Quarterly Report for Quarter Ending September 30, 2025 (Form 10-Q)

Management's Discussion and Analysis ofFinancial Condition and Results of Operations.

The following discussion and analysis of our financial condition and results of operations should be read in conjunction with our condensed consolidated financial statements and related notes appearing elsewhere in this Quarterly Report. Some of the information contained in this discussion and analysis or set forth elsewhere in this Quarterly Report, such as statements regarding our plans, objectives, expectations, intentions and projections, includes forward-looking statements that involve risks and uncertainties. As a result of many factors, including those factors set forth in the "Risk Factors"section of this Quarterly Report, our actual results could differ materially from the results described in, or implied by, these forward-looking statements.

Overview

We are a clinical-stage company focused on improving patient outcomes in medically vulnerable populations through novel live biotherapeutics. We led the successful development and approval of VOWST, the first FDA-approved orally administered microbiome therapeutic, which was sold to Société des Produits Nestlé S.A., or SPN, and with certain of its affiliates, collectively, Nestlé Health Science, in September 2024. We are progressing the development of SER-155, an investigational, oral, live biotherapeutic designed to decolonize gastrointestinal, or GI, pathogens, improve GI epithelial barrier integrity, and induce immune homeostasis to prevent bacterial bloodstream infections, or BSIs, including those that can harbor antimicrobial resistance, or AMR, as well as other pathogen-associated negative clinical outcomes in patients undergoing allogeneic hematopoietic stem cell transplantation, or allo-HSCT. We also continue to develop another proprietary live biotherapeutic composition, SER-147, designed to prevent bacterial bloodstream and spontaneous bacterial peritonitis, or SBP, infections in patients with metabolic disease, including chronic liver disease, or CLD. SER-155 and our other pipeline programs are designed to target multiple disease-relevant pathways and are manufactured from standard clonal cell banks via single-strain cultivation, rather than from the donor-sourced production process used for VOWST.

In our placebo-controlled Phase 1b study of SER-155 in allo-HSCT, Cohort 2 results demonstrated that 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. In December 2024, the FDA granted Breakthrough Therapy designation to SER-155 for the reduction of BSIs in patients 18 years and older undergoing allo-HSCT. In January 2025, we reported exploratory translational biomarker data from the SER-155 Phase 1b study which provided evidence supporting the intended therapeutic mechanisms, including promotion of intestinal epithelial barrier integrity to reduce the potential of bacterial translocation into the bloodstream, and reduction of systemic inflammatory responses.

Based on prior FDA feedback, we are progressing start-up activities for our SER-155 Phase 2 study in allo-HSCT that could provide a time and capital-efficient path to obtaining clinical results. We require additional capital to begin this study. In May 2025, we filed the SER-155 Phase 2 protocol with the FDA. In September 2025, the FDA provided us with feedback on the SER-155 Phase 2 protocol and we continue to work with the FDA to finalize the study protocol. The SER-155 Phase 2 study will incorporate a well-powered, placebo-controlled design, which provides for a planned interim analysis to enable an expedited initial data readout. The SER-155 Phase 2 study is expected to enroll approximately 248 participants and incorporate an adaptive design and an interim data analysis when approximately half of the enrolled participants have reached the primary endpoint. We expect to obtain the interim clinical results within twelve months following study initiation, which we believe will facilitate timely engagement with the FDA on the design of a Phase 3 study and inform development in adjacent medically vulnerable patient populations. We believe that positive results, if achieved, from the Phase 2 study could enable advancement into a single Phase 3 trial to support registration.

We continue our efforts to obtain capital and other resources to support further development of SER-155 and our broader portfolio of live biotherapeutic product candidates with applications for inflammatory diseases. We are evaluating a range of potential deal structures that we believe could leverage our live biotherapeutics expertise and success, as demonstrated by bringing VOWST from early development through FDA approval.

Our live biotherapeutic candidates are consortia of bacteria designed to optimize specific, targeted pharmacological properties, and are formulated for oral delivery. We maintain a differentiated live biotherapeutics drug discovery and development platform that includes good manufacturing practices, or GMP, manufacturing capabilities for this novel drug modality. We are designing live biotherapeutic candidates optimized to prevent the colonization and overgrowth of pathogens in the gastrointestinal tract and modulate host function to increase epithelium integrity and to induce immune homeostasis and tolerance. We believe clinical and nonclinical data across our programs support the development of live biotherapeutics to target the prevention and treatment of a broad swath of infections, and in inflammatory and immune diseases. We believe that the scientific and clinical data from the development of VOWST (our then product candidate SER-109 program) and the data from the SER-155 Phase 1b study validate this novel therapeutic approach in the context of infection. We believe this approach may be replicable across different bacterial pathogens to develop live biotherapeutics with the potential to protect a range of medically compromised patients from infections, including pathogens that harbor AMR.

Our business development discussions are focused on supporting SER-155 clinical advancement to reduce the risk of BSIs, including life-threatening and antimicrobial resistant infections, in medically vulnerable patient populations. We believe that SER-155 and other cultivated live biotherapeutic candidates could be developed in additional patient populations beyond allo-HSCT, including autologous-HSCT patients, cancer patients with neutropenia, chimeric antigen receptors therapy recipients, or CAR-T, individuals with chronic liver disease, or CLD, solid organ transplant recipients, as well as patients in the intensive care unit and long-term acute care facilities.

Additional efforts in the early-stage portfolio are focused on inflammatory bowel disease, or IBD, with programmatic objectives supported through a partnership with the Crohn's and Colitis Foundation, or CCF. These efforts aim to (i) confirm the functional phenotype and inflammatory state of patient subpopulations observed in our prior ulcerative colitis, or UC, clinical trials, and (ii) prioritize inflammatory targets and evaluate the potential to utilize biomarker-based patient selection and stratification for future studies. In addition, we continue to leverage microbiome pharmacokinetic and pharmacodynamic data from across our clinical and preclinical portfolios, using our reverse translational development platform to prioritize future drug targets and to identify opportunities for monotherapy treatment and in combination with existing therapies across various indications, including inflammatory and immune diseases, cancer, and metabolic diseases.

We have built and deploy a reverse translational platform and knowledge base, which we call our MbTx Platform, for the discovery and development of live biotherapeutics, and maintain 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 microbiological capabilities and a strain library that spans broad biological and functional breadth. This platform and knowledge base enables 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, we own a valuable intellectual property estate related to the development and manufacture of live biotherapeutics.

Since our inception in October 2010, we have devoted substantially all of our resources to developing our programs, platforms, and technologies, building our intellectual property portfolio, developing our supply chain, business planning, raising capital and providing general and administrative support for these operations.

Our product candidates are in early-stage clinical or preclinical development. Our ability to achieve profitability will depend heavily on the successful development and eventual commercialization of one or more of our product candidates. Since our inception, we have incurred significant operating losses. Our loss from operations was $74.6 million for the nine months ended September 30, 2025. As of September 30, 2025, we had an accumulated deficit of $957.1 million.

While we plan to focus our investment on progressing the development of SER-155 and advancing our other wholly-owned live biotherapeutic candidates in the near-term, our expenses may increase in connection with these future activities. See "Risk Factors-Risks Related to Our Financial Position and Need for Additional Capital-We are a clinical-stage company and have incurred significant losses since our inception. We expect to incur losses for the foreseeable future and may never achieve or maintain profitability."

In addition, if we obtain marketing approval for any of our product candidates, we expect to incur costs related to product manufacturing and commercialization, including marketing, sales and distribution. Furthermore, we expect to continue to incur additional costs associated with operating as a public company.

As a result, we will need additional financing to support our continuing operations. Until such time as we can generate significant revenue from product sales, if ever, we expect to finance our operations through a combination of collaborations with third parties, public or private equity or debt financings or other sources. Adequate additional financing may not be available to us on acceptable terms, or at all. For example, the trading prices for our and other biopharmaceutical companies' stock have been highly volatile as a result of factors such as the impacts of pandemics, such as COVID-19, and increases in inflation rates, interest rates and tariffs. As a result, we may face difficulties raising capital through sales of our common stock and any such sales may be on unfavorable terms. Our inability to raise capital or secure a partnership would have a negative impact on our financial condition and our ability to pursue our business strategy. We will need to generate significant revenue to achieve profitability, and we may never do so.

As of September 30, 2025, we had cash and cash equivalents totaling $47.6 million. Based on our currently available cash resources, including proceeds received in the fourth quarter from our at the market equity offering, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will fund our operations through the second quarter of 2026. In accordance with applicable accounting standards, we evaluated whether there are conditions and events, considered in the aggregate, that raise substantial doubt about our ability to continue as a going concern within 12 months after the date of the issuance of the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q. In performing this analysis, we excluded certain elements of our operating plan that cannot be considered probable of occurring. Under the applicable accounting standards, any future transactions or equity issuances cannot be considered probable, as these events are

outside our control. Accordingly, management has concluded that substantial doubt exists about our ability to continue as a going concern for 12 months from the date the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q, are issued. See "Risk Factors- Risks Related to Our Financial Position and Need for Additional Capital -We have identified conditions and events that raise substantial doubt regarding our ability to continue as a going concern."

On July 17, 2025, Eric D. Shaff, President, Chief Executive Officer and Director of the Company, resigned from his positions as President and Chief Executive Officer of the Company, effective July 31, 2025 (the "Effective Date"). Mr. Shaff continues in his role as a Class I member of the Company's board of directors (the "Board"). As of the Effective Date, each of the Company's Executive Vice President and Chief Financial Officer, Marella Thorell, and the Company's Executive Vice President and Chief Legal Officer, Thomas J. DesRosier, were appointed as the Co-Presidents and Co-Chief Executive Officers of the Company.

On September 23, 2025, we announced that we implemented cost reduction actions, including reducing our workforce by approximately 25% (including reductions that were effective in August 2025). During the three and nine months ended September 30, 2025, we incurred approximately $1.0 million in restructuring costs, primarily related to severance costs. These costs are expected to be paid out in the fourth quarter of 2025.

Sale of our VOWST Business to SPN

VOWST (previously referred to as SER-109) was approved by the FDA on April 26, 2023, to prevent recurrence of CDI in individuals 18 years of age or older following antibacterial treatment for recurrent CDI. We launched VOWST in the United States with our then collaborator, Nestlé Health Science, in June 2023. On August 5, 2024, we entered into an Asset Purchase Agreement, or Purchase Agreement, with Société des Produits Nestlé S.A., or SPN, a wholly-owned subsidiary of Nestlé S.A., pursuant to which, after approval by our stockholders at a special meeting of stockholders held on September 26, 2024, we sold our VOWST microbiome therapeutic business, or the VOWST Business, to SPN and its designated affiliates on September 30, 2024, or the Transaction. Following the completion of the Transaction, or the Closing, our headcount decreased by approximately 100 employees, principally due to the transition of manufacturing and quality team members from Seres to Nestlé Health Science, positioning us to efficiently progress SER-155 and our other wholly-owned cultivated live biotherapeutic candidates.

Under the terms of the Purchase Agreement, we 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 the microbiome product sold under the brand name VOWST, or the Product, to SPN, and SPN assumed certain liabilities from us. As consideration for the Transaction, SPN paid or agreed to pay us, as applicable, the following Transaction Consideration:

See Risk Factors- Risks Related to Our Financial Position and Need for Additional Capital- The total amount of the Milestone Payments we may receive from the Transaction, and the amounts payable or due under the Profit Sharing Payments, are subject to various risks and uncertainties.

As they are earned, the Milestone Payments will be satisfied as follows: (1) first, by set-off against all accrued interest on the Prepaid Milestone until the amount of such accrued interest has been paid in full, (2) second, by set-off against the outstanding balance of the Prepaid Milestone until the Prepaid Milestone has been repaid in full and (3) thereafter, in cash. If any amount of the

Prepaid Milestone (and any accrued interest thereon) remains outstanding as of following the last day of the Milestone Period (defined below), the balance thereof (together with any interest accrued thereon) will be forgiven and the right of set-off of SPN with respect thereto will be deemed forfeited. The installment payment received on July 1, 2025 was offset by $1.4 million we paid to Nestlé on the same date related to certain employment obligations assumed by SPN with respect to the period ending as of the Closing Date.

We and SPN share 50/50 in the net profit or net loss achieved during the period from the Closing Date until December 31, 2025, or the Profit Sharing Period, with the net profit or net loss calculated as (i) the net sales of VOWST in the United States and Canada, plus (ii) other income received in connection with the grant of a license or sublicense with respect to VOWST in the United States and Canada as described in the Purchase Agreement, minus (iii) allowable expenses directly attributable or reasonably allocable to certain development activities, commercialization activities, medical affairs activities, manufacturing activities or other relevant activities, as described in the Purchase Agreement. During the Profit Sharing Period, we will reimburse SPN for (i) certain payments under the exclusive license agreement between us and Memorial Sloan Kettering Cancer Center, (ii) certain costs incurred in connection with an ongoing post-marketing safety study of VOWST and (iii) 80.1% of all rent and other costs due to the landlord under the lease for our Waltham facility.

We estimated the costs associated with these future payments and recorded them within accrued liabilities due to SPN - related party on our condensed consolidated balance sheets as of the Closing. The contingent liabilities 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. As of September 30, 2025, the contingent liabilities included $1.7 million associated with the Profit Sharing Payments, $2.2 million associated with the MSK Agreement, $0.4 million associated with our obligation to pay 80.1% of the costs associated with the lease of the Waltham facility through December 31, 2025, and $0.2 million associated with the ongoing post-marketing safety study of VOWST. We recorded a gain of $2.2 million for the three months ended September 30, 2025 primarily as a result of SPN's actual and forecasted Profit Sharing Payments as compared to the previous estimate.
At Closing, in exchange for a payment to be made by SPN to Bacthera AG, the Long Term Manufacturing Agreement, dated November 8, 2021, between the Company and Bacthera AG, or the Bacthera Manufacturing Agreement, was terminated and each of Bacthera and Seres released one another from any and losses, liabilities or other obligations arising thereunder with respect to the period ending as of the Closing Date, including without limitation any milestone payments required to be paid to Bacthera thereunder.

In connection with the Closing, we and SPN entered into a securities purchase agreement, or the Securities Purchase Agreement, pursuant to which SPN purchased 714,285 shares of our common stock, or the Shares, at Closing, at a purchase price per share of $21.00, for an aggregate purchase price of $15 million. Under the terms of the Securities Purchase Agreement, SPN agreed not to sell or transfer the Shares for a period of six months after Closing, subject to certain customary exceptions. We agreed to register the resale of the Shares by SPN within 90 days of Closing. On October 1, 2024, we 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 our outstanding shares of common stock, we agreed to take such action within our control to include one individual designated by SPN in the slate of nominees recommended by our Board (or the applicable committee of the board of directors) to our stockholders for election to the Board at the applicable stockholder meeting. SPN designated Hans-Juergen Woerle, M.D., Ph.D., and on February 4, 2025, our Board appointed Dr. Woerle to the Board as a Class III director, with a term expiring at our 2027 annual meeting of stockholders. The Securities Purchase Agreement contains customary representations and warranties and closing conditions.

In connection with the Closing, we entered into a Transition Services Agreement, or the TSA, with NESA, which provides for services to be performed by us in order to facilitate a transition of the business associated with the VOWST Business to NESA and its affiliates. The scope of the transition services includes the provision of certain manufacturing services and certain administrative functions related to the VOWST Business and operations, including the maintenance of certain manufacturing services and the related facility in which such services are currently conducted. NESA has agreed to pay us for certain fixed costs, including a monthly fixed fee and a variable per batch fee for preserved raw material suspension manufacturing, or PRMS, and will reimburse us for certain costs of the transition services performed by us under the TSA, including labor. We will provide the manufacturing services until December 31, 2025 and other services for the duration specified in the schedule to the TSA for each service. Following the completion of PRMS manufacturing in the second quarter of 2025, manufacturing services primarily consist of costs incurred to ensure compliance of the facility and management of in-process inventories and samples. The know-how and other intellectual property generated in connection with the performance of the TSA will be owned by NESA with us having a non-exclusive license to such know-how and other intellectual property under the Cross-License Agreement. During the term of the TSA, upon NESA's request, we will transfer the specifications for materials and documentation necessary to enable PRMS manufacturing services to a third party service provider designated by NESA. In the event of a material failure by us to deliver PRMS under the TSA, NESA will have step-in rights to negotiate to enter into a direct lease with the landlord of the manufacturing facility with respect to the portion of such facility used in connection with the VOWST Business or to cause such services to be performed, with any reasonable out-of-pocket costs and expenses incurred in connection therewith reimbursed by us.

In connection with the Closing, we entered into a cross-license agreement with SPN under which, we granted to SPN a perpetual, worldwide, non-exclusive, fully paid-up license under certain Seres patents that have been issued or will issue in the future and current know-how controlled by us that is not transferred to SPN pursuant to the Purchase Agreement. In the field of the treatment of Clostridioides difficileinfections, or CDI, and rCDI and associated complications, or collectively, the CDI Field, the license to SPN under such Seres patents and know-how is exclusive to SPN for five years after the Closing and co-exclusive between SPN and Seres following that five year period. The license from Seres to SPN is to issued Seres patents that currently or in the future cover the Product or improvements thereof and know-how that is used or reasonably useful in connection with the exploitation of the VOWST Business. See "Intellectual Property" below.

In connection with the Closing, the parties entered into assignment and assumption of lease agreements, or the Assignment and Assumption Agreements. Under the Assignment and Assumption Agreements, we assigned to SPN or its designated affiliates, our rights in, to and under certain real property leases, and SPN or its designated affiliates assumed the liabilities related thereto.

In connection with the Closing, the parties entered into an employee support agreement, or the Employee Support Agreement. Under the Employee Support Agreement, among other things and subject to the terms and conditions therein, certain of our employees related to the VOWST Business who accepted employment with SPN or one of its designated affiliates provided the services they provided to us prior to the Transaction to SPN, as well as other services as SPN may reasonably request, from Closing until the day prior to the beginning of SPN's or its designated affiliate's next pay period following the Closing. SPN will reimburse our out of pocket costs in connection with such employees' services, including certain compensation and benefits paid or provided to such employees pursuant to the terms of the Employee Support Agreement. All such employees have transferred to SPN as of December 31, 2024.

Infection Risk Reduction

We believe that the scientific and clinical data from our SER-109 program validate our novel approach of using live biotherapeutics to decolonize GI pathogens and improve GI epithelial barrier integrity, resulting in reduced rate of infections in medically compromised patients. Data from the SER-109 ECOSPOR III and ECOSPOR IV Phase 3 trial published in the New England Journal of Medicine(Feuerstadt et al., 2022) and Journal of the American Medical Association(Sims et al., 2023) suggest that live biotherapeutics have the potential to restructure the gut microbiome and shift the gut metabolic landscape. Additional data show that SER-109 rapidly reduced the abundance of bacteria associated with common antibiotic resistance genes, or ARGs, and reduced ARG abundance in the gut (Straub et al., 2023). Collectively, we believe these data suggest the potential for live biotherapeutics to prevent the colonization and overgrowth of pathogens that can establish in the gut and ultimately to reduce infections. We believe that reducing pathogen colonization in the GI tract and improving GI epithelial barrier integrity to reduce the risk of infection may be replicable in a range of medically compromised patients, protecting them from infections and resulting downstream clinical sequelae. We believe this approach may also enable us to reduce AMR, which the World Health Organization declared as a top ten global public health threat facing humanity, and with estimates that yearly deaths may reach 10 million by 2050, putting mortality due to AMR on par with deaths due to cancer.

SER-155

We are developing SER-155, an investigational, oral, live biotherapeutic designed to decolonize GI pathogens, improve GI epithelial barrier integrity, and induce immune homeostasis to prevent bacterial BSIs, including those that can harbor AMR, as well as other pathogen associated negative clinical outcomes in patients undergoing allo-HSCT. SER-155 contains 16 bacterial strains selected using our reverse translation discovery and development platform technologies to optimize SER-155's functional profile. The design incorporates biomarker data from human clinical data and screening data from nonclinical human cell-based assays and in vivo disease models. The bacteria consortia is designed to optimize: (i) the prevention of the growth of various Enterococcaceaeand Enterobacteriaceaespecies known to potentially dominate the GI tract and lead to downstream negative clinical outcomes in medically compromised patients and that can harbor antibacterial resistance, (ii) the production of multiple bacterial metabolites that can promote mucosal and epithelial barrier integrity with the goal of reducing the likelihood of harmful bacteria translocating from the gut to the bloodstream through a compromised epithelium, and (iii) the production of multiple bacterial metabolites that can modulate immune pathways to induce immune tolerance with a potential impact on graft versus host disease, or GvHD.

The rationale for this program is based in part on published clinical evidence from our collaborators at Memorial Sloan Kettering Cancer Center showing that allo-HSCT patients with decreased diversity of commensal microbes and pathogen domination in the gastrointestinal tract were significantly more likely to die due to infection and/or lethal GvHD (Peled et al., 2020). There are an estimated 40,000 allo-HSCT procedures annually worldwide, and infection is one of the most common causes of mortality in these patients. The Center for International Blood & Marrow Transplant Research, or CIBMTR, reports that 19-28% of deaths in allo-HSCT patients over 18 years of age within 100 days post-transplant are caused by infections and 5-14% by GvHD. In December 2023, we received Fast Track Designation for SER-155 to reduce the risk of infection and GvHD in allo-HSCT patients. In December 2024, the FDA granted Breakthrough Therapy designation to SER-155 for the reduction of BSIs in patients 18 years and older undergoing allo-HSCT.

SER-155 Phase 1b Study

SER-155 has been evaluated in a Phase 1b study in patients undergoing allo-HSCT. The SER-155 Phase 1b study included two cohorts. Cohort 1 was designed to assess safety and drug pharmacology, specifically the drug strain engraftment in the gastrointestinal tract. Cohort 1 included 13 subjects who received any dosing of the SER-155 regimen, with 11 subjects subsequently receiving an allo-HSCT. Results from this cohort, announced in May 2023, showed SER-155 was generally well tolerated and resulted in successful drug strain engraftment and a reduction in pathogen domination in the GI microbiome relative to a historical control cohort.

Study Cohort 2 utilized a randomized, double-blinded 1:1 placebo-controlled design to further evaluate safety and drug strain engraftment, as well as key secondary and exploratory endpoints such as the incidence of bacterial bloodstream infections and related medical consequences such as febrile neutropenia and antibiotic use. Cohort 2 included 45 patients in the intention-to-treat (ITT) population. Of the ITT population, 20 received SER-155 and 14 received placebo, each of whom subsequently received an allo-HSCT, with data available for clinical evaluation through day 100, the study's prespecified primary observation point. Exploratory hypothesis testing was conducted at the two-sided α=0.05 level. Ninety-five percent (95%) 2-sided confidence intervals (CIs) were determined, where specified. No adjustment for multiplicity was done. A subset of patient samples was available for drug pharmacology analysis.

The median age in Cohort 2 was 63, and most subjects had acute myeloid leukemia, acute lymphocytic leukemia, myelodysplastic syndrome or myeloproliferative neoplasia as their primary disease and received reduced-intensity conditioning pre-transplant. Most patients received peripheral blood stem cells from a matched unrelated donor. A majority received post-transplant cyclophosphamide as part of their graft-versus-host disease (GvHD) prophylaxis.

Results from Cohort 2, announced in September 2024, were consistent with the observations from Cohort 1. SER-155 was generally well tolerated, and no treatment-emergent serious adverse events related to drug were observed. SER-155 bacterial strains engrafted into the gastrointestinal tract of patients following the administration of SER-155.

The incidence of BSIs was significantly lower in the SER-155 arm compared with the placebo arm (2/20 (10%) vs. 6/14 (42.9%), respectively; [Odds Ratio: 0.15; 95% CI: 0.01, 1.13, p=0.0423]), which represents a relative risk reduction of approximately 77% and an absolute risk reduction of approximately 33%, resulting in a number needed to treat (NNT) of 3 for SER-155 to prevent a BSI event. In addition, while antibiotic starts were similar in each arm, patients administered SER-155 were treated with antibiotics for a significantly shorter duration compared to patients in the placebo arm (9.2 days vs. 21.1 days, respectively, with a mean difference of -11.9 days [95% CI: -23.85, -0.04; p=0.0494]). The incidence of febrile neutropenia was lower in patients administered SER-155 compared to placebo (65% vs. 78.6%, respectively; [Odds Ratio: 0.51; 95% CI: 0.07, 2.99; p=0.4674]). Six cases of gastrointestinal infections (C. difficile infections) were observed in the study, with four cases (20%) in the SER-155 arm and two cases (14.3%) in the placebo arm.

Recent changes in the allo-HSCT standard of care and the increasing use of post-transplant cyclophosphamide as part of prophylactic therapy for GvHD have reduced rates of GvHD overall in this patient population. The rates of GvHD in the study were low, with two cases of grade 2 GvHD observed in each arm, and no cases of grade 3 or 4 GvHD were observed.

In Cohort 2, the ability to detect pathogen domination (i.e., relative abundance in the GI ≥30%) in the placebo arm, and differences between the study arms, was constrained due to the limited number of placebo stool samples (placebo patients submitted fewer stool samples) and an imbalance in the number of available stool samples between the arms. Observed pathogen domination events were low in the placebo and SER-155 arms with no significant differences identified. In a comparison of the prevalence of pathogen domination versus a larger allo-HSCT historical control cohort, pathogen domination in SER-155 subjects was substantially lower, providing further evidence of SER-155 activity.

We believe the available study data from Cohort 1 suggest that SER-155 administration results in significantly lower incidence rates of gastrointestinal dominations with pathogens of clinical concern, such as Enterococcaceae, Enterobacteriaceae, Streptococcaceae, and Staphylococcaceae. We further believe the resulting Cohort 2 data, together with the Cohort 1 SER-155 Phase 1b study results provide encouraging evidence to support further development of SER-155 to potentially reduce GI associated bloodstream and AMR infections as well as increase immune tolerance in individuals undergoing allo-HSCT for cancers and other serious conditions.

Proposed SER-155 Phase 2 Study

Based on prior FDA feedback, we are progressing start-up activities for our SER-155 Phase 2 study in allo-HSCT that could provide a time and capital-efficient path to obtaining clinical results. We require additional capital to begin this study. In May 2025, we filed the SER-155 Phase 2 protocol with the FDA. In September 2025, the FDA provided us with feedback on the SER-155 Phase 2 protocol and we continue to work with the FDA to finalize the study protocol. The SER-155 Phase 2 study will incorporate a well-powered, placebo-controlled design, which provides for a planned interim analysis to enable an expedited initial data readout. The SER-155 Phase 2 study is expected to enroll approximately 248 participants and incorporate an adaptive design and an interim data analysis when approximately half of the enrolled participants have reached the primary endpoint. We expect to obtain the interim clinical results within twelve months following study initiation, which we believe will facilitate timely engagement with the FDA on

the design of a Phase 3 study and inform development in adjacent medically vulnerable patient populations. We believe that positive results, if achieved, from the Phase 2 study could enable advancement into a single Phase 3 trial to support registration.

We continue our efforts to obtain capital and other resources to support further development of SER-155 and our broader portfolio of live biotherapeutic product candidates with applications for inflammatory diseases. We are evaluating a range of potential deal structures that we believe could leverage our live biotherapeutics expertise and success, as demonstrated by bringing VOWST from early development through FDA approval.

Other recent updates

In addition to SER-155 development in allo-HSCT, we are expanding our understanding of the broader SER-155 therapeutic opportunity through an ongoing investigator-sponsored trial (IST) with Memorial Sloan Kettering Cancer Center to evaluate SER-155 in patients with immune checkpoint related enterocolitis (irEC). IrEC is among the most frequent and severe immune-related adverse events (irAEs) in recipients of immune checkpoint-inhibitor therapy and can be observed in up to 50% of patients with rates varying based on cancer drug and treatment regimen. Immune checkpoint inhibitors can cause a wide range of irAEs with links to T cell biology and epithelial barrier inflammation, both of which are biological functions shown in our preclinical and clinical pharmacology data to be positively impacted by SER-155. We believe that supportive data from this study could provide further support for the expansion of indications that may be well suited for our biotherapeutic approach. Enrollment in the study is ongoing and is expected to complete by the end of 2025 with a clinical readout expected in early 2026.

In July 2025, we were awarded a grant from CARB-X to support the development of an oral liquid formulation of SER-155 for medically vulnerable patient populations at risk of BSIs, including antimicrobial resistant infections, who cannot be dosed with oral capsules, such as intubated patients in the ICU. The CARB-X grant provides us with up to $3.6 million of funding for research, manufacture, and design of a Phase 1 clinical trial in ICU patients. The Company recognized $0.4 million of grant revenue from CARB-X in the three months ended September 30, 2025.

In October 2025, we presented new post hoc data from our SER-155 Phase 1b trial in an oral presentation at IDWeek in Atlanta, Georgia. The presentation included new post-hoc analysis from the completed SER-155 Phase 1b study describing differences between the SER-155 and placebo groups, including the bacterial and fungal organisms causing BSIs, BSI event clinical outcomes, antibacterial prophylaxis use, and patterns of AMR among the bacterial BSI organisms. These new data illustrated that BSIs occurred despite antibacterial prophylaxis, and that BSI bacteria exhibited AMR. Resistance to multiple antibacterial agents was observed only in the BSI bacteria from placebo-treated participants, two of whom had fatal outcomes related to their BSIs. These new data further support the potential of SER-155 as an innovative alternative approach to the significant unmet medical need for prevention of BSIs in HSCT patients, especially those BSIs associated with AMR that increases the risk of morbidity and mortality.

Exploratory biomarker data

In January 2025, we reported exploratory translational biomarker data from the SER-155 Phase 1b study which provided evidence supporting the intended therapeutic mechanisms, including promotion of intestinal epithelial barrier integrity to reduce the potential of bacterial translocation into the bloodstream, and reduction of systemic inflammatory responses. Results from this exploratory biomarker analysis showed that SER-155 was associated with lower levels of fecal albumin and lower concentrations of various plasma biomarkers associated with systemic inflammation (i.e., IFN-y, TNF-α, IL-17, and IL-8) in the HSCT peri-transplant period, the period from the end of the first SER-155 treatment course through to neutrophil engraftment. The results support SER-155's intended mechanisms of action and reinforce the previously reported promising clinical study efficacy and safety data. These systemic inflammatory response observations further support the potential to develop our live biotherapeutics to address inflammatory and immune diseases, including ulcerative colitis and Crohn's disease.

In February 2025, clinical and biomarker results from our biotherapeutic programs were presented as a poster at the 2025 Tandem Transplantation & Cellular Therapy Meetings of the American Society for Transplantation and Cellular Therapy (ASTCT) and Center for International Blood and Marrow Transplant Research (CIBMTR). SER-155 Phase 1b clinical study data were also featured in an oral presentation in the Best Abstracts in Infectious Diseases track at the Tandem meeting.

In April 2025, we presented SER-155 Phase 1b clinical and exploratory biomarker results at the 51st annual meeting of the European Society for Blood and Marrow Transplantation, or EBMT. Our presented poster was recognized by the EBMT scientific organizing committee and obtained the "Best Clinical Poster Award."

In May 2025, we presented data at the Digestive Disease Week, or DDW conference highlighting preclinical and clinical data that enable identification of patients with a disease etiology linked to the gastrointestinal microbiome, and the identification of microbiome-based biomarkers that are predictive of response and suitable for patient selection and stratification in clinical trials. Our poster, entitled "Candidate Biomarkers of Microbiome Disruption for Patient Selection or Stratification in Clinical Trials of Microbiome Therapies in Ulcerative Colitis" received a Poster of Distinction award in the Microbiome and Microbial Therapies subgroup. We believe that the data generated suggest that live biotherapeutics could provide a novel treatment modality that could benefit patients living with gut-related inflammatory and immune diseases that are not effectively addressed today. Furthermore,

research indicates that specific patient subpopulations optimally suited for biotherapeutic-based treatments may be identifiable. We are exploring options, including potential partnerships, to advance the development of our biotherapeutics in inflammatory and immune diseases, including ulcerative colitis and Crohn's disease.

In May 2025, we presented new exploratory biomarker data from the SER-155 Phase 1b study in a poster session at the 2025 American Society of Clinical Oncology, or ASCO, Annual Meeting. The biomarker data presented at ASCO demonstrate the potential of SER-155 to promote immune reconstitution following allo-HSCT by modulating homeostatic cytokines and peripheral T-cell expansion. In post hoc analyses from the SER-155 Phase 1b study, significantly higher levels of the homeostatic cytokine IL-7 were observed both after the second course of SER-155 (administered after neutrophil recovery) and at HSCT Day 100, as compared to placebo. Additionally, a higher frequency of CD4+ T cells was observed in peripheral blood at these same timepoints in the SER-155 arm. We believe the results support the ability of SER-155 to promote peripheral T-cell recovery and immune reconstitution to support favorable outcomes post allo-HSCT.

We believe that exploratory biomarker data presented at recent medical meetings have supported the intended mechanisms of SER-155 and demonstrated the broader potential of live biotherapeutics in inflammatory and immune mediated diseases.

SER-147 and other pipeline programs

We continue to develop another proprietary live biotherapeutic composition, SER-147, designed to prevent bacterial bloodstream and spontaneous bacterial peritonitis, or SBP, infections in patients with metabolic disease, including chronic liver disease, or CLD. SER-147 was designed and optimized using our reverse translational therapeutics development platform. CLD is a progressive condition marked by deterioration of liver function and is reaching epidemic proportions affecting nearly 1.7 billion people worldwide, causing substantial health burden on afflicted countries (GBD 2017 Cirrhosis Collaborators, 2020, Clinical Liver Disease, 2021). In the advanced stages of CLD, known as decompensated cirrhosis, patients exhibit significant immune dysfunction, microbiome disruption, and increased contact with the healthcare system, all of which drive increased susceptibility to bacterial infections (Bajaj et al., 2021, Albillos et al., 2022). The Company is conducting IND-enabling activities for SER-147.

Nasdaq Notice and Compliance

On November 7, 2024, we received a letter from the Listing Qualifications Department of The Nasdaq Stock Market LLC, or Nasdaq, notifying us that, for the last 30 consecutive business days, the bid price for our common stock had closed below the $1.00 per share minimum bid price requirement for continued inclusion on The Nasdaq Global Select Market pursuant to Nasdaq Listing Rule 5450(a)(1), or the Bid Price Requirement.

On April 10, 2025, at our 2025 annual meeting of stockholders, our stockholders approved an amendment to our certificate of incorporation to effect a reverse stock split of all outstanding shares of our common stock. On April 21, 2025, we effected a 1-for-20 reverse stock split of our common stock. The reverse stock split had no impact on the number of authorized shares or the par value of preferred and common stock. Trading of our common stock on The Nasdaq Global Select Market commenced on a split-adjusted basis on April 22, 2025. On May 6, 2025, we were notified by the Nasdaq Listing Qualifications staff that the closing bid price of our common stock had been at $1.00 per share or greater for 10 consecutive business days, from April 22, 2025 to May 5, 2025. Accordingly, we have regained compliance with the Bid Price Requirement and this matter is now closed.

All shares of our common stock, stock-based instruments, and per-share data included in this Quarterly Report on Form 10-Q have been retroactively adjusted as though the reverse stock split had been effected prior to all periods presented.

Intellectual Property

Patent Portfolio

We have an extensive patent portfolio directed to rationally designed ecologies of spores and microbes. The portfolio includes both company-owned patents and applications, and those that we have rights to as licensee. The patents and applications included in our portfolio cover both composition of matter and methods (e.g., method of treating). Our intellectual property rights related to SER-155 and SER-147 extend through at least 2043 (not including any potential term extension). We plan on continuing to broaden our patent portfolio. Currently, we have 24 active patent families, which includes 20 nationalized applications and four at the provisional stage. To date, we have obtained issuance of 33 U.S. patents (which includes three as licensee). Of the issued U.S. patents, 13 U.S. patents (including one as licensee) have been assigned to Nestlé Health Science as part of its purchase of VOWST.

In connection with the Transaction and pursuant to the Purchase Agreement, we transferred certain patents and trademarks affiliated with the VOWST Business to SPN at Closing. In addition, in connection with Closing, we entered into a cross-license agreement, or the Cross-License Agreement, with SPN. Under the Cross-License Agreement, we granted to SPN a perpetual, worldwide, non-exclusive, fully paid-up license under certain Seres patents that have been issued or will issue in the future and current know-how controlled by us that was not transferred to SPN pursuant to the Purchase Agreement. In the field of the treatment of CDI and recurrent CDI and associated complications, or collectively, the CDI Field, the license to SPN under such Seres patents and know-how is exclusive to SPN for five years after the Closing and co-exclusive between SPN and Seres following that five year period. The

license from Seres to SPN is to issued Company patents that currently or in the future cover the Product or improvements thereof and know-how that is used or reasonably useful in connection with the exploitation of the VOWST Business. We also granted SPN an exclusive, perpetual, worldwide, fully paid-up license under issued Seres patents that currently or in the future cover the Product and improvements thereof and know-how that is used or reasonably useful in connection with the exploitation of the Product to exploit SER-262 in the CDI Field. SPN granted to us a perpetual, worldwide, non-exclusive license under the patents and know-how that are transferred to SPN pursuant to the Purchase Agreement or developed under the TSA, for Seres' products for use outside of the CDI Field, and after five years from Closing for Seres products containing designed, cultivated, bacterial consortia not manufactured using human stool (excluding SER-262) in the CDI Field. From and after Closing, certain license agreements between us, SPN, and/or their respective affiliates terminated and are of no further force or effect, except as contemplated by the Purchase Agreement.

Regulatory Exclusivity

If we obtain marketing approval for any of our product candidates, we expect to receive reference product exclusivity against biosimilar products.

Financial Operations Overview

Revenue

To date we have not generated any revenues from the sale of products. Our revenues have been derived primarily from our agreements with our collaborators. See "-Liquidity and Capital Resources."

Operating Expenses

Our operating expenses since inception have consisted primarily of research and development activities and general and administrative costs. In connection with the TSA the Company entered into with NESA following the sale of the VOWST Business during the third quarter of 2024, our operating expenses also consisted of certain passthrough costs incurred in performing duties under the TSA and manufacturing services related to the VOWST Business and operations.

Research and Development Expenses

Research and development expenses consist primarily of costs incurred for our research activities, including our discovery efforts, and the development of our product candidates and other obligations, which include:

We expense research and development costs as incurred. We recognize external development costs based on an evaluation of the progress to completion of specific tasks using information provided to us by our vendors and our clinical investigative sites. Payments for these activities are based on the terms of the individual agreements, which may differ from the pattern of costs incurred, and are reflected in our unaudited condensed consolidated financial statements as prepaid or accrued research and development expenses.

Our primary focus of research and development since inception has been on our reverse translational platform and the subsequent development of our product candidates. Our direct research and development expenses are tracked on a program-by-program basis and consist primarily of external costs, such as fees paid to investigators, consultants, CROs in connection with our preclinical studies and clinical trials, lab supplies and consumables, and regulatory fees. We do not allocate employee-related costs and other indirect costs to specific research and development programs because these costs are deployed across multiple product programs under development.

Research and development activities are central to our business model. Product candidates in later stages of clinical development generally have higher development costs than those in earlier stages of clinical development, primarily due to the increased size and duration of later-stage clinical trials. We anticipate an overall decrease in research and development expenses in 2025 as compared to 2024, following the sale of the VOWST Business and completion of the Phase 1b study of SER-155 in allo-HSCT. Research and development expenses may increase in the future if and as we continue the clinical development of SER-155 in patients undergoing allo-HSCT and for other medically vulnerable populations and resume development of any other clinical or preclinical programs. In 2025, research and development expenses continue to include labor and passthrough costs, reimbursable by Nestlé, incurred in performing obligations under the TSA.

General and Administrative Expenses

General and administrative expenses consist primarily of salaries and other related costs, including stock-based compensation, for personnel in our executive, finance, commercial, business development and administrative functions. General and administrative expenses also include legal fees relating to patent and corporate matters; professional fees for accounting, auditing, tax and consulting services; insurance costs; travel expenses; and facility-related expenses, which include direct depreciation costs and allocated expenses for rent and maintenance of facilities and other operating costs. Beginning in the fourth quarter of 2024, general and administrative expenses also include labor and passthrough costs, reimbursable by Nestlé, incurred in performing duties under the TSA.

We expect that our general and administrative expenses will decrease in 2025 as compared to 2024, following the sale of VOWST Business, reduction of our workforce and overall cost containment efforts. General and administrative expenses may increase in the future as we continue to incur increased expenses associated with being a public company, including increased costs of accounting, audit, legal, regulatory and tax-related services associated with maintaining compliance with exchange listing rules and the requirements of the SEC, director and officer insurance costs and investor and public relations costs. In 2025, general and administrative expenses continue to include labor and passthrough costs, reimbursable by Nestlé, incurred in performing obligations under the TSA.

Manufacturing Services

Under the TSA with NESA, beginning in the fourth quarter of 2024, we provide certain manufacturing services and related functions of the VOWST Business and operations. Expenses associated with the manufacturing services include certain facility-related, labor, lab supplies and consumables, and other manufacturing costs that would have been capitalized into inventory prior to the sale of VOWST Business.

We will provide the manufacturing services until December 31, 2025. We expect manufacturing services expenses to increase in 2025 as compared to 2024, given the TSA obligations exist for the full year in 2025 as compared to one quarter in 2024.

Other Income, Net

Interest Income

Interest income consists of interest earned on our cash, cash equivalents and investments.

Other Income, Net

Other income, net primarily consists of:

Discontinued Operations

We completed the sale of the VOWST Business to SPN on September 30, 2024. The financial results of the VOWST Business have been classified as discontinued operations in the condensed consolidated statements of operations and the related assets and liabilities of the VOWST Business have been classified as assets and liabilities of discontinued operations in the condensed consolidated balance sheets. Unless otherwise noted, amounts and disclosures in this section relate to our continuing operations (except for the Liquidity and Capital Resources section).

Income Taxes

Since our inception in 2010, we have not recorded any U.S. federal or state income tax benefits for the net losses we have incurred in each year or our earned research and development tax credits, due to our uncertainty of realizing a benefit from those items. We did not provide for any income taxes in the three and nine months ended September 30, 2025 or 2024.

Critical Accounting Policies and Significant Judgments and Estimates

Our condensed consolidated financial statements are prepared in accordance with accounting principles generally accepted in the United States. The preparation of these condensed consolidated financial statements requires the application of appropriate technical accounting rules and guidance, as well as the use of estimates. The application of these policies necessarily involves judgments regarding future events. These estimates and judgments, in and of themselves, could materially impact the condensed consolidated financial statements and disclosures based on varying assumptions. The accounting policies discussed in our Annual Report on Form 10-K for the fiscal year ended December 31, 2024, filed with the SEC on March 13, 2025, or the Annual Report, are considered by management to be the most important to an understanding of the consolidated financial statements because of their significance to the portrayal of our financial condition and results of operations. There have been no material changes to that information disclosed in our Annual Report during the three and nine months ended September 30, 2025.

Results of Operations

Comparison of Three Months Ended September 30, 2025 and 2024

The following table summarizes our results of operations for the three months ended September 30, 2025 and 2024:

Revenue

Total revenue was $0.4 million for the three months ended September 30, 2025 consisting of costs reimbursable under the CARB-X grant that we were awarded in the third quarter of 2025.

Research and Development Expenses

Research and development expenses were $12.6 million for the three months ended September 30, 2025 and $16.5 million for the three months ended September 30, 2024. The decrease of $3.8 million was primarily due to the following:

General and Administrative Expenses

General and administrative expenses were $9.5 million for the three months ended September 30, 2025 compared to $12.7 million for the three months ended September 30, 2024. The decrease of $3.2 million was primarily due to the following:

Manufacturing Services

Manufacturing services costs began with the effectiveness of the TSA with Nestlé in the fourth quarter of 2024 and resulted in $0.7 million of expenses for the three months ended September 30, 2025. The expenses are associated with the PRMS manufacturing performed on behalf of Nestlé, including labor, materials, allocated facility-related, lab supplies and other manufacturing costs that would have been capitalized into inventory prior to the sale of VOWST Business.

Other Income (Expense), Net

Other income (expense) , net was $30.7 million of income and $21.9 million of expense for the three months ended September 30, 2025 and 2024, respectively. The increase of $52.6 million in other income, net was due to the $27.2 million gain on sale of the VOWST business primarily due to the installment payment received from Nestlé in July 2025 that was conditioned on our material compliance with obligations under the TSA, as well as $2.0 million of reimbursement income associated with the performance of TSA services. Additionally, the three months ended September 30, 2024 included a $23.4 million loss associated with the extinguishment of the Oaktree Term Loan recorded in connection with the sale of the VOWST Business to SPN.

Comparison of Nine Months Ended September 30, 2025 and 2024

The following table summarizes our results of operations for the nine months ended September 30, 2025 and 2024:

Revenue

Total revenue was $0.4 million for the nine months ended September 30, 2025, consisting of costs reimbursable under the CARB-X grant that we were awarded in the third quarter of 2025.

Research and Development Expenses

Research and development expenses were $37.4 million for the nine months ended September 30, 2025 and $51.8 million for the nine months ended September 30, 2024. The decrease of $14.4 million was primarily due to the following:

General and Administrative Expenses

General and administrative expenses were $31.6 million for the nine months ended September 30, 2025 compared to $40.7 million for the nine months ended September 30, 2024. The decrease of $9.1 million was primarily due to the following:

These decreases were partially offset by an increase in professional fees of $0.4 million due to an increase in legal and consulting fees.

Manufacturing Services

Manufacturing services costs began with the effectiveness of the TSA with Nestlé in the fourth quarter of 2024 and resulted in $6.0 million of expenses for the nine months ended September 30, 2025. The expenses are associated with the PRMS manufacturing performed on behalf of Nestlé, including labor, materials, allocated facility-related, lab supplies and other manufacturing costs that would have been capitalized into inventory prior to the sale of VOWST Business.

Other Income (Expense), Net

Other income (expense), net was $95.6 million of income and $17.7 million of expense for the nine months ended September 30, 2025 and 2024, respectively. The $113.3 million increase in other income, net was primarily due to the $50.0 million and $25.0 million installment payments received from Nestlé in January 2025 and July 2025, respectively, which were conditioned on our material compliance with obligations under the TSA, $11.8 million of reimbursement income from Nestlé associated with the performance of TSA services, as well as a $4.6 million gain as a result of a change in estimate of the accrued liabilities due to SPN - related party, and $0.6 million increase in sublease income. The increases were partially offset by a decrease in interest income of $1.7 million due to our lower cash balance. Additionally, the nine months ended September 30, 2024 included a $23.4 million loss associated with the extinguishment of the Oaktree Term Loan recorded in connection with the sale of the VOWST Business to SPN.

Liquidity and Capital Resources

Since our inception, we have generated revenue only from collaborations and have incurred recurring losses from operations. We anticipate that we will continue to incur losses for at least the next several years. We will need additional capital to fund our operations, which include our research and development and general and administrative expenses, which we may obtain from additional financings, public offerings, research funding, additional collaborations, contract and grant revenue or other sources.

On August 5, 2024, we entered into the Purchase Agreement with SPN, pursuant to which we agreed to sell our 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 Product to SPN and its designated affiliates, and SPN and its designated affiliates assumed certain liabilities from us. Our stockholders approved the Transaction at a special meeting of stockholders held on September 26, 2024, and the Transaction closed on September 30, 2024. As consideration for the Transaction, SPN agreed to pay us:

As they are earned, the Milestone Payments will be satisfied as follows: (i) first, by set-off against all accrued interest on the Prepaid Milestone until the amount of such accrued interest has been paid in full, (ii) second, by set-off against the outstanding balance of the Prepaid Milestone until the Prepaid Milestone has been repaid in full and (iii) thereafter, in cash. If any amount of the Prepaid Milestone (and any accrued interest thereon) remains outstanding as of following the last day of the Milestone Period (defined below), the balance thereof (together with any interest accrued thereon) will be forgiven and the right of set-off of SPN with respect thereto will be deemed forfeited. The installment payment received on July 1, 2025 was offset by $1.4 million that we paid to Nestlé on the same date related to certain employment obligations assumed by SPN through the period prior to the Closing Date.

We and SPN share 50/50 in the net profit or net loss achieved during the Profit Sharing Period, with the net profit or net loss calculated as (i) the net sales of VOWST in the United States and Canada, plus (ii) other income received in connection with the grant of a license or sublicense with respect to VOWST in the United States and Canada as described in the Purchase Agreement, minus (iii) allowable expenses directly attributable or reasonably allocable to certain development activities, commercialization activities, medical affairs activities, manufacturing activities or other relevant activities, as described in the Purchase Agreement. During the Profit Sharing Period, we will reimburse SPN for (i) certain payments under the exclusive license agreement between us and Memorial Sloan Kettering Cancer Center, (ii) certain costs incurred in connection with an ongoing post-marketing safety study of VOWST and (iii) 80.1% of all rent and other costs due to the landlord under the lease for our Waltham facility.

As a condition to Closing, we and SPN entered into the Securities Purchase Agreement, pursuant to which SPN purchased 714,285 shares of Common Stock at Closing, at a purchase price per share of $21.00, for an aggregate purchase price of $15.0 million.

In May 2021, we entered into a Sales Agreement, or the Sales Agreement, with Cowen and Company, LLC, or Cowen, to sell shares of our common stock, with aggregate gross sales proceeds of up to $150.0 million, from time to time, through an "at the market" equity offering program under which Cowen acts as sales agent. As of October 31, 2025, we have sold 1,772,037 shares of common stock under the Sales Agreement, at an average price of approximately $30.66 per share, raising aggregate net proceeds of approximately $52.2 million after deducting an aggregate commission of approximately 3% and other issuance costs.

As of September 30, 2025, we had cash and cash equivalents totaling $47.6 million and an accumulated deficit of $957.1 million. For the nine months ended September 30, 2025, we incurred a loss from operations of $74.6 million. We expect that our operating losses and negative cash flows will continue for the foreseeable future.

Under applicable accounting standards, we have the responsibility to evaluate whether conditions or events raise substantial doubt about our ability to meet our future financial obligations as they become due within 12 months after the date the consolidated financial statements are issued. The ability to obtain sufficient proceeds from additional equity offerings, collaborations or other financing with terms favorable or acceptable to us cannot be considered probable, as these events are outside of our control. Based on our currently available cash resources, including proceeds received in the fourth quarter from our at the market equity offering, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will fund our operations through the second quarter of 2026. Accordingly, management has concluded that these circumstances raise substantial doubt about our ability to continue as a going concern. Substantial doubt about our ability to continue as a going concern may materially and adversely affect the price per share of our common stock, and it may be more difficult for us to obtain financing. If potential collaborators decline to do business with us or potential investors decline to participate in any future financings due to such concerns, our ability to increase our cash position may be limited. We will need to generate significant revenues to achieve profitability, and we may never do so. Because of the numerous risks and uncertainties associated with the development of our current and any future product candidates, the development of our platform and technology and because the extent to which we may enter into collaborations with third parties for development of any of our product candidates is unknown, we are unable to estimate the amounts of increased capital outlays and operating expenses required for completing the research and development of our product candidates.

Cash Flows

The following table summarizes our sources and uses of cash for each of the periods presented:

Operating Activities

During the nine months ended September 30, 2025, cash provided by operating activities was $15.8 million due to net income of $21.0 million and non-cash charges of $17.1 million, partially offset by changes in our operating assets and liabilities of $22.3 million. Non-cash charges consisted of stock-based compensation expense of $7.6 million, $6.2 million related to the amortization of right-of-use assets, and $3.2 million of depreciation and amortization. Changes in our operating assets and liabilities during the nine months ended September 30, 2025 consisted of a decrease in accrued liabilities due to SPN of $13.3 million, a decrease in operating lease liabilities of $6.4 million, a decrease in accrued expenses and other current and long-term liabilities of $4.2 million, a decrease in accounts payable of $2.4 million, and an increase in accounts receivable relating to the CARB-X program of $0.4 million, partially offset by a decrease in prepaid expenses and other current and other non-current assets of $2.7 million, and a decrease in accounts receivable due from SPN of $1.6 million.

During the nine months ended September 30, 2024, operating activities used $109.7 million of cash, primarily due to non-cash charges of $90.1 million and changes in our operating assets and liabilities of $35.4 million, partially offset by net income of $15.8 million. Non-cash charges consisted of stock-based compensation expense of $17.2 million, $7.2 million related to the amortization of right-of-use assets, $4.4 million of depreciation and amortization, $1.4 million of amortization of debt issuance costs, $23.4 million of loss associated with the extinguishment of the Oaktree Term Loan, $0.3 million loss on disposal of fixed assets, and $3.3 million of impairment charges related to our long-lived assets. These were partially offset by the $146.7 million gain on sale of VOWST Business and $0.5 million decrease in the fair value of warrants. Changes in our operating assets and liabilities during the nine months ended September 30, 2024 consisted of a decrease in operating lease liabilities of $4.4 million, a decrease in deferred income - related party of $4.1 million, a decrease in accrued expenses and other current and long-term liabilities of $3.3 million, and a decrease in inventories of $33.8 million in connection with the sale of the VOWST Business to SPN, partially offset by a decrease in collaboration receivable - related party of $8.7 million, a decrease in prepaid expenses and other current and other non-current assets of $0.3 million, and an increase in accounts payable of $1.2 million.

Investing Activities

During the nine months ended September 30, 2025, net cash used in investing activities was $0.2 million, consisting entirely of purchases of property and equipment.

During the nine months ended September 30, 2024, net cash provided by investing activities was $142.4 million, consisting of $141.3 million of proceeds from the sale of the VOWST Business and a $1.4 million sale of a restricted investment relating to a security deposit on one of our leases that was reclassified as restricted cash, partially offset by $0.3 million of purchases of property and equipment.

Financing Activities

During the nine months ended September 30, 2025, net cash provided by financing activities was $1.2 million, consisting of $1.0 million from the issuance of common stock under our at the market equity program, net of issuance costs and $0.2 million from the issuance of common stock under our 2015 Employee Stock Purchase Plan, or ESPP.

During the nine months ended September 30, 2024, net cash used in financing activities was $92.1 million, consisting of $127.9 million repayment of the Oaktree Term Loan, partially offset by $21.8 million from the issuance of common stock under our at the market equity program, net of issuance costs, $13.5 million from the issuance of common stock in connection with the sale of the VOWST Business to SPN,and $0.5 million from the issuance of common stock under our 2015 ESPP.

Funding Requirements

Our expenses may increase in connection with our ongoing clinical development activities and research and development activities. In addition, we expect to continue to incur additional costs associated with operating as a public company. We anticipate that our future expenses will increase if and as we:

Because of the numerous risks and uncertainties associated with the development of our product candidates, we are unable to estimate the amounts of increased capital outlays and operating expenses associated with completing the research and development of our product candidates. Our future capital requirements will depend on many factors, including:

Identifying potential product candidates and conducting preclinical testing and clinical trials is a time-consuming, expensive and uncertain process that takes years to complete, and we may never generate the necessary data or results required to obtain marketing approval for our current or future product candidates and achieve product sales. In addition, our product candidates, if approved, may not achieve commercial success. Additionally, part of our commercial revenues, if any, will be derived from sales of product candidates that we do not expect to be commercially available for many years, if ever. Accordingly, we will need to obtain substantial additional funds to achieve our business objectives.

Adequate additional funds may not be available to us on acceptable terms, or at all. Additionally, market volatility resulting from macroeconomic conditions, or other factors could also adversely impact our ability to access capital as and when needed. To the extent that we raise additional capital through the sale of equity or convertible debt securities, our stockholders' ownership interest will be diluted, and the terms of these securities may include liquidation or other preferences that adversely affect our stockholders' rights as common stockholders. Any debt financing and preferred equity financing, if available, may involve agreements that include, covenants limiting or restricting our ability to take specific actions, such as incurring additional debt, making capital expenditures or declaring dividends. Additional debt or preferred equity financing may also require the issuance of warrants, which could potentially dilute our stockholders' ownership interest.

If we raise additional funds through collaborations, strategic alliances or licensing arrangements with third parties, in addition to our existing collaboration agreements, we may have to relinquish valuable rights to our technologies, future revenue streams, research programs, or product candidates or grant licenses on terms that may not be favorable to us. If we are unable to raise additional funds through equity, debt financings, or collaborations when needed, we may be required to delay, limit, reduce or terminate our product development programs or any potential future commercialization efforts or grant rights to develop and market product candidates that we would otherwise prefer to develop and market ourselves.

As discussed in Note 1 of the condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q, we have the responsibility to evaluate whether conditions or events raise substantial doubt about our ability to meet our future financial obligations as they become due within 12 months after the date the condensed consolidated financial statements are issued. The ability to obtain sufficient proceeds from additional equity offerings, collaborations or other financing with terms favorable or acceptable to us cannot be considered probable, as these events are outside of our control. Accordingly, management has concluded that these circumstances raise substantial doubt about our ability to continue as a going concern. Based on our currently available cash resources, including proceeds received in the fourth quarter from our at the market equity offering, and considering our future operating plans and our ongoing obligations related to the Transaction, we anticipate that we will fund our operations through the second quarter of 2026.

Contractual Obligations and Commitments

The disclosure of our contractual obligations and commitments was included in our Annual Report. There have been no material changes from the contractual commitments and obligations previously disclosed in our Annual Report.