7. Common Stock and Stock-Based Awards

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.

Additionally, at the 2025 Annual Meeting, stockholders approved the Seres Therapeutics, Inc. 2025 Incentive Award Plan (the “2025 Plan”) as an amendment and restatement of the Seres Therapeutics, Inc. 2015 Incentive Award Plan (the “2015 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.

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 May 21, 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 six months ended June 30, 2025, the Company sold 54,806 shares of common stock under the Sales Agreement, at an average price of approximately $18.60 per share, raising aggregate net proceeds of approximately $996 after deducting an aggregate commission of approximately 3% and other issuance costs. During the six months ended June 30, 2024, the Company sold 768,331 shares of common stock under the Sales Agreement, at an average price of approximately $24.60 per share, raising aggregate net proceeds of approximately $18,409 after deducting an aggregate commission of approximately 3% and other issuance costs.

Stock Options

The weighted average grant date fair value of stock options granted during the three and six months ended June 30, 2025 and 2024 was $10.18, $13.49, $13.06 and $18.67 per share, respectively.

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 three and six months ended June 30, 2025 and 2024, the Company recognized $188, $261, $284, and $426, respectively, of compensation expense related to these awards, respectively.

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 following table summarizes the Company’s RSU and PSU activity since December 31, 2024:

During the three and six months ended June 30, 2025 and 2024, the Company granted 0, 11,250, 258, and 64,316 RSUs, respectively. During the three and six months ended June 30, 2025 and 2024, the Company did not grant any PSUs. 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 three months ended March 31, 2023, the Company granted PSUs to employees for the purchase of 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 $267 and $527 in compensation expense during the three and six months ended June 30, 2024, with respect to these PSUs. The remaining compensation expense associated with these PSUs was fully recognized as of December 31, 2024.

Stock-based Compensation Expense