Quarterly Report for Quarter Ending June 30, 2026 (Form 10-Q)

Management's Discussion and Analysis of Financial 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.

On April 21, 2025, we effected a 1-for-20 reverse stock split of our common stock. 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.

Overview

We are a clinical-stage company focused on improving patient outcomes in medically compromised populations, including oncology patients and those suffering from inflammatory and immune, or I&I, diseases through discovery and development of novel live biotherapeutic product, or LBP, candidates. We led the successful development and approval of VOWST, the first FDA-approved orally administered microbiome biotherapeutic and a Breakthrough Therapy designated drug, 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 have established field-leading capabilities and platforms that are powered by best-in-field human data sets to advance a portfolio of products that can uniquely address diseases by targeting host pathways that are modulated by microbes in the human body, and, in particular, diseases associated with mucosal epithelial barrier-immune interface targets. We believe clinical and nonclinical data across our programs support the development of LBPs to address unmet medical needs in oncology that can lead to interruption to patients' cancer treatment and/or mortality (by targeting the prevention and treatment of a broad swath of infection risks faced by cancer patients and by treating irEC), and to treat I&I diseases. Our pipeline consists of SER-155, SER-603, SER-428, and SER-147, as well as other potential candidates in earlier development.

We are designing LBP candidates to modulate 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, or GI, tract. 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 in allo-HCT and the SER-155 IST in irEC (both further described below) validate our novel therapeutic approach 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.

In the context of preventing infection for patients undergoing allo-HCT for hematological cancer, we believe that our technology may be replicable across different bacterial pathogens with the potential to develop live biotherapeutics to protect a range of medically compromised patients at risk of antimicrobial resistance, or AMR, infections and bloodstream infections, or BSIs, that can result from a compromised mucosal epithelial barrier and that can be a major cause of mortality. SER-155, our most advanced LBP candidate, is an investigational, oral, live biotherapeutic designed to decolonize GI pathogens, improve GI mucosal epithelial barrier integrity, and induce immune homeostasis to prevent bacterial BSIs, including those that can harbor antimicrobial resistance, as well as other pathogen-associated negative clinical outcomes in patients undergoing allogeneic hematopoietic stem cell transplantation, or allo-HCT. In our 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 our CRO, and manufacturing of drug substance, we have paused additional investment in that program while continuing to seek funding for the Phase 2 study.

We are also evaluating SER-155 in 15 patients with moderate-to-severe (Grade 2- 3) immune checkpoint-related enterocolitis, or irEC, through an investigator-sponsored trial, or IST, with Memorial Sloan Kettering Cancer Center, an institution with whom we have had a decade-long collaboration. irEC is among the most frequent and severe immune-related adverse events, or 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. Moderate to severe irEC occurs in approximately 25% of all ICI therapy recipients in the United States. In 2026, it is estimated that there are a total of 300,000 patients on ICI cancer therapy in the United States, and this figure is increasing as ICI are being used across multiple cancer types, in earlier intervention and in combination with other cancer therapies. ICIs 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. 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. In addition, drug pharmacology translational biomarkers of gastrointestinal inflammation (fecal calprotectin) and of mucosal epithelial barrier integrity (fecal albumin), which were elevated in participants at baseline, prior to SER-155 dosing, both showed decreases post SER-155 treatment, with statistically significant reductions achieved by Day 43, reflecting improvement in two mechanistically linked dimensions of irEC disease. Participants in the study were on a wide range of ICI types, including PD-1 inhibitors (Keytruda®, Opdivo®, Zynyz®), PD-L1 inhibitors (Imfinzi®, Bavencio®), CTLA-4 inhibitors (Yervoy®, Imjudo®), LAG-3 inhibitor (Opdualag®), and combinations thereof. Clinical guidelines for these patients stipulate halting of ICI cancer treatment and initiation of systemic immunosuppressive corticosteroids, which are associated with clinically meaningful toxicities and other negative consequences, including: systemic immunosuppression, increased infection risk, metabolic complications, and potential interference with cancer treatment.

We believe there remains a significant unmet need for systemic immunosuppressive-free therapeutic approaches that reduce gastrointestinal inflammation and diarrhea and may allow patients who develop irEC to avoid disruption of their life-saving ICI cancer treatment and the promising study results support continued development of SER-155 to treat irEC. We are engaging with potential partners, including companies with ICI franchises, as we evaluate next steps for the development of SER-155 in irEC.

We have meaningfully advanced over the past decade our scientific understanding of how microbes in the GI functionally modulate pathways at the mucosal epithelial barrier-immune interface that are associated with inflammatory and immune-related disease. The clinical data from our SER-155 Phase 1b study in allo-HCT and the IST in irEC, in particular the drug pharmacology translational biomarker data, along with our extensive preclinical and translational clinical data compiled over the past decade support and inform the advancement of our earlier stage programs targeting I&I diseases and our current strategy continues to prioritize these indications. We are developing SER-603, broadly in inflammatory bowel disease, or IBD, including ulcerative colitis, or 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 epithelial 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. We believe that our LBPs could represent a non-immunosuppressive treatment option for I&I diseases that are linked to colitis and could broadly address immune therapy toxicities, both of which represent significant unmet medical needs and potential commercial opportunities. We are currently exploring potential collaborations related to those I&I disease programs.

We believe that SER-155 and other cultivated live biotherapeutic candidates could be developed in additional patient populations in which mucosal epithelial barrier compromise is implicated. For example, in bloodstream and AMR infections, there are numerous medically compromised patients beyond allo-HCT, including autologous-HCT patients, cancer patients with neutropenia, chimeric antigen receptors therapy, or CAR-T, recipients, individuals with chronic liver disease, or CLD, solid organ transplant recipients, as well as patients in the intensive care unit, or ICU, and long-term acute care facilities. In 2025, we received a non-dilutive award from CARB-X (Combating Antibiotic-Resistant Bacteria Biopharmaceutical Accelerator) for up to $3.6 million, representing our 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. We have advanced development and manufacturing of SER-428 and are 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. Additionally, 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 CLD. 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 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 a strain library and associated microbiological capabilities that span 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, 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 net loss from operations was $42.2 million for the six months ended June 30, 2026. As of June 30, 2026, we had an accumulated deficit of $987.7 million.

We plan to focus our investment in the near-term on advancing our early-stage live biotherapeutic candidates, including advancing IND-enabling studies for SER-603, evaluating the next stage of development for SER-155 in irEC, and, subject to receiving additional funding, progressing the development of SER-155 into a Phase 2 study in allo-HCT. 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 business development transactions including 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, 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 as and when needed 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 June 30, 2026, we had cash and cash equivalents totaling $15.6 million. Based on our currently available cash resources, the $12.5 million Milestone Termination Payment received from SPN in July 2026, and the expected receipt of the additional $12.5 million Milestone Termination Payment due from SPN in October 2026, and considering our future operating plans, we anticipate that we will require additional funding following the first quarter of 2027. 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."

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.

On February 12, 2026, we announced that we implemented cost reduction actions, including reducing our workforce by approximately 30%. During the three months ended March 31, 2026, we incurred approximately $0.9 million in restructuring costs, primarily related to severance costs, of which $0.7 million was paid during the first quarter of 2026, and the remainder was paid out in the second quarter of 2026.

On June 5, 2026, we announced that we amended our lease with our landlord for a portion of our space in Cambridge, Massachusetts, under which we reduced our leased space, rental rate and facility operating expenses. The restructured lease is expected to materially reduce the Company's ongoing annual facility-related costs and long-term obligations. Refer to Note 6, Leases, included elsewhere in this Quarterly Report on Form 10-Q for more information.

Our Product Pipeline

Addressing unmet medical needs in oncology patients

Treatment of Immune checkpoint-related enterocolitis (irEC)

SER-155 for irEC patients

We have been collaborating with Memorial Sloan Kettering Cancer Center for over a decade on the impact of the GI microbiome on immune related diseases and cancer; recently this long-standing collaboration included a single arm, open-label Phase 1b investigator-sponsored trial, or IST, evaluating SER-155 as a potential first-line treatment in irEC. The study evaluated SER-155 in 15 patients with moderate-to-severe (Grade 2- 3) irEC. irEC is among the most frequent and severe immune-related adverse events, or 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. Moderate to severe irEC occurs in approximately 25% of all ICI therapy recipients in the United States. ICIs 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. Participants in the study were on a wide range of ICI types, including PD-1 inhibitors (Keytruda®, Opdivo®, Zynyz®), PD-L1 inhibitors (Imfinzi®, Bavencio®), CTLA-4 inhibitors (Yervoy®, Imjudo®), LAG-3 inhibitor (Opdualag®), and combinations thereof. Clinical guidelines for these patients who experience Grade 2-3 irEC stipulate halting of ICI cancer treatment and initiation of systemic immunosuppressive corticosteroids, which are associated with clinically meaningful toxicities and other negative consequences, including systemic immunosuppression, increased infection risk, metabolic complications, and potential interference with cancer treatment. There remains a significant unmet need for systemic, immunosuppressive-free therapeutic approaches that reduce gastrointestinal inflammation and diarrhea and may allow patients who develop irEC to avoid disruption of their life-saving ICI cancer treatment. SER-155 is designed to promote mucosal healing and modulate inflammation without systemic immunosuppressives, which carry the risk of toxicity and ICI efficacy impact.

In July 2026, we reported initial clinical results, including preliminary safety, efficacy, pharmacology, and exploratory biomarker data. Top-line data from the IST showed that 80% of SER-155 recipients, or 12 of 15 participants, 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). Notably, 8 of these 12 responders (67%) achieved greater than or equal to a 2-grade improvement in diarrhea symptoms without immunosuppressive therapy at Day 15. At Day 15, 5 of 15 participants (33%) achieved immunosuppressive-free complete clinical remission, defined as total resolution of diarrhea symptoms to Grade 0, without immunosuppressive therapy. At Day 43, 5 of 15 participants (33%) maintained immunosuppressive-free clinical response, and, notably, 2 of 15 participants (13%) maintained immunosuppressive-free complete clinical remission. All 12 participants with immunosuppressive-free clinical response at Day 15 had the same, or better, diarrhea grade at Day 43. As noted, 5 maintained immunosuppressive-free clinical response at Day 43. The other 7 were treated with non-systemically acting, gastrointestinal-targeted immunosuppressives after Day 15. SER-155 was generally well tolerated through Day 43, with no safety concerns identified, consistent with the outcome in Seres' Phase 1b study of SER-155 in participants undergoing allo-HCT. There were no serious adverse events assessed as related to SER-155 and no bloodstream infections reported in the study through Day 43. Two participants experienced 2 non-serious adverse events each, assessed as possibly related to vancomycin and SER-155. All 4 adverse events were moderate in severity and were resolved. SER-155 bacterial strain engraftment (a measure of drug pharmacokinetics and strain growth in the gastrointestinal tract) was robust, with the majority of SER-155 strains observed across the study participants, and with kinetics, magnitude, and durability comparable to that observed in our prior clinical studies.

Biomarker data also supported that SER-155 was functioning as designed. At baseline, participants in the study showed evidence of epithelial barrier disruption and severe gastrointestinal inflammation as evidenced in the biomarkers fecal albumin and fecal calprotectin respectively. Fecal albumin is a biomarker that indicates protein leakage from the bloodstream into the gut lumen and provides direct evidence of mucosal epithelial barrier compromise. Fecal calprotectin is a well-established clinical biomarker of immune activation that indicates the presence of activated neutrophils in the intestinal mucosa. At study entry participants had elevated fecal albumin and calprotectin levels that are characteristic of individuals with colitis. Following SER-155 treatment, both albumin and calprotectin biomarkers show early, durable, and concordant reductions over time with significant reductions in both measures achieved by Day 43, reflecting consistent improvement across two mechanistically linked dimensions of irEC disease. These biomarker improvements were directionally consistent with the clinical observations and provide additional support for SER-155's potential biologic activity in this setting. Importantly, the pharmacological and translational results suggest that SER-155 may act on core disease-relevant biology rather than simply produce a symptomatic effect. We believe the drug pharmacology data provide supportive evidence of our live biotherapeutic candidates operating as designed to repair the mucosal epithelial barrier and reduce gastrointestinal inflammation, which supports possible expansion into multiple other inflammatory and immune diseases.

We believe data from this IST further supports the potential for live biotherapeutics to address a significant unmet need among the large population of cancer patients receiving ICIs for systemic immunosuppressive-free therapeutic approaches that have the potential to reduce gastrointestinal inflammation and diarrhea and may allow patients who develop irEC to avoid disruption of their life-saving ICI cancer treatment.

Infection Risk Reduction

Oncology patients are particularly vulnerable to risk of infection due to their cancer treatment and conditioning procedure as well as compromised immune system. We believe that the scientific and clinical data from our VOWST program (our then product candidate SER-109 program) validate our novel approach of using live biotherapeutics to decolonize pathogens and improve mucosal epithelial barrier integrity, resulting in reduced rate of infections in medically compromised patients. Data from the 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 VOWST 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 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. Recently, two manuscripts were published in Nature Medicine (Bryant et al. 2026) and the Journal of Infectious Diseases (Bryant et al. 2025) highlighting new insights into the functional mechanism and clinical impact of VOWST. The Nature Medicine article, titled "The impact of an oral purified microbiome therapeutic on the GI microbiome", confirmed our pharmacological hypotheses from earlier VOWST studies, with higher VOWST dosing associated with enhanced pharmacokinetics, as assessed by faster and more robust therapeutic species engraftment in the gut. Treatment also significantly altered the composition of the intestinal microbiome and microbe-associated metabolites, including decreased primary and increased secondary bile acids, as well as elevated short- and medium-chain fatty acids, functional changes that inhibit C. difficile spore germination and vegetative growth. Further, in vitro analyses confirmed that VOWST batches induced production of these metabolites that disrupt C. difficile life cycle and growth. Collectively, these findings support VOWST's role in restoring microbe-associated metabolic functions critical to preventing CDI recurrence. A complementary publication in the Journal of Infectious Diseases, titled "Comparability of Gastrointestinal Microbiome and Bile Acid Profiles in Patients With First or Multiply Recurrent Clostridioides difficile Infection", reported a post hoc analysis of the ECOSPOR IV Phase 3 trial, evaluating differences in gastrointestinal microbiome and bile acid profiles between patients experiencing a first recurrence C. difficile infection (frCDI) versus multiply recurrence infection (mrCDI). These data demonstrate that the underlying functional disease etiology is consistent in both first and multiply recurrent CDI patient populations, with VOWST demonstrating similar efficacy and drug pharmacology across the broad patient population.

We believe these data provide important clinical translation and further demonstrate the potential of live biotherapeutics to target specific microbiome functions that are linked to serious disease, including those that are not effectively treated with other drug modalities. The underlying data supporting these publications was developed using Seres' MbTx platform, which provides high-resolution assessment of drug pharmacology and functional mechanism of action. These data on bacterial function and pharmacology anchored the preclinical development of SER-155 and inform the continued development of Seres' pipeline of next-generation live biotherapeutic products.

SER-155 for allo-HCT patients

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-HCT. SER-155 is a live biotherapeutic candidate designed to prevent frequent, expensive, and fatal infections in blood cancer patients.

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 Enterococcaceae and Enterobacteriaceae species 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-HCT 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-HCT 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-HCT 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-HCT 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-HCT.

SER-155 Phase 1b Study (including placebo-controlled Cohort)

SER-155 has been evaluated in a Phase 1b study in patients undergoing allo-HCT. 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-HCT. 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-HCT, 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-HCT 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-HCT 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-HCT for cancers and other serious conditions.

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 agent classes 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 HCT patients, especially those BSIs associated with AMR that increases the risk of morbidity and mortality.

In April 2026, we presented SER-155 Phase 1b study results, including biomarker and clinical pharmacology data, at the 2026 European Society of Clinical Microbiology and Infectious Diseases (ESCMID) global congress. Data showed that administration of SER-155 induced a significant and durable shift in GI microbiome composition relative to placebo, characterized by high relative abundance of SER-155 species. This shift is associated with improved GI epithelial barrier integrity that could reduce the likelihood of bacterial translocation from the GI to the bloodstream. These pharmacology results are consistent with the intended SER-155 mechanisms of action as well as the observation of significantly lower bloodstream infection incidence post allo-HCT in SER-155-administered participants.

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 HCT 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 2025, clinical and biomarker results from our biotherapeutic programs were presented at multiple leading industry meetings and conferences, including 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), European Society for Blood and Marrow Transplantation (EBMT), Digestive Disease Week (DDW), and the 2025 American Society of Clinical Oncology (ASCO). We believe that exploratory biomarker data presented at recent medical meetings have supported the intended mechanisms of SER-155. 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.

Proposed SER-155 Phase 2 Study

The SER-155 Phase 2 study is expected to 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.

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 our CRO, and manufacturing of drug substance, we have paused additional investment in that program while continuing to seek funding for the Phase 2 study.

SER-428 - liquid formulation for ICU patients

In July 2025, we were awarded a grant from CARB-X to support the development of SER-428, an oral liquid formulation of an LBP based on SER-155 strains for medically vulnerable patient populations at risk of BSIs, including AMR infections, who cannot be dosed with oral capsules, such as intubated patients in the medical 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. SER-428 is designed to target the prevention of bloodstream infections in medical ICU patients by Escherichia coli and other gut-derived bacteria capable of harboring antibiotic resistance. Up to 50% of all preventable medical ICU deaths have been attributed to infections with E. coli and other gut-derived bacteria (Mayr, 2006). These infections are also the leading cost in the medical ICU (Neidell, 2012). When ICU patients with multidrug resistant, or MDR, infections survive hospitalization, they have high long-term morbidity with over 20% 30-day readmission rates (Chang, 2015; Mayr, 2017). Over 5 million patients are admitted to ICUs in the U.S. annually, and these admissions account for approximately 20% of all acute care hospitalizations (Barrett et al. 2024).

Infections with pathogenic, often MDR, bacteria are the leading cause of mortality in the medical ICU, causing up to 9 deaths for every 100 ICU patients admitted (Vincent, 2009). Most patients are admitted to the medical ICU with a known or suspected

infection (i.e., sepsis) but, with targeted or empiric antibiotics, most recover from this initial infection. Once in the ICU, secondary, healthcare-associated infections frequently develop during the prolonged recovery from sepsis and are a significant driver of mortality. SER-428 is a novel approach that addresses both gut colonization and subsequent translocation by E. coli and other gut-derived pathogens to prevent a significant proportion of these secondary hospital acquired infections. SER-428 is in preclinical development, with IND-enabling activities ongoing and IND-readiness targeted by the end of 2026. We have advanced development and manufacturing of SER-428 and are designing a Phase 1b open label trial in collaboration with Columbia University to evaluate this therapeutic candidate in medical ICU patients at high risk of infection.

SER-147 for cirrhosis patients

We are also developing 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 such as SBP and BSIs (Bajaj et al., 2021, Albillos et al., 2022). Over 40% of patients with decompensated cirrhosis experience an infection within the first year of diagnosis. Antibiotics are the only prophylactic option for patients at high risk of infections like SBP, resulting in exposure to antibiotics for months or years. To combat increasing rates of AMR, antibacterial prophylaxis for primary SBP is no longer recommended for the majority of patients outside of those at very high-risk, leaving significant unmet need. Many cultivated live biotherapeutics currently in clinic are constrained by formulation technologies incompatible with concomitant medications commonly used in CLD.

SER-147 is in preclinical development. The program is ready to progress to IND-enabling activities, including manufacturing, in order to advance to clinical development, pending availability of funding.

Immunology and Inflammation

SER-603 for IBD patients

SER-603 is a novel, LBP candidate designed to improve response rates and durability of remission in patients with IBD, including ulcerative colitis, or UC, and Crohn's disease. SER-603 is 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. Our research on SER-603 has been primarily 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.

Emerging clinical and preclinical evidence suggests that microbiome functional disruption contributes to disease activity in a defined subset of IBD patients. Observational and translational data from our prior SER-287 Phase 2b study and SER-301 Phase 1b study indicate that pharmacodynamic responses were greater in microbiome-defined subpopulations. These findings, along with external data demonstrating heterogeneity in microbiome-associated inflammatory responses, support the development of targeted, biomarker-informed live biotherapeutic strategies. We have discovered more than fifty GI bacterial features linked to inflammatory outcomes and have nominated and validated microbe associated biomarkers that can predict a response to current advanced therapies for IBD. Leveraging these biomarkers and our integrated preclinical and clinical data sets, SER-603 is optimized to address epithelial barrier dysfunction and microbiome-driven inflammation without systemic immunosuppression.

SER-603 is in preclinical development, with IND-enabling activities ongoing. SER-603 is being developed for use as a stand-alone therapy and/or as a mechanism-distinct adjunctive therapy in combination with biologics or small molecules. We continue to evaluate biomarker-based patient selection approaches and functional characterization strategies to inform future clinical development.

In April 2026, Dr. Ines Moura of the University of Leeds gave a presentation at the 2026 European Society of Clinical Microbiology and Infectious Diseases (ESCMID) global congress describing the use of an in vitro colonic model (MiGut) to recapitulate patient-specific microbiome composition and inflammatory responses in IBD. We are co-developing with Leeds models to evaluate drug strain engraftment in different patient microbiome backgrounds and measure resulting metabolic and immune functional responses. The collaboration with Leeds on MiGut enables the modeling of patient stratification, conditioning, and live biotherapeutic effects in a pharmacological model, to inform clinical development in IBD and broader opportunities in other diseases.

In May 2026, we presented data at the Digestive Disease Week, or DDW conference highlighting preclinical data supporting the design and potential of SER-603 in IBD. The poster, titled "The Rational Design of SER-603: A Next Generation Cultivated Microbial Consortia to Treat IBD," which was selected as a DDW 'Poster of Distinction,' highlights our integrated approach to the design of microbiome therapeutics, combining rational strain selection and biomarker-driven patient stratification. SER-603 incorporates strains selected for engraftment and delivery of clinically relevant metabolites, including short-chain fatty acids, secondary bile acids, and tryptophan-derived molecules, with a therapeutic goal of inducing mucosal healing and regulating inflammatory pathways central to IBD pathophysiology, without immunosuppression. Its design integrates insights from human clinical datasets and reverse translational approaches to identify strains linked to key functional outputs, potentially enabling targeted modulation of inflammatory microbiome features, and is complemented by microbiome-based biomarkers associated with GI inflammation, to support patient stratification and to enrich for those patients most likely to benefit.

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, SER-147 and/or SER-603 extend through at least part of 2046 (not including any potential term extension). We plan on continuing to broaden our patent portfolio. Currently, we have 20 active patent families, which includes 16 nationalized applications, three at the PCT stage, and one 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 we entered into with NESA following the sale of the VOWST Business during the third quarter of 2024 through December 31, 2025, 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 2026 as compared to 2025, following the conclusion of the TSA, completion of the Phase 1b study of SER-155 in allo-HCT, and the cost reduction actions that were implemented in September 2025 and February 2026, including pausing investment in the SER-155 Phase 2 study and headcount reductions. Research and development expenses may increase in the future if and as we resume development of any clinical or preclinical programs. In 2025, research and development expenses included labor and passthrough costs, reimbursable by Nestlé, incurred in performing obligations under the TSA. Given the conclusion of the TSA as of December 31, 2025, these costs and related reimbursements are not expected to reoccur in 2026.

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, information technology costs and other operating costs. In 2025, general and administrative expenses also included 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 2026 as compared to 2025, following the conclusion of the TSA as of December 31, 2025, reductions of our workforce and overall cost containment efforts. Over the longer term, 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.

Manufacturing Services

Under the TSA with NESA, beginning in the fourth quarter of 2024, we provided certain manufacturing services and related functions of the VOWST Business and operations. Expenses associated with the manufacturing services included 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 provided the manufacturing services until December 31, 2025. We do not expect to incur any expenses related to manufacturing services related to the VOWST business in the future, as the TSA and other Transaction-related obligations concluded on December 31, 2025.

Impairment of Long-Lived Assets

We recognized an impairment loss of $5.8 million, related to one of our operating leases and the associated leasehold improvements as an indicator of impairment was deemed to exist and the carrying value of the asset group exceeded its fair value. Refer to Note 6, Leases, included elsewhere in this Quarterly Report on Form 10-Q, for more information.

Other Income (Expense), Net

Interest Income

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

Other Income (Expense), Net

Other income, net primarily consists of:

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 six months ended June 30, 2026 or 2025.

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, 2025, filed with the SEC on March 12, 2026, 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 six months ended June 30, 2026.

Results of Operations

Comparison of Three Months Ended June 30, 2026 and 2025

The following table summarizes our results of operations for the three months ended June 30, 2026 and 2025:

Revenue

Total revenue was $0.7 million for the three months ended June 30, 2026 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 $9.1 million for the three months ended June 30, 2026 and $12.9 million for the three months ended June 30, 2025. The decrease of $3.8 million was primarily due to the following:

General and Administrative Expenses

General and administrative expenses were $7.1 million for the three months ended June 30, 2026 compared to $10.3 million for the three months ended June 30, 2025. The decrease of $3.2 million was primarily due to the following:

Manufacturing Services

Manufacturing services costs were incurred between the fourth quarter of 2024 and the end of 2025 as we performed PRMS manufacturing on behalf of Nestlé in accordance with the TSA. The expenses associated with manufacturing services included 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. Following the conclusion of the TSA on December 31, 2025, no further manufacturing services costs were incurred and none are expected moving forward.

Impairment of Long-Lived Assets

Impairment of long-lived assets was $5.8 million for the three months ended June 30, 2026, consisting of $5.6 million related to right-of-use assets and $0.2 million related to the associated leasehold improvements. Refer to Note 6, Leases, included elsewhere in this Quarterly Report on Form 10-Q, for more information.

Other Income (Expense), Net

Other income (expense), net was $25.9 million of income and $5.0 million of income for the three months ended June 30, 2026 and 2025, respectively. The increase of $20.8 million in other income, net was primarily due to the $25.0 million Gain on sale of VOWST business related to the Milestone Termination Payment expected to be received from SPN in July and October 2026, partially offset by $3.5 million of reimbursement income associated with the performance of TSA services in the second quarter of 2025 that did not reoccur due to the conclusion of the TSA at the end of 2025, and a decrease in interest income of $0.3 million due to our lower cash balance.

Comparison of Six Months Ended June 30, 2026 and 2025

The following table summarizes our results of operations for the six months ended June 30, 2026 and 2025:

Revenue

Total revenue was $1.1 million for the six months ended June 30, 2026 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 $22.3 million for the six months ended June 30, 2026 and $24.8 million for the six months ended June 30, 2025. The decrease of $2.4 million was primarily due to the following:

General and Administrative Expenses

General and administrative expenses were $15.1 million for the six months ended June 30, 2026 compared to $22.1 million for the six months ended June 30, 2025. The decrease of $7.0 million was primarily due to the following:

Manufacturing Services

Manufacturing services costs were incurred between the fourth quarter of 2024 and the end of 2025 as we performed PRMS manufacturing on behalf of Nestlé in accordance with the TSA. The expenses associated with manufacturing services included 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. Following the conclusion of the TSA on December 31, 2025, no further manufacturing services costs were incurred and none are expected moving forward.

Impairment of Long-Lived Assets

Impairment of long-lived assets was $5.8 million for the six months ended June 30, 2026, consisting of $5.6 million related to right-of-use assets and $0.2 million related to the associated leasehold improvements. Refer to Note 6, Leases, included elsewhere in this Quarterly Report on Form 10-Q, for more information.

Other Income, Net

Other income (expense), net was $26.8 million of income and $64.9 million of income for the six months ended June 30, 2026 and 2025, respectively. The decrease of $38.1 million in other income, net was due to the lower gain on sale of VOWST business in 2026 compared to 2025 of $27.4 million, as well as $9.8 million of reimbursement income associated with the performance of TSA services in the first half of 2025 that did not reoccur due to the conclusion of the TSA at the end of 2025, and a decrease in interest income of $0.7 million due to our lower cash balance. The $52.4 million gain on sale of the VOWST business recognized in the six months ended June 30, 2025 was primarily due to the $50.0 million installment payment received from Nestlé in January 2025 that was conditioned on our material compliance with obligations under the TSA, while the $25.0 million gain on sale of VOWST business recognized in the six months ended June 30, 2026 was related to the Milestone Termination Payment expected to be received from SPN in July and October 2026.

Liquidity and Capital Resources

Since our inception, we have generated revenue only from collaborations and have incurred recurring net 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.

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.

On June 2, 2026, we entered into Amendment No. 1 (the "APA Amendment") to the Purchase Agreement. Pursuant to the APA Amendment, the parties agreed to terminate SPN's obligations with respect to the Milestone Payments described above and eliminate the milestone interest payments that would have been due from us to SPN. In consideration for the foregoing, SPN agreed to a one-time payment to us of $25.0 million (the "Milestone Termination Payment"), which amount is payable in two equal installments of $12.5 million, with the first installment paid on July 1, 2026 and the second installment payable on October 1, 2026.

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. During the three and six months ended June 30, 2026, we 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, raising aggregate net proceeds of approximately $1.7 million and $2.1 million after deducting an aggregate commission of approximately 3%. During the six months ended June 30, 2025, we sold 54,806 of common stock under the Sales Agreement, at an average price of approximately $18.60 per share, raising aggregate net proceeds of approximately $1.0 million after deducting an aggregate commission of approximately 3% and other issuance costs. As of June 30, 2026, we have sold 2,446,777 shares of common stock under the Sales Agreement, at an average price of approximately $26.16 per share, raising aggregate net proceeds of approximately $61.4 million after deducting an aggregate commission of approximately 3% and other issuance costs.

As of June 30, 2026, we had cash and cash equivalents totaling $15.6 million and an accumulated deficit of $987.7 million. For the six months ended June 30, 2026, we incurred a loss from operations of $42.2 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, the $12.5 million Milestone Termination Payment received from SPN in July 2026, and the expected receipt of the additional $12.5 million Milestone Termination Payment due from SPN in October 2026, and considering our future operating plans, we anticipate that we will require additional funding following the first quarter of 2027. 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 six months ended June 30, 2026, cash used in operating activities was $38.8 million due to a net loss of $15.3 million and changes in our operating assets and liabilities of $38.5 million, partially offset by non-cash charges of $15.1 million. Non-cash charges consisted of the impairment loss of $5.8 million, stock-based compensation expense of $3.5 million, $4.1 million related to the amortization of right-of-use assets, $1.5 million of depreciation and amortization, and $0.1 million loss on disposal of fixed assets. Changes in our operating assets and liabilities during the six months ended June 30, 2026 consisted of an increase in accounts receivable due from SPN of $24.6 million related to the APA Amendment, a decrease in operating lease liabilities of $14.8 million, primarily related to $10.8 million of termination payments related to the Lease Amendment, a decrease in accounts payable of $0.5 million, a decrease in accrued expenses and other current and long-term liabilities of $0.1 million, and an increase in accounts receivable relating to the CARB-X program of $0.1 million, partially offset by a decrease in prepaid expenses and other current and other non-current assets of $1.6 million.

During the six months ended June 30, 2025, cash provided by operating activities was $13.6 million due to net income of $12.8 million and non-cash charges of $11.4 million, partially offset by changes in our operating assets and liabilities of $10.6 million. Non-cash charges consisted of stock-based compensation expense of $5.2 million, $4.1 million related to the amortization of right-of-use assets, and $2.1 million of depreciation and amortization. Changes in our operating assets and liabilities during the six months ended June 30, 2025 consisted of a decrease in accrued liabilities due to SPN of $4.3 million, a decrease in operating lease liabilities of $4.2 million, a decrease in accrued expenses and other current and long-term liabilities of $4.8 million, and a decrease in accounts payable of $1.9 million, partially offset by a decrease in prepaid expenses and other current and other non-current assets of $3.4 million and a decrease in accounts receivable due from SPN of $1.2 million.

Investing Activities

During the six months ended June 30, 2026, net cash provided by investing activities was less than $0.1 million, consisting entirely of proceeds received from sales of property and equipment to unrelated third parties.

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

Financing Activities

During the six months ended June 30, 2026, net cash provided by financing activities was $2.1 million, consisting of $2.1 million from the issuance of common stock under our at the market equity program, net of issuance costs and less than $0.1 million from the issuance of common stock under our 2015 Employee Stock Purchase Plan, or ESPP.

During the six months ended June 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.

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, the $12.5 million Milestone Termination Payment received from SPN in July 2026, and the expected receipt of the additional $12.5 million Milestone Termination Payment due from SPN in October 2026, and considering our future operating plans, we anticipate that we will require additional funding following the first quarter of 2027.

Contractual Obligations and Commitments

The disclosure of our contractual obligations and commitments was included in our Annual Report. Except for the Lease Amendment described in Note 6, Leases, to our condensed consolidated financial statements included elsewhere in this Quarterly Report on Form 10-Q there have been no material changes from the contractual commitments and obligations previously disclosed in our Annual Report.