Seres Therapeutics, Inc.

(Amounts in thousands, except share and per share data)

(Unaudited)

1. Nature of the Business and Basis of Presentation

Seres Therapeutics, Inc. (the “Company”) was incorporated under the laws of the State of Delaware in October 2010 under the name Newco LS21, Inc. In October 2011, the Company changed its name to Seres Health, Inc., and in May 2015, the Company changed its name to Seres Therapeutics, Inc. The Company is a clinical-stage company focused on improving patient outcomes in medically compromised populations, including oncology patients and those suffering from inflammatory and immune (“I&I”) diseases through discovery and development of novel live biotherapeutics. The Company led the successful development and approval of VOWST (previously referred to as SER-109), the first FDA-approved orally administered microbiome therapeutic and a Breakthrough Therapy designated drug, which was sold to Nestlé Health Science (as defined below) in September 2024. The Company's live biotherapeutic product (“LBP”) candidates, including SER-155, SER-603, SER-428, SER-147, and other potential candidates in earlier development, are consortia of bacteria designed to optimize specific, targeted pharmacological properties, and are formulated for oral delivery. The Company is designing LBP candidates to address unmet medical needs in oncology that can lead to interruption to patients' cancer treatment and/or mortality, and to treat I&I diseases, bymodulating host function to protect and improve mucosal epithelial barrier integrity, induce immune homeostasis and tolerance, and prevent the colonization and overgrowth of pathogens in the gastrointestinal (“GI”) tract.

The Company's initial focus in oncology is in two areas: (1) to prevent bacterial bloodstream infections (“BSIs”), including those that can harbor antimicrobial resistance (“AMR”), as well as other pathogen-associated negative clinical outcomes in patients undergoing allogeneic hematopoietic stem cell transplantation (“allo-HCT”), and (2) to treat immune checkpoint-related enterocolitis (“irEC”), a frequent and often severe side effect of immune checkpoint inhibitor (“ICI”) therapy.

SER-155, the Company's most advanced LBP candidate, is an investigational, oral, live biotherapeutic currently in development to address unmet medical needs in oncology that cause interruptions to cancer treatment and/or mortality. In the Company's placebo-controlled Phase 1b study of SER-155 in allo-HCT, SER-155 was associated with a 77% relative risk reduction in bacterial BSIs and a significant reduction in systemic antibiotic exposure as well as a lower incidence of febrile neutropenia, as compared to placebo through day 100 post HCT. SER-155 was generally well tolerated, with no observed treatment-related serious adverse events. Drug pharmacology data demonstrated that SER-155 significantly promoted mucosal epithelial barrier integrity and had a positive impact on biomarkers of systemic inflammation and immune homeostasis. Following advancement of key startup activities for the SER-155 Phase 2 study in allo-HCT, including the submission of a final protocol to the FDA in January 2026, study site evaluation and qualification with its CRO, and manufacturing of drug substance, the Company has paused additional investment in that program while continuing to seek funding for the Phase 2 study.

SER-155 is also being evaluated in 15 patients with moderate-to-severe (Grade 2- 3) irEC, through an investigator-sponsored trial (“IST”), with Memorial Sloan Kettering Cancer Center, with whom the Company has had a decade-long collaboration. irEC is among the most frequent and severe immune-related adverse events (“irAEs”), in recipients of ICI therapy, and can be observed in up to 50% of patients, with rates varying based on cancer drug and treatment regimen. Moderate to severe irEC occurs in approximately 25% of all ICI therapy recipients in the United States. Top-line data from the IST showed that 80% of SER-155 recipients achieved an immunosuppressive-free clinical response of diarrhea (a primary symptom of irEC) at Day 15, which met the primary endpoint, defined as at least a 1-grade improvement in diarrhea symptoms without immunosuppressive therapy (i.e., a corticosteroid and/or biologic immunomodulator drug). All 12 participants with immunosuppressive-free clinical response at Day 15 had the same, or better, diarrhea grade at Day 43. SER-155 was well tolerated, with no drug-related serious adverse events observed.

Clinical data from the SER-155 Phase 1b study in allo-HCT and the IST in irEC, in particular the drug pharmacology translational biomarker data, along with the Company's extensive preclinical and other translational clinical data compiled over the past decade support and inform the advancement of the Company's earlier stage programs targeting I&I diseases. The Company is developing SER-603, broadly in inflammatory bowel disease (“IBD”), including ulcerative colitis (“UC”), and Crohn's disease. SER-603 is a novel, LBP candidate optimized to address disruptions in the GI microbiome and to improve GI mucosal barrier integrity through the inhibition of inflammatory bacteria and associated metabolites, the promotion of epithelial barrier integrity to reduce the translocation of inflammatory molecules and barrier inflammation, and to induce immune homeostasis through non-immunosuppressive regulatory T cell, or T-reg, induction via T cell signaling. The Company is currently exploring potential collaborations related to I&I disease programs.

In 2025, the Company was awarded a grant from Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator (“CARB-X”) for up to $3,583, representing the Company’s second CARB-X award, to support the development of an oral liquid formulation based on SER-155 strains, now referred to as SER-428, for dosing in patients who cannot take oral capsules such as intubated patients in the medical ICU, and other medically vulnerable patients at high risk of AMR infections. The Company began recognizing revenue from this grant in the third quarter of 2025. The Company has advanced development and manufacturing of SER-428 and is designing a Phase 1b open label trial in collaboration with Columbia University to evaluate this LBP candidate in medical ICU patients at high risk of infection.

The Company has built and deploys a reverse translational platform and knowledge base for the discovery and development of LBPs, and maintains extensive proprietary know-how that may be used to support future research and development efforts. This platform incorporates high-resolution analysis of human clinical data to identify microbiome biomarkers associated with disease and non-disease states; preclinical screening using human cell-based assays and in vitro/ex vivo and in vivo disease models customized for live biotherapeutics; and a strain library and associated microbiological capabilities that spans broad biological and functional breadth. This platform and knowledge base are integrated through a proprietary knowledge graph and agentic artificial intelligence, enabling rapid identification of specific microbes, microbial genes, and microbial metabolites/peptides associated with disease and the design of therapeutic consortia of bacteria for specific pharmacological properties to restructure the gut microbiome and modulate functional pathways associated with disease. In addition, the Company owns a valuable intellectual property estate related to the development and manufacture of live biotherapeutics.

On February 12, 2026, the Company announced that it implemented cost reduction actions, including reducing its workforce by approximately 30%. During the six months ended June 30, 2026, the Company incurred approximately $914 in restructuring costs, primarily related to severance costs, of which $718 was paid in the first quarter of 2026, and the remainder of these costs were paid out in the second quarter of 2026.

Going Concern

The Company is subject to risks common to companies in the biotechnology industry including, but not limited to, new technological innovations, protection of proprietary technology, dependence on key personnel, compliance with government regulations and the need to obtain additional financing. The Company operates in an environment of rapid change in technology and substantial competition from pharmaceutical and biotechnology companies. In addition, the Company is dependent upon the services of its employees and consultants.

The accompanying condensed consolidated financial statements have been prepared on a basis which assumes that the Company will continue as a going concern and which contemplates the realization of assets and satisfaction of liabilities and commitments in the normal course of business. As of June 30, 2026, the Company had an accumulated deficit of$987,735 and cash and cash equivalents of$15,594.

The Company’s product candidates are in development, and will require significant additional research and development efforts, including extensive preclinical and clinical testing and regulatory approval, prior to potential commercialization. There can be no assurance that the Company’s research and development will be successfully completed, that adequate protection for the Company’s intellectual property will be obtained, or maintained, that any product candidate developed will obtain necessary government regulatory approval, or that any approved product will be commercially viable. Even if the Company’s product development efforts are successful, it is uncertain when, if ever, the Company will generate significant revenue from product sales.

Primarily as a result of the costs associated with the discovery and development of novel live biotherapeutics, the Company incurred a net loss from operations of $42,180 for thesix months ended June 30, 2026. The Company expects that its operating losses and negative cash flows will continue for the foreseeable future. Based on the Company’s currently available cash resources, the $12,500 Milestone Termination Payment (as defined below in Note 3, Discontinued Operations and TSA) received from SPN (as defined below) in July 2026, and the expected receipt of the additional $12,500 Milestone Termination Payment due from SPN in October 2026, current and forecasted level of operations, and forecasted cash flows for the 12-month period subsequent to the date of issuance of these condensed consolidated financial statements, the Company will require additional funding to support its ongoing operations and meet its obligations as they come due. These conditions raise substantial doubt about the Company’s ability to continue as a going concern.

The Company’s ability to continue as a going concern is dependent upon its ability to obtain the necessary financing to meet its obligations and repay its liabilities arising from normal business operations when they come due, and to generate profitable operations in the future. Management plans to provide for the Company’s capital requirements through financing or other strategic transactions, including potential business development transactions, and selling shares under the Company’s at the market equity offering. There can be no assurance that the Company will be able to access additional capital to fund operations with terms acceptable to the Company, or at all. Because certain elements of management’s plans to mitigate the conditions that raised substantial doubt about the Company’s ability to continue as a going concern are outside of the Company’s control, including the ability to raise capital through an equity or other financing, those elements cannot be considered probable according to Accounting Standards Codification (“ASC”) 205-40, Going Concern (“ASC 205-40”), and therefore cannot be considered in the evaluation of mitigating factors. As a result, management has concluded that substantial doubt exists about the Company’s ability to continue as a going concern for 12 months from the date these condensed consolidated financial statements are issued. The accompanying condensed consolidated financial statements do not include any adjustments that may result from the outcome of this uncertainty.

Unaudited Interim Financial Information

The accompanying unaudited condensed consolidated financial statements as of June 30, 2026 and for the six months ended June 30, 2026 and 2025 have been prepared by the Company, pursuant to the rules and regulations of the Securities and Exchange Commission (the “SEC”) for interim financial statements. Certain information and footnote disclosures normally included in financial statements prepared in accordance with accounting principles generally accepted in the United States of America (“GAAP”) have been condensed or omitted pursuant to such rules and regulations. However, the Company believes that the disclosures are adequate to make the information presented not misleading. These unaudited condensed consolidated financial statements should be read in conjunction with the Company’s audited consolidated financial statements and the notes thereto for the year ended December 31, 2025 included in the Company’s annual report on Form 10-K for the fiscal year ended December 31, 2025, which was filed with the SEC on March 12, 2026 (the “Annual Report”).

The unaudited condensed consolidated interim financial statements have been prepared on the same basis as the audited consolidated financial statements. The condensed consolidated balance sheet at December 31, 2025 was derived from audited annual financial statements, but does not contain all of the footnote disclosures from the annual financial statements. In the opinion of management, the accompanying unaudited interim condensed consolidated financial statements contain all adjustments which are necessary for a fair statement of the Company’s financial position, results of operations, and cash flows for the periods presented. Such adjustments are of a normal and recurring nature. The results of operations for the three and six months ended June 30, 2026 are not necessarily indicative of the results of operations that may be expected for the year ending December 31, 2026.

The Company’s condensed consolidated financial statements include its accounts and the accounts of its wholly owned subsidiaries. All intercompany transactions have been eliminated in consolidation. The condensed consolidated financial statements have been prepared in conformity with U.S. GAAP.

On April 21, 2025, the Company effected a 1-for-20 reverse stock split of the Company’s common stock. All share and per share amounts in the financial statements and notes thereto have been retroactively adjusted for all periods presented to give effect to this reverse stock split. The reverse stock split had no impact on the number of authorized shares or the par value of preferred and common stock. Therefore, the Company reclassified an amount equal to the reduction in the number of shares of common stock at par value to additional paid-in capital. No fractional shares were issued in connection with the reverse split, and stockholders who would otherwise be entitled to receive a fractional share instead received a cash payment equal to the fraction of a share of common stock in lieu of such fractional share. Proportionate adjustments were made to the number of shares authorized under the Company’s equity incentive plans, the number of shares subject to any award or purchase right under the Company’s equity incentive plans, and the exercise price or purchase price with respect to any stock option award or purchase right under the Company’s equity incentive plans. See Note 7, Stockholders' Equity, for further information.

2. Summary of Significant Accounting Policies

The significant accounting policies and estimates used in preparation of the unaudited condensed consolidated financial statements are described in the Company’s audited financial statements as of and for the year ended December 31, 2025, and the notes thereto, which are included in the Annual Report. There have been no material changes to the Company’s significant accounting policies during the six months ended June 30, 2026.

Use of Estimates

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the unaudited condensed consolidated financial statements and the reported amount of expenses during the reporting periods. In the unaudited condensed consolidated financial statements, the Company uses estimates and assumptions related to the accrual of research and development expenses. Estimates are periodically reviewed in light of changes in circumstances, facts and experience. Actual results could differ from those estimates.

Restricted Cash

The Company held restricted cash of$2,243 and $8,668 as of June 30, 2026 and December 31, 2025, respectively, which represents cash held for the benefit of the landlords for the Company’s leases. The Company has classified the restricted cash as long-term on its condensed consolidated balance sheets as the terms of the underlying leases are greater than one year.

Cash, cash equivalents and restricted cash were comprised of the following (in thousands):

Recently Adopted Accounting Pronouncements

In September 2025, the FASB issued ASU No. 2025-07, Derivatives and Hedging and Revenue from Contracts with Customers - Derivatives Scope Refinements and Scope Clarification for Share-Based Noncash Consideration from a Customer in a Revenue Contract, which applies to all entities that enter into non-exchange-traded contracts with underlyings based on operations or activities specific to one of the parties to the contract. The guidance in ASU 2025-07 expands the scope exceptions within ASC Topic 815, Derivatives and Hedging, to include certain nonexchange-traded contracts with underlyings that are based on operations or activities specific to one of the parties to the contract, including research and development funding arrangements. The Company early-adopted ASU 2025-07 effective January 1, 2026, and will account for the new ASU on a prospective basis to any new contracts entered into after the effective date. The adoption of ASU 2025-07 did not have a material impact on the Company's condensed consolidated financial statements or financial statement disclosures.

Recently Issued Accounting Pronouncements

In November 2024, the FASB issued ASU 2024-03, Disaggregation of Income Statement Expenses (Topic 220), which requires disclosure in the notes to financial statements about specific types of expenses included in the expense captions presented on the face of the statement of operations. The requirements of the ASU are effective for annual periods beginning after December 15, 2026, and for interim periods beginning after December 15, 2027, with early adoption permitted. The requirements will be applied prospectively with the option for retrospective application. The Company is currently evaluating the impact related to the adoption of ASU 2024-03 on its financial statement disclosures.

In December 2025, the FASB issued ASU 2025-10, Government Grants (Topic 832): Accounting for Government Grants Received by Business Entities, which standardizes the accounting for government grants and distinguishes between a grant related to an asset and a grant related to income. The requirements of the ASU are effective for annual periods beginning after December 15, 2028, and for interim periods within those annual periods, with early adoption permitted. The requirements can be applied using a modified prospective or a modified retrospective approach. The Company does not expect the impact of ASU 2025-10 to be material to its financial statement disclosures as it is consistent with the Company's current accounting policy for government grants.

3. Discontinued Operations and TSA

On September 30, 2024, the Company completed the sale (the “Transaction”) of its VOWST microbiome therapeutic business (the “VOWST Business”), including inventory and equipment, certain patents and patent applications, know-how, trade secrets, trademarks, domain names, marketing authorizations and related rights, documents, materials, business records and data and contracts that are used or held for use primarily in the development, commercialization and manufacturing of the microbiome product sold under the brand name VOWST as provided for in accordance with the terms of the Purchase Agreement (the “Product”), to Société des Produits Nestlé S.A. (“SPN”), a wholly-owned subsidiary of Nestlé S.A., and its designated affiliates (collectively, “Nestlé Health Science”) pursuant to the Asset Purchase Agreement, dated as of August 5, 2024 (the “Purchase Agreement”), by and among the Company and SPN, and a wholly-owned subsidiary of Nestlé S.A.

The Company also entered into a Transition Services Agreement (“TSA”) with Nestlé Enterprises S.A., (“NESA”), an affiliate of SPN, in connection with the Transaction, through which the Company provided certain manufacturing services until December 31, 2025, and other transition services, for the duration specified in the schedule to the TSA for each service. The Company's obligations under the TSA are now complete. For the three and six months ended June 30, 2026 and 2025, the Company recognized$0,$0,$3,490, and$9,799 respectively, of TSA reimbursement income in other income in the Company’s condensed consolidated statements of operations and comprehensive (loss) income. For the three and six months ended June 30, 2026 and 2025, the Company incurred$0,$0,$1,689, and$5,216, respectively, of expenses related to manufacturing services and$0,$0,$1,261, and$3,509, respectively, of TSA labor and passthrough expenses to support the transition services, including finance and accounting, information technology, human resources, operations, and other services.

For the three and six months ended June 30, 2026 and 2025,$0,$0,$4,585, and$11,987, respectively, was billed to NESA related to transition services performed by the Company, and the Company received$0,$360,$6,464, and$63,173 from NESA during the periods, respectively. The payments received in the first quarter of 2025 included the installment payment of $50,000 received in January 2025 which wasconditioned on the Company’s material compliance with obligations under the TSA. The installment payment was recognized in Gain on sale of VOWST Business within continuing operations in the Company’s condensed consolidated statements of operations and comprehensive income for the six months ended June 30, 2025 as the gain was realizable.

The Company has estimated costs associated with certain accrued liabilities due to SPN - related party as a loss contingency in accordance with ASC 450, Contingencies. These contingent liabilities are presented as Accrued Liabilities due to SPN - related party from continuing operations on the condensed consolidated balance sheet as of June 30, 2026 and December 31, 2025 and consist of the following (in thousands):

The contingent liabilities accrued on the Company's condensed consolidated balance sheet are remeasured at each reporting period based on i) cash payments made by the Company to reduce the accrued liabilities due to SPN - related party and ii) revised estimates of the total remaining liabilities due to SPN - related party. For the three and six months ended June 30, 2026 and 2025, the Company recognized a gain on sale of VOWST Business of $0, $0, $185, and $2,366, respectively, as a result of the change in accrued liabilities due to SPN - related party.

On June 2, 2026, the Company entered into Amendment No. 1 (the “APA Amendment”) to the Purchase Agreement. Pursuant to the Purchase Agreement, SPN agreed to pay the Company certain one-time contingent milestone payments during the Milestone Period (as defined in the Purchase Agreement) if and following the first time that the worldwide annual net sales of the Product (as defined in the Purchase Agreement) reached the following thresholds: (i) a $125,000 milestone payment upon the first calendar year in which annual worldwide net sales of the Product equal or exceed $400,000 (the “Second Sales Milestone Payment”); and (ii) a $150,000 milestone payment upon the first calendar year in which annual worldwide net sales of the Product equal or exceed $750,000 (the “Third Sales Milestone Payment”). Pursuant to the Purchase Agreement, the Prepaid Milestone (as defined in the Purchase Agreement) accrued interest during the Milestone Period, which would reduce the Second Milestone Payment to Seres if and when it became payable (the “Milestone Interest Payments”). Pursuant to the APA Amendment, the parties agreed to terminate SPN’s obligations with respect to the Second Sales Milestone Payment, the Third Sales Milestone Payment and eliminate the Milestone Interest Payments that would have been due from the Company to SPN. In consideration for the foregoing, SPN agreed to a one-time payment to the Company of $25,000 (the “Milestone Termination Payment”), which amount is payable in two equal installments of $12,500, with the first installment paid on July 1, 2026 and the second installment payable on October 1, 2026.

As there are no conditions under which the Company would be required to repay the $25,000, or any portion of the interest that was accruing on the Prepaid Milestone under the Purchase Agreement, and there are no circumstances under which SPN would be relieved of its obligation to make this payment to the Company, the gain is considered realizable in June 2026 when the APA Amendment was signed. The Company recorded a Gain on Sale of VOWST Business within continuing operations of $25,000 during the three months ended June 30, 2026 because the amount is fixed consideration and is no longer contingent on a future event. As of June 30, 2026 and December 31, 2025, the Company had$25,000 and $360 in accounts receivable due from SPN - related party in the Company’s condensed consolidated balance sheets.

4. Property and Equipment, Net

Property and equipment, net consisted of the following (in thousands):

Depreciation and amortization expense was$670,$1,451,$1,059, and$2,135 for the three and six months ended June 30, 2026 and 2025, respectively. During the three and six months ended June 30, 2026, the Company disposed of certain assets with a cost basis of $3,155 and a net book value of $386, primarily related to assets that were returned to the landlord in connection with the Lease Amendment as defined in Note 6, Leases. The Company didnot dispose of any assets during the three andsix months ended June 30, 2025.

5. Accrued Expenses and Other Current Liabilities

Accrued expenses and other current liabilities consisted of the following (in thousands):

6. Leases

The Company leases real estate, primarily laboratory, office and manufacturing space. The Company’s leases have remaining terms ranging from approximately three toten years. Certain leases include one or more options to renew, exercisable at the Company’s sole discretion, with renewal terms that canextend the lease from approximatelyone year to ten years. The Company evaluated the renewal options in its leases to determine if it was reasonably certain that the renewal option would be exercised, given the Company’s current business structure, uncertainty of future growth, and the associated impact to real estate, the Company concluded that it is not reasonably certain that any renewal options would be exercised. Therefore, the operating lease assets and operating lease liabilities only contemplate the initial lease terms. All the Company’s leases qualify as operating leases.

In June 2026, in order to reduce the Company's ongoing annual rent costs and facilities footprint, the Company entered into the First Amendment to Lease (the “Lease Amendment”) with 101 CPD LLC (f/k/a HCP/King 101 CPD LLC), a Delaware limited liability company (the “Landlord”), which amends the Lease Agreement, dated September 22, 2021, by and between the Company and the Landlord (as amended, the “Lease”), pursuant to which the Company leases approximately 82,714 rentable square feet of office and laboratory space in Cambridge, Massachusetts.

Effective as of May 1, 2026, the Lease Amendment reduced the amount of space subject to the lease from 82,714 rentable square feet of space to 36,882 rentable square feet, extended the term of the renewal premises to December 31, 2036, and reducedthe base rent the Company is obligated to pay the Landlord for the renewal premises to $79.70 per rentable square foot per year, subject to an annual adjustment of 3%. Concurrent with the execution of the Lease Amendment, the Company entered into a separate lease for the portion of the space under the Lease that was not retained (the “Early Termination Premises”) with a lease term that ends on December 31, 2027. There are no ongoing legal or economic liabilities of the Company related to this lease of the Early Termination Premises apart from the termination payments described below related to the Lease Amendment. The Company accounted for the Lease Amendment and the lease of the Early Termination Premises as a single contract with two lease components, as the agreements were negotiated simultaneously.

As consideration for the Lease Amendment, the Company agreed to pay the following: (i) a $4,500 termination fee payable on the execution of the Lease Amendment, and (ii) on or before January 4, 2027, a deferred payment of $5,201 which may be satisfied either as an unconditional letter of credit or in cash, of which $1,967 represents the Company’s rent obligations for the period from May 1, 2026 through December 31, 2026 and $3,234 represents an additional termination payment. Further, the Company permitted the Landlord to draw the existing letter of credit held by Landlord under the Lease equal to $6,266. Minimum lease payments total $36,763 throughout the term of the Lease Amendment, for total consideration of $50,763 inclusive of termination fees and the letter of credit draw. The Company identified two lease components, the retained space subject to the Lease Amendment, and the Early Termination Premises. Consideration was allocated to each lease component based on their relative standalone selling prices.

The Company accounted for the Lease Amendment as a modification to the existing lease and not a new contract separate from the existing contract, and accordingly decreased the associated lease liability and right-of-use asset by $11,538.

During the three months ended June 30, 2026, the Company identified an indicator of impairment relating to the Early Termination Premises, as the Company is not planning to use the Early Termination Premises; additionally, the Company is prohibited under the lease from marketing the Early Termination Premises for sublease. The Company determined that this represents a significant adverse change in the extent in which the long-lived asset was being used. The Company concluded that the carrying value of the Early Termination Premises, which represents a single asset group, was not recoverable as there are zero future cash flows that are expected to be generated from the assets within the asset group. The Company recognized an impairment loss of $5,807, consisting of $5,574 on the operating lease right-of-use asset and $233 on the leasehold improvements, in the three andsix months ended June 30, 2026. The impairment loss is disaggregated in the accompanying condensed consolidated statements of operations and comprehensive income (loss) as a separate line, impairment of long-lived assets.

The following table summarizes the presentation in the Company’s condensed consolidated balance sheets of its operating leases (in thousands):

The following table summarizes the effect of lease costs in the Company’s condensed consolidated statements of operations and comprehensive (loss) income (in thousands):

During the three and six months ended June 30, 2026 and 2025, the Company made cash payments for operating leases of$14,166,$19,147,$4,837, and$9,715, respectively.

As of June 30, 2026, future payments of operating lease liabilities are as follows (in thousands):

As of June 30, 2026, the weighted average remaining lease term was 7.10 years and the weighted average incremental borrowing rate used to determine the operating lease liability was 11.4%. As of June 30, 2025, the weighted average remaining lease term was 6.52 years and the weighted average incremental borrowing rate used to determine the operating lease liability was 13%.

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 July 8, 2026, at the Company's reconvened 2026 annual meeting of stockholders (the “2026 Annual Meeting”), stockholders approved an amendment and restatement of the 2025 Plan to increase the number of authorized shares available for issuance under the Plan by 900,000.

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 thethree and six months ended June 30, 2026, the Company sold 232,286 and 258,082 shares of common stock under the Sales Agreement, at an average price of approximately$7.99 and$8.78 per share, respectively, raising aggregate net proceeds of approximately$1,715 and$2,115 after deducting an aggregate commission of approximately 3% and other issuance costs. During thesix 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.

Stock Options

The following table summarizes the Company’s stock option activity since December 31, 2025:

The weighted average grant date fair value of stock options granted during the six months ended June 30, 2026 and the three and six months ended June 30, 2025 was$7.79,$10.18, and$13.49 per share, respectively. The Company didnot grant any stock options during the three months ended June 30, 2026.

During 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 thethree and six months ended June 30, 2026 and 2025, the Company recognized $82, $248,$188 and $261, respectively, 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. RSUs generally vest over four years, with 25% vesting afterone 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.

The following table summarizes the Company’s RSU and PSU activity since December 31, 2025:

During the three and six months ended June 30, 2026 and 2025, the Company granted 0,173,385,0, and 11,250 RSUs, respectively. During the three and six months ended June 30, 2026 and 2025, the Company didnot grant any PSUs.

In February 2026, the Company issued retention awards to non-executive employees of the Company in the form of RSUs covering 173,385 shares of common stock with a grant date fair value of $8.74 per share. The retention RSUs will become fully vested on September 30, 2026 subject to the employee's continued employment with the Company through such date. The compensation expense associated with these awards is being recognized ratably over the vesting period. For thethree and six months ended June 30, 2026, the Company recognized $523 and $741 in compensation expense with respect to the retention RSUs.

Stock-based Compensation Expense

The Company recorded stock-based compensation expense in the following expense categories of its condensed consolidated statements of operations andcomprehensive (loss) income (in thousands):

8. Net Income (Loss) per Share

Basic and diluted net income (loss) per share attributable to common stockholders was calculated as follows (in thousands, except share and per share data):

The Company’s potential dilutive securities include stock options, unvested restricted common stock and shares issuable under the 2015 Employee Stock Purchase Plan. The effect of dilutive securities was calculated using the treasury stock method. The anti-dilutive potential common stock equivalents for the six months ended June 30, 2026 and the three months ended June 30, 2025 were excluded from the computation of diluted net loss per share attributable to common stockholders because those stock options to purchase common stock, restricted stock units, and shares issuable under employee stock purchase plan had an anti-dilutive impact as the Company reported a net loss from continuing operations attributable to common stockholders for those periods. The anti-dilutive potential common stock equivalents for the three months ended June 30, 2026 and the six months ended June 30, 2025 were excluded from the computation of diluted net income per share attributable to common stockholders because those stock options to purchase common stock and restricted stock units had an anti-dilutive impact due to the assumed proceeds per share using the treasury stock method being greater than the average fair value of the Company’s common shares for those periods. For that same period, the warrants to purchase common stock were excluded because the exercise price of the Tranche A Warrants is greater than the average fair value of the Company’s common shares.

9. Commitments and Contingencies

Leases

Refer to Note 6, Leases, for discussion of the commitments associated with the Company’s lease portfolio.

Indemnification Agreements

In the ordinary course of business, the Company may provide indemnification of varying scope and terms to vendors, lessors, business partners and other parties with respect to certain matters including, but not limited to, losses arising out of breach of such agreements or from intellectual property infringement claims made by third parties. In addition, the Company has entered into indemnification agreements with members of its board of directors and its officers that will require the Company, among other things, to indemnify them against certain liabilities that may arise by reason of their status or service as directors or officers. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is, in many cases, unlimited. To date, the Company has not incurred any material costs as a result of such indemnifications. The Company does not believe that the outcome of any claims under indemnification arrangements will have a material effect on its financial position, results of operations or cash flows, and it hasnot accrued any liabilities related to such obligations in its consolidated financial statements as of June 30, 2026 or December 31, 2025.

Legal Contingencies

The Company accrues a liability for legal contingencies when it believes that it is both probable that a liability has been incurred and that the Company can reasonably estimate the amount of the loss. The Company reviews these accruals and adjusts them to reflect ongoing negotiations, settlements, rulings, advice of legal counsel and other relevant information. To the extent new information is obtained and the views on the probable outcomes of claims, suits, assessments, investigations or legal proceedings change, changes in the Company’s accrued liabilities will be recorded in the period in which such determination is made.

In addition, in accordance with the relevant authoritative guidance, for any matters in which the likelihood of material loss is at least reasonably possible, the Company will provide disclosure of the possible loss or range of loss. If a reasonable estimate cannot be made, however, the Company will provide disclosure to that effect. The Company expenses legal costs as they are incurred.

The Company didnot accrue any liabilities related to legal contingencies in its consolidated financial statements as of June 30, 2026 or December 31, 2025.

10. Income taxes

The Company didnot provide for any income taxes in its condensed consolidated state ment of operations and comprehensive (loss) income for the three and six months ended June 30, 2026 and 2025. Management considered the Company’s history of cumulative net losses incurred since inception, its early stage of development of its product candidates, and its projection of book and tax losses for the year ending December 31, 2026. Based on its evaluation of the positive and negative evidence bearing upon its ability to realize its deferred tax assets, the Company determined that it is more likely than not that it will not realize such benefits. Accordingly, the Company has recorded a full valuation allowance against its deferred tax assets as of June 30, 2026 and December 31, 2025, and has not recorded any income taxes for the three and six months ended June 30, 2026 and 2025. Management reevaluates the positive and negative evidence at each reporting period.

11. Related Party Transactions

As described in Note 3, Discontinued Operations and TSA, in September 2024, the Company sold the VOWST Business, including inventory and equipment, certain patents and patent applications, know-how, trade secrets, trademarks, domain names, marketing authorizations and related rights, documents, materials, business records and data and contracts that are used or held for use primarily in the development, commercialization and manufacturing of VOWST, to SPN, and SPN assumed certain liabilities from the Company. As consideration for the Transaction, the Company received an upfront cash payment of $139,788, which consisted of$100,000, less $17,857 owed by the Company to an affiliate of SPN under the prior license agreement between the Company and the SPN affiliate, less approximately $2,355 in satisfaction of fees due under the Bacthera Manufacturing Agreement; plus a prepayment of the $60,000 milestone payment tied to the achievement of worldwide annual net sales of VOWST of $150,000; plus an equity investment of $15,000 based on the Securities Purchase Agreement pursuant to which SPN purchased 714,285 shares of common stock at a purchase price of$21.00 per share.

As of June 30, 2026 and December 31, 2025, there was$3,278 included in Accrued Liabilities due to SPN - related party on the Company’s condensed consolidated balance sheet, which represents amounts due to SPN pursuant to the Purchase Agreement, which are further described in Note 3, Discontinued Operations and TSA. During the three and six months ended June 30, 2026 and 2025, the Company paid $0, $0, $0, and $1,309, to SPN related to the Purchase Agreement during the periods, respectively.

As described in Note 3, Discontinued Operations and TSA, the Company entered into the TSA with NESA, an affiliate of SPN, in connection with the Transaction, through which the Company provided certain manufacturing services until December 31, 2025, and other transition services, for the duration specified in the schedule to the TSA for each service. For the three and six months ended June 30, 2026 and 2025, the Company recognized$0,$0,$3,490, and$9,799, respectively, of TSA reimbursement income in other income in the Company’s condensed consolidated statements of operations and comprehensive (loss) income. For the three and six months ended June 30, 2026 and 2025, the Company incurred$0,$0,$1,689, and$5,216, respectively, of expenses related to manufacturing services and$0,$0,$1,261, and$3,509, respectively, of TSA labor and passthrough expenses to support the transition services, including finance and accounting, information technology, human resources, operations, and other services.

During the three and six months ended June 30, 2026 and 2025,$0,$0,$4,585, and$11,987, respectively, was billed to NESA related to transition services performed by the Company, and the Company received payments of$0,$360,$6,464, and$63,173, respectively, related to transition services performed. The payments received in the first quarter of 2025 included the installment payment of $50,000 received in January 2025 which wasconditioned on the Company’s material compliance with obligations under the TSA. As of June 30, 2026 and December 31, 2025, the Company had$25,000 and $360 in accounts receivable due from SPN - related party, respectively, and$0 and $169 included in prepaid expenses and other current assets, respectively, relating to the sale ofcertain manufacturing and laboratory equipment, in the Company’s condensed consolidated balance sheets.

As described in Note 3, Discontinued Operations and TSA, the Company entered into the APA Amendment with SPN pursuant to which the parties agreed to terminate SPN’s obligations with respect to the Second Sales Milestone Payment, the Third Sales Milestone Payment and eliminate the Milestone Interest Payments that would have been due from the Company to SPN. In consideration for the foregoing, SPN agreed to a one-time payment to the Company of $25,000 (the “Milestone Termination Payment”), which amount is payable in two equal installments of $12,500, with the first installment paid on July 1, 2026 and the second installment payable on October 1, 2026. The Company recorded a Gain on Sale of VOWST Business within continuing operations and the corresponding receivable due from SPN of $25,000 during the three months ended June 30, 2026 because the amount is fixed consideration and is no longer contingent on a future event.

12. Segment Reporting

The Company’s interim Chief Executive Officer, who is the Chief Operating Decision Maker (“CODM”), manages and allocates resources to the operations of the Company on a total company basis by assessing the overall level of resources available and how to best deploy these resources across functions and research and development projects that are in line with the Company’s long-term company-wide strategic goals. The CODM uses the Company’s consolidated net income (loss) to monitor actual results versus the budget in assessing segment performance and the allocation of resources. The measure of segment assets is reported on the consolidated balance sheets as total assets.

The Company's reportable segment net income (loss) for the three andsix months ended June 30, 2026 and 2025, consisted of the following (in thousands):

[1] Other segment (income) expense includes manufacturing services expenses, research and development expenses on early stage programs, interest income and other (income) expense, net.

[2] See Note 3, Discontinued Operations and TSA, for further details.

13. Subsequent Events

On July 31, 2026, the Company entered into the Third Amendment to Lease and Termination Agreement (the “Termination

Agreement”)with BMR-Sidney Research Campus LLC, a Delaware limited liability company (the “Sidney Street Landlord”), the purpose of which is to effect an early termination of one of the Company’s leases, reducing the Company’s ongoing annual facilities costs and materially eliminating the Company’s primary restoration obligations. The Termination Agreement amends the Lease Agreement, dated November 11, 2015, by and between the Company and the Sidney Street Landlord (as amended, the “Lease”), pursuant to which the Company leases approximately 68,636 rentable square feet of office, laboratory, and manufacturing space located at 200 Sidney Street, Cambridge, Massachusetts (the “Existing Premises”).

The Termination Agreement provides for (i) effective as of August 1, 2026, the surrender by the Company to the Landlord of an aggregate area of approximately 21,295 rentable square feet of the Existing Premises (the “Early Termination Premises”), and (ii) the revision of the expiration date of the term of the Lease with respect to the remaining 47,341 rentable square feet of the Existing Premises (the “Renewal Premises”) from January 13, 2031 to December 31, 2026. As consideration for the Termination Agreement, the Company agreed to pay the following: (i) an increase to the letter of credit held by the Sidney Street Landlord in the amount of $2,238 (for a total letter of credit of $3,638), which the Sidney Street Landlord will apply toward rent and operating expenses through the term of the Renewal Premises, (ii) on or before January 4, 2027, a deferred payment of $3,850 representing an additional termination payment, and (iii) an equity issuance of shares of the Company's common stock valued at $500 (the “Share Issuance”).

On July 31, 2026, in connection with the Share Issuance, the Company entered into a Stock Issuance Agreement (the “Stock Issuance Agreement”) with the Sidney Street Landlord, pursuant to which the Company agreed to issue 103,520 shares of Common Stock (the “Shares”) to the Sidney Street Landlord at a price per share of $4.83, which was the closing price of the Common Stock on the Nasdaq Global Select Market (“Nasdaq”) on July 31, 2026.

The Shares are to be issued no later than five business days after the Execution Date. The Shares are registered under the Company’s registration statement on Form S-3 (File No. 333-273794), pursuant to a prospectus supplement, dated July 31, 2026 and the accompanying base prospectus, dated August 15, 2023, and will be freely tradeable when issued. In the event the value of the Shares on the date of issuance (calculated using the closing price on Nasdaq on such date) (the “Issuance Date Value”) is less than $500, the Company is obligated to pay to the Sidney Street Landlord, in cash, the difference between $500, and the Issuance Date Value. The Stock Issuance Agreement contains customary representations and warranties of the Company and the Sidney Street Landlord and customary conditions to the share issuance.