7. Stock and Stock-Based Awards

On July 1, 2015, in connection with the closing of the initial public offering of the Company’s common stock (“IPO”), the Company effected its Restated Certificate of Incorporation, which authorizes the Company to issue 10,000,000 shares of preferred stock, $0.001 par value per share.

On April 10, 2025, at the Company's 2025 annual meeting of stockholders (the “2025 Annual Meeting”), stockholders approved an amendment to the Company’s Restated Certificate of Incorporation in order to effect a reverse stock split of all outstanding shares of the Company's common stock. On April 21, 2025, the Company effected a 1-for-20 reverse stock split of its common stock. The reverse stock split had no impact on the number of authorized shares or the par value of preferred and common stock. As of the effective time of the reverse stock split, the number of shares of common stock issuable upon exercise, vesting or settlement of outstanding awards, the exercise price of all outstanding options and any stock price vesting goals with respect to any outstanding awards under the Company’s equity plans (including the 2025 Plan, as defined below) was proportionately adjusted (and rounded down to the nearest whole share in the case of shares and up to the nearest whole cent in the case of exercise prices, as applicable) based on the 1-for-20 ratio. In addition, the number of shares available for future issuance and any share‑based award limits under the Company’s equity plans were proportionately reduced based on the 1-for-20 ratio. Trading of the Company's common stock on The Nasdaq Global Select Market commenced on a split-adjusted basis on April 22, 2025.

On September 30, 2024, the Company entered into the Securities Purchase Agreement with SPN, pursuant to which SPN purchased 714,285 shares at the Closing at a purchase price per share of $21.00, for an aggregate purchase price of $15,000. Under the terms of the Securities Purchase Agreement, SPN has agreed not to sell or transfer the shares for a period of six months after Closing, subject to certain customary exceptions. The Company agreed to register the resale of the Shares by SPN within 90 days of Closing. On October 1, 2024, the Company filed a registration statement to register the Shares, which became effective on October 11, 2024. In addition, under the terms of the Securities Purchase Agreement, for as long as SPN, together with its affiliates, beneficially owns at least 10% of the Company's outstanding shares of common stock, the Company has agreed to take such action within its control to include one individual designated by SPN in the slate of nominees recommended by the Company's board of directors (or the applicable committee of the board) to the Company's stockholders for election to the board at the applicable stockholder meeting. The Securities Purchase Agreement contains customary representations and warranties and closing conditions. The aggregate fair value of $13,516 for the common stock issued to SPN was recorded in equity, with the remaining $1,484 cash received from SPN under the Securities Purchase Agreement allocated to the consideration transferred for the VOWST Business.

On February 22, 2024, the Company’s board of directors adopted a resolution to amend the Restated Certificate of Incorporation, subject to stockholder approval, by increasing the number of authorized shares of the Company’s Common Stock from 240,000,000 shares to 360,000,000 shares (the “Share Increase Amendment”). At the Company’s annual meeting of stockholders held on April 4, 2024, the Company’s stockholders approved the Share Increase Amendment. On April 5, 2024, the Company amended its Restated Certificate of Incorporation to reflect the Share Increase Amendment.

In May 2021, the Company entered into a Sales Agreement (the “Sales Agreement”) with Cowen and Company, LLC ("Cowen") to sell shares of the Company’s common stock, with aggregate gross sales proceeds of up to $150,000, from time to time, through an "at-the-market" equity offering program (“ATM”) under which Cowen acts as sales agent. During the year ended

December 31, 2025, the Company sold 739,545 shares of common stock under the 2021 Sales Agreement, at an average price of approximately $18.48 per share, raising aggregate net proceeds of approximately $13,167 after deducting an aggregate commission of approximately 3% and other issuance costs. During the year ended December 31, 2024, the Company sold 1,030,846 shares of common stock under the 2021 Sales Agreement, at an average price of approximately $23.67 per share, raising aggregate net proceeds of approximately $23,530 after deducting an aggregate commission of approximately 3% and other issuance costs.

2015 and 2025 Incentive Award Plans

On June 16, 2015, the Company’s stockholders approved the 2015 Incentive Award Plan (the “2015 Plan”), which became effective on June 25, 2015. The 2015 Plan was subsequently amended on December 14, 2022, and provides for the grant of incentive stock options, nonqualified stock options, stock appreciation rights, restricted stock awards, restricted stock units and other stock-based awards. The number of shares initially reserved for issuance under the 2015 Plan was the sum of (i) 110,000 shares of common stock and (ii) the number of shares subject to awards outstanding under the 2012 Plan that expire, terminate or are otherwise surrendered, canceled, forfeited or repurchased by the Company on or after the effective date of the 2015 Plan. In addition, the number of shares of common stock that may be issued under the 2015 Plan was subject to increase on the first day of each calendar year, beginning in 2016 and ending in 2025, equal to the lesser of (i) 4% of the number of shares of the Company’s common stock outstanding on the last day of the preceding applicable calendar year and (ii) an amount determined by the Company’s board of directors.

On April 10, 2025, the Company's stockholders approved the 2025 Incentive Award Plan (the “2025 Plan”) as an amendment and restatement of the Seres Therapeutics, Inc. 2015 Incentive Award Plan. The amendment, among other things, authorized the issuance of 2,230,243 shares of the Company’s common stock for awards under the 2025 Plan, which includes 1,750,493 shares previously authorized for issuance under the 2015 Plan plus an increase of 479,750 shares (in each case, which amounts reflect the 1-for-20 reverse stock split), and extended the term of the 2025 Plan to March 3, 2035, the tenth anniversary of the approval of the 2025 Plan by the Company’s board of directors.

Stock awards granted under the 2025 Plan generally vest over four years and expire after ten years, although options have been granted with vesting terms less than four years. As of December 31, 2025, there were 740,410 shares available for future grant under the 2025 Plan.

2015 Employee Stock Purchase Plan

On June 16, 2015, the Company’s stockholders approved the 2015 Employee Stock Purchase Plan (the “ESPP”), which became effective on June 25, 2015. A total of 18,250 shares of common stock were reserved for issuance under the ESPP. In addition, the number of shares of common stock that may be issued under the ESPP automatically increase on the first day of each calendar year, beginning in 2016 and ending in 2025, by an amount equal to the lesser of (i) 20,000 shares, (ii) 1% of the number of shares of the Company’s common stock outstanding on the last day of the applicable preceding calendar year and (iii) an amount determined by the Company’s board of directors. Offering periods under the ESPP will commence when determined by the plan administrator. During the year ended and as of December 31, 2025, there were 17,839 shares issued and 106,064 shares were reserved and available for issuance under the ESPP, respectively.

The ESPP provides that eligible employees may contribute up to 15% of their eligible earnings toward the semi-annual purchase of the Company's common stock. Purchase rights issued under the ESPP are intended to be qualified under Section 423 of the Internal Revenue Code of 1986, as amended ("IRC"). The employee's purchase price is derived from a formula based on the closing price of the common stock on the first day of the offering period versus the closing price on the date of purchase (or, if not a trading day, on the immediately preceding trading day). The offering period under the ESPP has a duration of six months, and the purchase price with respect to each offering period beginning on or after such date is, until otherwise amended, equal to 85% of the lesser of (i) the fair market value of the Company's common stock at the commencement of the applicable six-month offering period or (ii) the fair market value of the Company's common stock on the purchase date.

2022 Employment Inducement Award Plan

On December 14, 2022, the Company’s board of directors approved the 2022 Employment Inducement Award Plan (the "2022 Plan"), which became effective on such date without stockholder approval pursuant to Rule 5635(c)(4) of The Nasdaq Stock Market LLC listing rules (“Rule 5635(c)(4)”). The 2022 Plan provides for the grant of nonqualified stock options, stock appreciation rights, restricted stock awards, restricted stock units and other stock- or cash-based awards. In accordance with Rule 5635(c)(4), awards under the 2022 Plan may only be made to a newly hired employee who has not previously been a member of our board of directors, or an employee who is being rehired following a bona fide period of non-employment by us as a material inducement to the employee’s entering into employment with us. A total of 125,000 shares of common stock were reserved for issuance under the 2022 Plan. Any shares subject to awards previously granted under the 2022 Plan that expire, terminate or are otherwise surrendered, canceled, or forfeited in any case, in a manner that results in the Company acquiring the shares covered by the award at a price not greater than the price (as adjusted to reflect any equity restructuring) paid by the Participant for such shares or not issuing any shares covered by the award, the unused shares covered by the award will again be available for award grants under the 2022 Plan.

As of December 31, 2025, there were 86,644 shares available for future grant under the 2022 Plan.

Stock Options

In February 2024, the Company approved a repricing of certain stock option awards to reduce the original exercise price to the Company’s current fair market value as of February 12, 2024 (the “Repricing”). The Repricing became effective 18 months from the approval date, or August 2025. The remaining terms and conditions of each option affected by the Repricing remained the same, including the expiration date, vesting commencement date, vesting schedule and any vesting acceleration. As the Repricing was retrospective to February 2024, the weighted average exercise price for stock options outstanding as of December 31, 2024 in the table above has been adjusted to reflect the Repricing. The Repricing was accounted for as a modification, and an immaterial amount of incremental fair value is being recognized from the date the Repricing was approved over the remaining vesting term of the options.

The weighted average grant-date fair value of stock options granted during the years ended December 31, 2025, 2024, and 2023 was $13.30, $18.58, and $90.37 per share, respectively. The total intrinsic value of stock options exercised during the years ended December 31, 2025, 2024, and 2023 was $98, $0, and $438, respectively.

The aggregate intrinsic value of stock options is calculated as the difference between the exercise price of the stock options and the fair value of the Company’s common stock for those stock options that had exercise prices lower than the fair value of the Company’s common stock.

During the year ended December 31, 2021, the Company granted performance-based stock options to employees for the purchase of an aggregate of 28,100 shares of common stock with a grant date fair value of $110.60 per share. These stock options are exercisable only upon achievement of specified performance targets. In April 2023, the performance target associated with 50% of the performance-based stock options was achieved. Accordingly, the Company recorded $0, $8 and $2,051 of compensation expense during the years ended December 31, 2025, 2024 and 2023, respectively, with respect to these performance-based stock options, which represents a cumulative catch-up from the grant date through the achievement of the performance targets, and vesting of the remaining 50% of the options beginning in April 2023. The remaining compensation expense associated with these performance-based stock options was recognized as of April 2024, for all such options for which ongoing performance targets were achieved and service requirements were met.

During the three months ended March 31, 2024, the Company granted stock options to certain executives for the purchase of an aggregate of 127,500 shares of common stock. These awards will vest only to the extent that the 30-day trailing simple average public market closing price of the Company's common stock reaches certain price thresholds. These awards have an exercise price of $22.00 and vest and become exercisable when the market conditions are satisfied or, if later, on the first anniversary of the grant date. These awards expire 10 years from the date of grant. The fair value of these market-based stock options was estimated using a Monte Carlo valuation method. During the years ended December 31, 2025 and 2024, the Company recognized $641 and $775 of compensation expense related to these awards.

Restricted Stock Units

The Company has granted restricted stock units with service-based vesting conditions ("RSUs") and restricted stock units with performance-based vesting conditions ("PSUs"). RSUs and PSUs represent the right to receive shares of common stock upon meeting specified vesting requirements. Restricted stock units may not be sold or transferred by the holder and vest according to the vesting conditions of each award. The table below summarizes the Company’s RSU and PSU activity for the year ended December 31, 2025:

During the years ended December 31, 2025, 2024, and 2023, the Company granted 79,846, 75,066 and 154,904 RSUs, respectively. RSUs generally vest over four years, with 25% vesting after one year, and the remaining 75% vesting quarterly over the next 3 years, subject to continued service to the Company through the applicable vesting date. PSUs vest according to the performance requirements of the awards, generally when the Company has determined that the specified performance targets have been achieved.

During the year ended December 31, 2023, the Company granted PSUs to employees covering an aggregate of 66,135 shares of common stock with a grant date fair value of $110.00. These PSUs begin to vest ratably only upon achievement of specified performance targets, which were achieved in April 2023. Accordingly, the Company recorded $0, $792 and $4,293 in compensation expense during the years ended December 31, 2025, 2024, and 2023 respectively, with respect to these PSUs.

The aggregate intrinsic value of RSUs, including PSUs for which the performance conditions have been met, that vested during the years ended December 31, 2025, 2024 and 2023 was $1,903, $1,899, and $4,729, respectively.

Retention Awards

In September 2025, the Company issued retention awards to employees of the Company in the form of RSUs covering 68,596 shares of common stock with a grant date fair value of $18.93 per share. The retention RSUs fully vested on November 15, 2025 subject to the employee's continued employment with the Company through such date. The compensation expense associated with these awards was recognized ratably over the vesting period. For the year ended December 31, 2025, the Company recognized $1,299 in compensation expense with respect to the retention RSUs.

In November 2023, as part of the corporate restructuring described in Note 9, Restructuring, the Company issued retention awards to employees of the Company in the form of RSUs, which vested as to the first tranche on August 15, 2024 and as to the second tranche on May 15, 2025, subject to remaining actively employed with the Company through such date. The compensation expense associated with these awards was recognized ratably over the vesting period. For the years ended December 31, 2025, 2024, and 2023, the Company recognized $163, $655 and $92, respectively, in compensation expense with respect to the retention awards.

Stock-based Compensation Valuation

The Company estimates the fair value of rights to acquire common stock under the ESPP using a Black-Scholes valuation model on the date of grant and the straight-line attribution approach to recognize the expense. The assumptions that the Company used to determine the fair value of rights to acquire common stock under the ESPP were as follows, presented on a weighted average basis:

Stock-based Compensation

As of December 31, 2025, the Company had an aggregate of $9,986 of unrecognized stock-based compensation cost, which is expected to be recognized over a weighted average period of 3.2 years.