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 vulnerable populations 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 target the prevention and treatment of a broad swath of infections, and to treat inflammatory and immune (“I&I”) diseases by modulating host function to increase epithelium integrity and to induce immune homeostasis and tolerance, as well as to prevent the colonization and overgrowth of pathogens in the gastrointestinal (“GI”) tract.

SER-155, the Company's most advanced LBP candidate, is an investigational, oral, live biotherapeutic designed to decolonize GI pathogens, improve GI epithelial barrier integrity, and induce immune homeostasis 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-HSCT”). In the Company's placebo-controlled Phase 1b study of SER-155 in allo-HSCT, 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 HSCT. SER-155 was generally well tolerated, with no observed treatment-related serious adverse events. Following advancement of key startup activities for the SER-155 Phase 2 study in allo-HSCT, 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.

The clinical data from the SER-155 Phase 1b study in allo-HSCT, along with the Company's extensive preclinical and 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 evaluating SER-155 in immune checkpoint-related enterocolitis (“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 immune checkpoint inhibitor, or ICI, therapy and can be observed in up to 50% of patients, with rates varying based on cancer drug and treatment regimen. The Company expects to report initial clinical results, including preliminary safety, efficacy, pharmacology, and exploratory biomarker data in the coming weeks. The Company is also 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 three months ended March 31, 2026, the Company incurred approximately $914 in restructuring costs, primarily related to severance costs, of which $718 has been paid as of March 31, 2026. The remainder of these costs are expected to be 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 March 31, 2026, the Company had an accumulated deficit of $992,316 and cash and cash equivalents of $29,834.

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 of $19,913 for the three months ended March 31, 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, 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 March 31, 2026 and for the three months ended March 31, 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 months ended March 31, 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.