, dissolution, or sale, transfer, exchange or other disposition of all or substantially all of the assets of the Company, or sale or exchange of Common Stock or other securities of
the Company, issuance of warrants or other rights to purchase Common Stock or other securities of the Company, or other similar corporate transaction or event, as determined by the Administrator, affects the Common Stock such that an adjustment is
determined by the Administrator to be appropriate in order to prevent dilution or enlargement of the benefits or potential benefits intended by the Company to be made available under the Plan or with respect to any outstanding purchase rights under
the Plan, the Administrator shall make equitable adjustments, if any, to reflect such change with respect to (i) the aggregate number and type of Shares (or other securities or property) that may be issued under the Plan (including, but not
limited to, adjustments of the limitations in Section 3(a) and the limitations established in each Offering Document pursuant to Section 4(b) on the maximum number of Shares that may be purchased); (ii) the class(es) and number of
shares and price per Share subject to outstanding rights; and (iii) the Purchase Price with respect to any outstanding rights. 

(b) Other Adjustments. Subject to Section 8(c), in the event of any transaction or event described in Section 8(a) or
any unusual or nonrecurring transactions or events affecting the Company, any affiliate of the Company, or the financial statements of the Company or any affiliate (including without limitation any Change in Control), or of changes in Applicable Law
or accounting principles, the Administrator, in its discretion, and on such terms and conditions as it deems appropriate, is hereby authorized to take any one or more of the following actions whenever the Administrator determines that such action is
appropriate in order to prevent the dilution or enlargement of the benefits or potential benefits intended to be made available under the Plan or with respect to any right under the Plan, to facilitate such transactions or events or to give effect
to such changes in laws, regulations or principles: 
 (i) To provide for either (x) termination of any outstanding right in
exchange for an amount of cash, if any, equal to the amount that would have been obtained upon the exercise of such right had such right been currently exercisable or (y) the replacement of such outstanding right with other rights or property
selected by the Administrator in its sole discretion; 
 (ii) To provide that the outstanding rights under the Plan shall be assumed by the
successor or survivor corporation, or a parent or subsidiary thereof, or shall be substituted for by similar rights covering the stock of the successor or survivor corporation, or a parent or subsidiary thereof, with appropriate adjustments as to
the number and kind of shares and prices; 
 (iii) To make adjustments in the number and type of Shares (or other securities or property)
subject to outstanding rights under the Plan and/or in the terms and conditions of outstanding rights and rights that may be granted in the future; 

  
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 (iv) To provide that Participants’ accumulated payroll deductions may be used to purchase
Common Stock prior to the next occurring Purchase Date on such date as the Administrator determines in its sole discretion and the Participants’ rights under the ongoing Offering Period(s) shall be terminated; and 

(v) To provide that all outstanding rights shall terminate without being exercised. 

(c) No Adjustment Under Certain Circumstances. No adjustment or action described in this Section 8 or in any other
provision of the Plan shall be authorized to the extent that such adjustment or action would cause the Plan to fail to satisfy the requirements of Section 423 of the Code. 

(d) No Other Rights. Except as expressly provided in the Plan, no Participant shall have any rights by reason of any subdivision
or consolidation of shares of stock of any class, the payment of any dividend, any increase or decrease in the number of shares of stock of any class or any dissolution, liquidation, merger, or consolidation of the Company or any other corporation.
Except as expressly provided in the Plan or pursuant to action of the Administrator under the Plan, no issuance by the Company of shares of stock of any class, or securities convertible into shares of stock of any class, shall affect, and no
adjustment by reason thereof shall be made with respect to, the number of Shares subject to outstanding rights under the Plan or the Purchase Price with respect to any outstanding rights. 

 

	9.	Amendment, Modification and Termination. 

 (a) Amendment, Modification
and Termination. The Administrator may amend, suspend or terminate the Plan at any time and from time to time; provided, however, that approval of the Company’s stockholders shall be required to amend the Plan to:
(i) increase the aggregate number, or change the type, of shares that may be sold pursuant to rights under the Plan under Section 3(a) (other than an adjustment as provided by Section 8); (ii) change the corporations or classes
of corporations whose employees may be granted rights under the Plan; or (iii) change the Plan in any manner that would cause the Plan to no longer be an “employee stock purchase plan” within the meaning of Section 423(b) of the
Code.  
 (b) Certain Changes to Plan. Without stockholder consent and without regard to whether any Participant rights
may be considered to have been adversely affected, to the extent permitted by Section 423 of the Code, the Administrator shall be entitled to change the Offering Periods, limit the frequency and/or number of changes in the amount withheld from
the Participant’s Compensation during an Offering Period, establish the exchange ratio applicable to amounts withheld from the Participant’s Compensation in a currency other than U.S. dollars, permit payroll withholding in excess of the
amount designated by a Participant in a properly completed subscription agreement in order to adjust for delays or mistakes in the Company’s processing of payroll withholding elections, establish reasonable waiting and adjustment periods and/or
accounting and crediting procedures to ensure that amounts applied toward the purchase of Common Stock for each Participant properly correspond with amounts withheld from the Participant’s Compensation, and establish such other limitations or
procedures as the Administrator determines in its sole discretion to be advisable that are consistent with the Plan.  
 (c)
Actions In the Event of Unfavorable Financial Accounting Consequences. In the event the Administrator determines that the ongoing operation of the Plan may result in unfavorable financial accounting consequences, the Administrator may, in its
discretion and, to the extent necessary or desirable, modify or amend the Plan to reduce or eliminate such accounting consequence including, but not limited to:  

(i) altering the Purchase Price for any Offering Period including an Offering Period underway at the time of the change in Purchase Price;

  
 10 

 (ii) shortening any Offering Period so that the Offering Period ends on a new Purchase Date,
including an Offering Period underway at the time of the Administrator action; and 
 (iii) allocating Shares. 

Such modifications or amendments shall not require stockholder approval or the consent of any Participant. 

(d) Payments Upon Termination of Plan. Upon termination of the Plan, the balance in each Participant’s Plan account shall
be refunded as soon as practicable after such termination, without any interest thereon. 
  

	10.	Term of Plan. 

 The Plan shall be effective on the Effective Date. The
effectiveness of the Plan shall be subject to approval of the Plan by the stockholders of the Company within twelve months following the date the Plan is first approved by the Board. No right may be granted under the Plan prior to such stockholder
approval. No rights may be granted under the Plan during any period of suspension of the Plan or after termination of the Plan. 
  

	11.	Administration. 

 (a) Administrator. Unless otherwise determined by
the Board, the Administrator of the Plan shall be the Compensation Committee of the Board (or another committee or a subcommittee of the Board to which the Board delegates administration of the Plan) (such committee, the
“Committee”). The Board may at any time vest in the Board any authority or duties for administration of the Plan.  

(b) Action by the Administrator. Unless otherwise established by the Board or in any charter of the Administrator, a majority of
the Administrator shall constitute a quorum. The acts of a majority of the members present at any meeting at which a quorum is present and, subject to Applicable Law and the Bylaws of the Company, acts approved in writing by a majority of the
Administrator in lieu of a meeting, shall be deemed the acts of the Administrator. Each member of the Administrator is entitled to, in good faith, rely or act upon any report or other information furnished to that member by any officer or other
Employee, the Company’s independent certified public accountants, or any executive compensation consultant or other professional retained by the Company to assist in the administration of the Plan. 

(c) Authority of Administrator. The Administrator shall have the power, subject to, and within the limitations of, the express
provisions of the Plan: 
 (i) To determine when and how rights to purchase Common Stock shall be granted and the provisions of each
offering of such rights (which need not be identical). 
 (ii) To designate from time to time which Subsidiaries of the Company shall be
Designated Subsidiaries, which designation may be made without the approval of the stockholders of the Company. 
 (iii) To construe and
interpret the Plan and rights granted under it, and to establish, amend and revoke rules and regulations for its administration. The Administrator, in the exercise of this power, may correct any defect, omission or inconsistency in the Plan, in a
manner and to the extent it shall deem necessary or expedient to make the Plan fully effective. 

  
 11 

 (iv) To amend the Plan as provided in Section 9. 

(v) Generally, to exercise such powers and to perform such acts as the Administrator deems necessary or expedient to promote the best
interests of the Company and its Subsidiaries and to carry out the intent that the Plan be treated as an “employee stock purchase plan” within the meaning of Section 423 of the Code. 

(d) Decisions Binding. The Administrator’s interpretation of the Plan, any rights granted pursuant to the Plan, any
subscription agreement and all decisions and determinations by the Administrator with respect to the Plan are final, binding, and conclusive on all parties. 
  

	12.	Miscellaneous. 

 (a) Restriction upon Assignment. A right granted
under the Plan shall not be transferable other than by will or the applicable laws of descent and distribution, and is exercisable during the Participant’s lifetime only by the Participant. Except as provided in Section 12(d) hereof, a
right under the Plan may not be exercised to any extent except by the Participant. The Company shall not recognize and shall be under no duty to recognize any assignment or alienation of the Participant’s interest in the Plan, the
Participant’s rights under the Plan or any rights thereunder.  
 (b) Rights as a Stockholder. With respect to
Shares subject to a right granted under the Plan, a Participant shall not be deemed to be a stockholder of the Company, and the Participant shall not have any of the rights or privileges of a stockholder, until such Shares have been issued to the
Participant or his or her nominee following exercise of the Participant’s rights under the Plan. No adjustments shall be made for dividends (ordinary or extraordinary, whether in cash securities, or other property) or distribution or other
rights for which the record date occurs prior to the date of such issuance, except as otherwise expressly provided herein or as determined by the Administrator. 

(c) Interest. No interest shall accrue on the payroll deductions or contributions of a Participant under the Plan. 

(d) Designation of Beneficiary. 

(i) A Participant may, in the manner determined by the Administrator, file a written designation of a beneficiary who is to receive any Shares
and cash, if any, from the Participant’s account under the Plan in the event of such Participant’s death subsequent to a Purchase Date on which the Participant’s rights are exercised but prior to delivery to such Participant of such
Shares and cash. In addition, a Participant may file a written designation of a beneficiary who is to receive any cash from the Participant’s account under the Plan in the event of such Participant’s death prior to exercise of the
Participant’s rights under the Plan. If the Participant is married and resides in a community property state, a designation of a person other than the Participant’s spouse as his or her beneficiary shall not be effective without the prior
written consent of the Participant’s spouse. 
 (ii) Such designation of beneficiary may be changed by the Participant at any time by
written notice to the Company. In the event of the death of a Participant and in the absence of a beneficiary validly designated under the Plan who is living at the time of such Participant’s death, the Company shall deliver such Shares and/or
cash to the executor or administrator of the estate of the Participant, or if no such executor or administrator has been appointed (to the knowledge of the 

  
 12 

 
Company), the Company, in its discretion, may deliver such Shares and/or cash to the spouse or to any one or more dependents or relatives of the Participant, or if no spouse, dependent or
relative is known to the Company, then to such other person as the Company may designate. 
 (e) Notices. All notices or other
communications by a Participant to the Company under or in connection with the Plan shall be deemed to have been duly given when received in the form specified by the Company at the location, or by the person, designated by the Company for the
receipt thereof. 
 (f) Equal Rights and Privileges. Subject to Section 5(g), all Eligible Employees will have equal
rights and privileges under this Plan so that this Plan qualifies as an “employee stock purchase plan” within the meaning of Section 423 of the Code. Subject to Section 5(g), any provision of this Plan that is inconsistent with
Section 423 of the Code will, without further act or amendment by the Company, the Board or the Administrator, be reformed to comply with the equal rights and privileges requirement of Section 423 of the Code. 

(g) Use of Funds. All payroll deductions received or held by the Company under the Plan may be used by the Company for any
corporate purpose, and the Company shall not be obligated to segregate such payroll deductions. 
 (h) Reports.
Statements of account shall be given to participating Eligible Employees at least annually, which statements shall set forth the amounts of payroll deductions, the Purchase Price, the number of Shares purchased and the remaining cash balance, if
any. 
 (i) No Employment Rights. Nothing in the Plan shall be construed to give any person (including any Eligible
Employee or Participant) the right to remain in the employ of the Company or any Parent or Subsidiary or affect the right of the Company or any Parent or Subsidiary to terminate the employment of any person (including any Eligible Employee or
Participant) at any time, with or without cause. 
 (j) Notice of Disposition of Shares. Each Participant shall give
prompt notice to the Company of any disposition or other transfer of any Shares purchased upon exercise of a right under the Plan if such disposition or transfer is made: (i) within two years from the Enrollment Date of the Offering Period in
which the Shares were purchased or (ii) within one year after the Purchase Date on which such Shares were purchased. Such notice shall specify the date of such disposition or other transfer and the amount realized, in cash, other property,
assumption of indebtedness or other consideration, by the Participant in such disposition or other transfer. 
 (k)
Governing Law. The Plan and any agreements hereunder shall be administered, interpreted and enforced under the internal laws of the State of Delaware without regard to conflicts of laws thereof or of any other jurisdiction. 

(l) Electronic Forms. To the extent permitted by Applicable Law and in the discretion of the Administrator, an Eligible Employee
may submit any form or notice as set forth herein by means of an electronic form approved by the Administrator. Before the commencement of an Offering Period, the Administrator shall prescribe the time limits within which any such electronic form
shall be submitted to the Administrator with respect to such Offering Period in order to be a valid election. 
 * * * * * 

  
 13EX-10.4

 Exhibit 10.4 

SERES THERAPEUTICS, INC. 

NON-EMPLOYEE DIRECTOR COMPENSATION PROGRAM 

Non-employee members of the board of directors (the “Board”) of Seres Therapeutics, Inc. (the
“Company”) shall receive cash and equity compensation as set forth in this Non-Employee Director Compensation Program (this “Program”). The cash and equity compensation described in this Program shall
be paid or be made, as applicable, automatically and without further action of the Board, to each member of the Board who is not an employee of the Company or any parent or subsidiary of the Company (each, a “Non-Employee
Director”) who is entitled to receive such cash or equity compensation, unless such Non-Employee Director declines the receipt of such cash or equity compensation by written notice to the Company. This Program shall remain in effect
until it is revised or rescinded by further action of the Board. This Program may be amended, modified or terminated by the Board at any time in its sole discretion. The terms and conditions of this Program shall supersede any prior cash and/or
equity compensation arrangements for service as a member of the Board between the Company and any of its Non-Employee Directors. No Non-Employee Director shall have any rights hereunder, except with respect to stock options granted pursuant to the
Program. This Program shall become effective on the date of the effectiveness of the Company’s Registration Statement on Form S-1 relating to the initial public offering of common stock (the “Effective Date”). 

 

	I.	CASH COMPENSATION 

 A. Annual Retainers. Each
Non-Employee Director shall receive an annual retainer of $35,000 for service on the Board. 
 B. Additional Annual Retainers. In
addition, each Non-Employee Director shall receive the following annual retainers: 
 1. Chairman of the Board or Lead Independent
Director. A Non-Employee Director serving as Chairman of the Board or Lead Independent Director shall receive an additional annual retainer of $20,000 for such service. 

2. Audit Committee. A Non-Employee Director serving as Chairperson of the Audit Committee shall receive an additional annual retainer
of $15,000 for such service. A Non-Employee Director serving as a member other than the Chairperson of the Audit Committee shall receive an additional annual retainer of $7,500 for such service. 

3. Compensation Committee. A Non-Employee Director serving as Chairperson of the Compensation Committee shall receive an additional
annual retainer of $10,000 for such service. A Non-Employee Director serving as a member other than the Chairperson of the Compensation Committee shall receive an additional annual retainer of $5,000 for such service. 

4. Nominating and Corporate Governance Committee. A Non-Employee Director serving as Chairperson of the Nominating and
Corporate Governance Committee shall receive an additional annual retainer of $7,000 for such service. A Non-Employee Director serving as a member other than the Chairperson of the Nominating and Corporate Governance Committee shall receive an
additional annual retainer of $3,500 for such service. 

 C. Payment of Retainers. The annual retainers described in Sections I(A) and I(B) shall be
earned on a quarterly basis based on a calendar quarter and shall be paid in cash by the Company in arrears not later than the fifteenth day following the end of each calendar quarter. In the event a Non-Employee Director does not serve as a
Non-Employee Director, or in the applicable positions described in Section I(B), for an entire calendar quarter, the retainer paid to such Non-Employee Director shall be prorated for the portion of such calendar quarter actually served as a
Non-Employee Director, or in such position, as applicable. 
  

	II.	EQUITY COMPENSATION 

 Non-Employee Directors shall be
granted the equity awards described below. The awards described below shall be granted under and shall be subject to the terms and provisions of the Company’s 2015 Incentive Award Plan or any other applicable Company equity incentive plan
then-maintained by the Company (the “Equity Plan”) and shall be granted subject to award agreements, including attached exhibits, in substantially the form previously approved by the Board. All applicable terms of the Equity
Plan apply to this Program as if fully set forth herein, and all grants of stock options hereby are subject in all respects to the terms of the Equity Plan and the applicable award agreement. For the avoidance of doubt, the share numbers in Sections
II(A) and II(B) shall be subject to adjustment as provided in the Equity Plan, including without limitation with respect to any stock dividend, stock split, reverse stock split or other similar event affecting the Company’s common stock that is
effected prior to the Effective Date. 
 A. Initial Awards. Each Non-Employee Director who is initially elected or appointed to the
Board after the Effective Date shall receive an option to purchase 30,000 shares of the Company’s common stock on the date of such initial election or appointment. The awards described in this Section II(A) shall be referred to as
“Initial Awards.” No Non-Employee Director shall be granted more than one Initial Award. 
 B. Subsequent
Awards. A Non-Employee Director who (i) has been serving as a Non-Employee Director on the Board for at least six months as of the date of any annual meeting of the Company’s stockholders after the Effective Date and (ii) will
continue to serve as a Non-Employee Director immediately following such meeting, shall be automatically granted an option to purchase 15,000 shares of the Company’s common stock on the date of such annual meeting. The awards described in this
Section II(B) shall be referred to as “Subsequent Awards.” For the avoidance of doubt, a Non-Employee Director elected for the first time to the Board at an annual meeting of the Company’s stockholders shall only receive
an Initial Award in connection with such election, and shall not receive any Subsequent Award on the date of such meeting as well. 
 C.
Termination of Service of Employee Directors. Members of the Board who are employees of the Company or any parent or subsidiary of the Company who subsequently terminate their service with the Company and any parent or subsidiary of the
Company and remain on the Board will not receive an Initial Award pursuant to Section II(A) 

 
above, but to the extent that they are otherwise entitled, will receive, after termination from service with the Company and any parent or subsidiary of the Company, Subsequent Awards as
described in Section II(B) above. 
 D. Terms of Awards Granted to Non-Employee Directors 

1. Exercise Price. The per share exercise price of each option granted to a Non-Employee Director shall equal the Fair Market Value (as
defined in the Equity Plan) of a share of common stock on the date the option is granted. 
 2. Vesting. Each Initial Award shall
vest and become exercisable in four substantially equal annual installments following the date of grant, such that the Initial Award shall be fully vested on the fourth anniversary of the date of grant, subject to the Non-Employee Director
continuing in service as a Non-Employee Director through each such vesting date. Each Subsequent Award shall vest and become exercisable on the earlier of the first anniversary of the date of grant or the day immediately prior to the date of the
next annual meeting of the Company’s stockholders occurring after the date of grant, in either case subject to the Non-Employee Director continuing in service on the Board as a Non-Employee Director through each such vesting date. Unless the
Board otherwise determines, any portion of an Initial Award or Subsequent Award which is unvested or unexercisable at the time of a Non-Employee Director’s termination of service on the Board as a Non-Employee Director shall be immediately
forfeited upon such termination of service and shall not thereafter become vested and exercisable. All of a Non-Employee Director’s Initial Awards and Subsequent Awards shall vest in full immediately prior to the occurrence of a Change in
Control (as defined in the Equity Plan), to the extent outstanding at such time. 
 3. Term. The maximum term of each stock option
granted to a Non-Employee Director hereunder shall be ten (10) years from the date the option is granted. 
 * * * * *

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