8-K

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 8-K

CURRENT REPORT

Pursuant to Section 13 or 15(d)

of the Securities Exchange Act of 1934

Date of Report (Date of earliest event reported): June 27, 2023

SERES THERAPEUTICS, INC.

(Exact name of Registrant as Specified in Its Charter)

Delaware	001-37465	27-4326290
(State or Other Jurisdiction of Incorporation)	(Commission File Number)	(IRS Employer Identification No.)

200 Sidney Street-4th Floor Cambridge, MA	02139
(Address of Principal Executive Offices)	(Zip Code)

Registrant’s Telephone Number, Including Area Code: (617) 945-9626

Not Applicable

(Former Name or Former Address, if Changed Since Last Report)

Check the appropriate box below if the Form 8-K filing is intended to simultaneously satisfy the filing obligation of the registrant under any of the following provisions:

☐ Written communications pursuant to Rule 425 under the Securities Act (17 CFR 230.425)

☐ Soliciting material pursuant to Rule 14a-12 under the Exchange Act (17 CFR 240.14a-12)

☐ Pre-commencement communications pursuant to Rule 14d-2(b) under the Exchange Act (17 CFR 240.14d-2(b))

☐ Pre-commencement communications pursuant to Rule 13e-4(c) under the Exchange Act (17 CFR 240.13e-4(c))

Securities registered pursuant to Section 12(b) of the Act:

Title of each class	Trading Symbol(s)	Name of each exchange on which registered
Common stock, $0.001 par value per share	MCRB	The Nasdaq Global Select Market

Indicate by check mark whether the registrant is an emerging growth company as defined in Rule 405 of the Securities Act of 1933 (§ 230.405 of this chapter) or Rule 12b-2 of the Securities Exchange Act of 1934 (§ 240.12b-2 of this chapter).

Emerging growth company ☐

If an emerging growth company, indicate by check mark if the registrant has elected not to use the extended transition period for complying with any new or revised financial accounting standards provided pursuant to Section 13(a) of the Exchange Act. ☐

Item 5.03 Amendments to Articles of Incorporation or Bylaws; Change in Fiscal Year.

On June 22, 2023, Seres Therapeutics, Inc. (the “Company”) held its 2023 Annual Meeting of Stockholders (the “Annual Meeting”), at which the Company’s stockholders approved an amendment (the “Amendment”) to the Company’s Restated Certificate of Incorporation to increase the number of authorized shares of the Company’s Common Stock, $0.001 par value per share, from 200,000,000 shares to 240,000,000 shares, as described in the Company’s Definitive Proxy Statement on Schedule 14A filed with the Securities and Exchange Commission on April 25, 2023.

The Company’s board of directors previously approved the Amendment and, on June 27, 2023, the Company filed a Certificate of Amendment to the Restated Certificate of Incorporation (the “Certificate of Amendment”) with the Secretary of State of the State of Delaware to effect the Amendment, which became effective upon filing with the Secretary of State.

The foregoing description of the Certificate of Amendment does not purport to be complete and is qualified in its entirety by reference to the full text of the Certificate of Amendment, which is filed as Exhibit 3.1 to this Current Report on Form 8-K (the “Current Report”) and is incorporated herein by reference.

Item 7.01. Regulation FD Disclosure.

On June 28, 2023, the Company posted an updated corporate presentation in the “Investors and Media” portion of its website at www.serestherapeutics.com. The presentation contains additional disclosure regarding the funding conditions of Tranche B and Tranche C pursuant to the Credit Agreement and Guarantee, dated April 27, 2023, by and among the Company, the subsidiary guarantors from time to time party thereto, the lenders from time to time party thereto (the “Lenders”) and Oaktree Fund Administration, LLC, in its capacity as administrative agent for the Lenders (the “Credit Facility”). The Company believes the funding requirements for Tranche B and Tranche C are achievable. A copy of the slide presentation is attached as Exhibit 99.1 to this Current Report and incorporated herein by reference.

The information in Item 7.01 of this Current Report is intended to be furnished and shall not be deemed “filed” for purposes of Section 18 of the Securities Exchange Act of 1934, as amended (the “Exchange Act”), or otherwise subject to the liabilities of that section, nor shall it be deemed incorporated by reference in any filing under the Securities Act of 1933, as amended, or the Exchange Act, except as expressly set forth by specific reference in such filing.

Forward-Looking Statements Disclaimer

This Current Report contains forward-looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. All statements contained in this Current Report that do not relate to matters of historical fact should be considered forward-looking statements, including statements regarding the Company’s belief that the funding requirements for Tranche B and Tranche C of the Credit Facility are achievable. These forward-looking statements are based on the Company’s management’s current expectations. These statements are neither promises nor guarantees, but involve known and unknown risks, uncertainties and other important factors that may cause the Company’s actual results, performance or achievements to be materially different from any future results, performance or achievements expressed or implied by the forward-looking statements, including, but not limited to, the following: the Company’s and Nestle’s ability to commercialize VOWST^TM and risks related to drug commercialization. These and other important factors discussed under the caption “Risk Factors” in the Company’s Quarterly Report on Form 10-Q filed with the Securities and Exchange Commission (the “SEC”), on May 9, 2023, and the Company’s other reports filed with the SEC could cause actual results to differ materially from those indicated by the forward-looking statements made in this Current Report. Any such forward-looking statements represent management’s estimates as of the date of this Current Report. While the Company may elect to update such forward-looking statements at some point in the future, the Company disclaims any obligation to do so, even if subsequent events cause the Company’s views to change. These forward-looking statements should not be relied upon as representing the Company’s views as of any date subsequent to the date of this Current Report.

Item 9.01. Financial Statements and Exhibits.

(d) Exhibits

The following Exhibit 99.1 relates to Item 7.01 and shall be deemed to be furnished, and not filed:

Exhibit No.	Description
3.1	Certificate of Amendment to Restated Certificate of Incorporation of Seres Therapeutics, Inc., dated June 27, 2023.
99.1	Seres Therapeutics, Inc. Corporate Presentation as of June 2023.
104	Cover Page Interactive Data File (embedded within the Inline XBRL document).

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the registrant has duly caused this report to be signed on its behalf by the undersigned hereunto duly authorized.

	SERES THERAPEUTICS, INC.
Date: June 28, 2023	By:	/s/ Thomas J. DesRosier
		Name: Thomas J. DesRosier
		Title: Executive Vice President and Chief Legal Officer

EX-3.1

Exhibit 3.1

CERTIFICATE OF AMENDMENT

TO

RESTATED CERTIFICATE OF INCORPORATION

OF

SERES THERAPEUTICS, INC.

Pursuant to Section 242 of the

General Corporation Law of the State of Delaware

Seres Therapeutics, Inc. (the “Corporation”), a corporation organized and existing under and by virtue of the General Corporation Law of the State of Delaware,

DOES HEREBY CERTIFY THAT:

1.    The Board of Directors of the Corporation duly adopted resolutions at a meeting recommending and declaring advisable that the Restated Certificate of Incorporation of the Corporation (the “Certificate of Incorporation”) be amended and that such amendment be submitted to the stockholders of the Corporation for their consideration, as follows:

RESOLVED, that the Certificate of Incorporation be amended by amending and restating the first sentence of Article FOURTH of the Certificate of Incorporation in its entirety to read as follows:

“The total number of shares of all classes of stock that the Corporation shall have authority to issue is 250,000,000 shares, consisting of (a) 240,000,000 shares of Common Stock, $0.001 par value per share (“Common Stock”), and (b) 10,000,000 shares of Preferred Stock, $0.001 par value per share (“Preferred Stock”).”

2.    The stockholders of the Corporation duly approved such amendment at an annual meeting of the stockholders of the Corporation.

3.    Such amendment has been duly adopted in accordance with Section 242 of the General Corporation Law of the State of Delaware.

IN WITNESS WHEREOF, this Certificate of Amendment to Restated Certificate of Incorporation has been executed by a duly authorized officer of the Corporation on this 27th day of June, 2023.

By:	/s/ Eric D. Shaff
Name:	Eric D. Shaff
Title:	President and Chief Executive Officer

EX-99.1

Exhibit 99.1 Seres Therapeutics June 2023 Corporate Overview

Forward Looking Statements Some of the statements in this presentation constitute “forward looking statements” under the Private Securities Litigation Reform Act of 1995, including, but not limited to the anticipated supply and degree of market acceptance of VOWST; the potential for microbiome therapeutics to protect against infection; the timing of clinical development; our development opportunities and plans; the ultimate safety and efficacy data for our products; access to additional debt tranches; and other statements which are not historical fact. Such statements are subject to important factors, risks and uncertainties, such as those discussed under the caption Risk Factors in the Company’s Quarterly Report on Form 10-Q filed on May 9, 2023, and its other filings with the SEC, that may cause actual results to differ materially from those expressed or implied by such forward looking statements. Any forward-looking statements included herein represent our views as of today only. We may update these statements, but we disclaim any obligation to do so. 2 Seres Therapeutics, Inc. © 2023

TM VOWST - First FDA Approved Orally Administered Commercially Microbiota-Based Therapeutic available TM VOWST is indicated to prevent the recurrence of C. difficile infection (CDI) in individuals 18 years of age or older following antibacterial treatment for recurrent CDI (rCDI). Seres is pioneering a new modality, led by VOWST 3 Seres Therapeutics, Inc. © 2023

Seres Mission: Transforming the Lives of Patients Worldwide with Revolutionary Microbiome Therapeutics Encapsulated consortia of commensal bacteria designed to target multiple disease-relevant pathways simultaneously Bacterial Consortia Orally-formulated, using current Good Disease Engraftment Restructure Change in Change Manufacturing susceptible of drug microbiome microbiome in host Practices (cGMP) baseline microbiome species composition function function Other Bile acids Tryptophan metabolites Short-chain fatty acids 4 Seres Therapeutics, Inc. © 2023

Strategic Priorities | Expanding Microbiome Therapeutic Leadership FDA approved on April 26, 2023; potential to transform management of recurrent • Successfully commercialize C. difficile infection TM VOWST , first-in-class orally administered microbiome Commercially available • therapeutic • Co-commercialization agreement with Nestlé Health Science • Ongoing SER-155 Phase 1b study in allo-HSCT* patients for prevention of bacterial infections and acute GvHD* Maximize opportunities in SER-155 Phase 1b Cohort 1 Day 100 data support continued development • Infection Protection Preclinical portfolio to prevent infection in medically compromised patients, including • cancer neutropenia, cirrhosis and solid organ transplant • Assessment of potential to utilize biomarker-based patient selection in Ulcerative Colitis Continue research to inform underway further development in ulcerative colitis and SER-155 GvHD results may further inform path forward in immune modulation • immune modulation * allo-HSCT: allogeneic hematopoietic stem cell transplant; GvHD: graft versus host disease 5 Seres Therapeutics, Inc. © 2023 SER-155 is an investigational microbiome therapeutic that has not been approved by any regulatory authority, including the U.S. Food and Drug Administration (FDA)

VOWST is the First Approval from Our Pipeline of Oral Microbiome Therapeutics INFECTION PROTECTION Preclinical Phase 1b Phase 2b Phase 3 FDA Approval Collaborators 1,2 VOWST Recurrent C. difficile (fecal microbiota spores, live-brpk) Bloodstream and antimicrobial-resistant bacterial infections & 3 Cohort 2 of Phase 1b proceeding SER-155 GvHD in allogeneic hematopoietic stem cell transplant patients Programs targeting antimicrobial-resistant infections in medically compromised groups (e.g., cancer neutropenia, solid organ transplant) IMMUNE MODULATION 1 4 SER-287 Ulcerative colitis Research and assessment ongoing to determine future ulcerative colitis 1 development plans 4 SER-301 Ulcerative colitis Modulate host immunity/inflammation to improve Oncology response and tolerability of cancer treatments Immunotherapy 1. Collaboration with Nestlé Health Science, announced Jan. 11, 2016, regarding C. difficile and IBD programs for markets outside of North America. 2. VOWST co-commercialization agreement for North America with Nestlé Health Science announced July 1, 2021 3. SER-155 preclinical work was supported in part by CARB-X 6 Seres Therapeutics, Inc. © 2023 4. No current clinical trials. Translational research activities are ongoing, informed by learnings from SER-287 Phase 2b and SER-301 Phase 1b study data, to evaluate the potential to utilize biomarker-based patient selection and stratification in future clinical development efforts

TM VOWST and Recurrent C. difficile Infection 7 Seres Therapeutics, Inc. © 2023

C. difficile Infections Are an Urgent Public Health Threat Spore-forming, toxin- Symptoms include colitis Acute onset of severe High probability of producing, gram-positive, and severe, watery symptoms leads to recurrence >20%, usually anaerobic bacteria diarrhea with up to 15 hospitalization for within 1-2 weeks after bowel movements a day many patients completion of antibiotic therapy CLOSTRIDIOIDES 40-50% DIFFICILE 20,000+ ~156K Risk of recurrence escalates Recurrent CDI cases CDI deaths per year once a patient has an initial THREAT LEVEL estimated for 2023 (U.S.) recurrence, which can trap URGENT patients in a vicious cycle (U.S.) 1. US CDC. Antibiotic Resistance Threats in the United States, 2019. US Department of Health and Human Services, CDC; 2019. doi:10.15620/cdc:82532 2. Feuerstadt P et al. J Med Econ. 2020;23(6):603-609. 3. Chilton CH et al. Clin Microbiol Infect. 2017;24(5):476-482. 4. Ofosu A. Ann Gastroenterol. 2016;29(2):147-154. 5. Cole SA, Stahl TJ. Clin Colon Rectal Surg. 2015;28(2):65-69. doi:10.1055/s-0035-1547333. 6. Wilcox MH et al. Open Forum Infect Dis. 2020;7(5):ofaa114. doi:10.1093/ofid/ofaa114 7. Centers for Disease Control and Prevention. Your risk of C. diff. Accessed January 28, 8 Seres Therapeutics, Inc. © 2023 2022. https://www.cdc.gov/cdiff/risk.html 8. Jiang ZD et al. Aliment Pharmacol Ther. 2017;45(7):899-908.9. McFarland LV et al. Am J Gastroenterol. 2002;97(7):1769-1775, https://www.fda.gov/news-events/press-announcements/fda-approves-first-fecal-microbiota-product.

VOWST Offers an Attractive Product Profile Highlights of Prescribing Information Broad product label covering adults with rCDI, including at Indication VOWST is indicated to prevent the recurrence of ✔ first recurrence statement Clostridioides difficile infection (CDI) in individuals 18 years of age and older following antibiotic treatment for recurrent CDI (rCDI) Approximately 88% recurrence-free ✔ at 8 weeks* Limitations of use VOWST is not indicated for the treatment of CDI Well-tolerated in Phase 3 clinical studies. The most ✔ common adverse reactions were mild to moderate in severity and transient in nature. Oral dosing - 4 capsules once daily for 3 consecutive days ✔ following antibiotic treatment and laxative No refrigeration requirements ✔ Full prescribing information available at vowst.com Note: Sustained clinical response % is calculated as 100% minus % with recurrence 9 * Compared to 60% in the placebo arm Feuerstadt P et al. N Engl J Med. 2022;386(3):220-229.

VOWST is Highly Anticipated by Healthcare Professionals TM HCP Intent to Prescribe VOWST Recurrent C. difficile infection is a highly “ debilitating and life-threatening disease, and 22% antibiotics alone do not address the underlying Definitely will cause of rCDI, dysbiosis of the gut microbiome. ~75% The approval of VOWST provides an important of surveyed HCPs new oral treatment option for this disease, and I definitely or probably am pleased to now be able offer this medicine 52% will prescribe to patients that have experienced a CDI Probably will TM VOWST recurrence. ” Dr. Carl Crawford, M.D. Assistant Professor of Clinical Medicine Division of Gastroenterology, Weill Cornell Medicine 25% Might or might not 1% Definitely or probably will not 10 Seres Therapeutics, Inc. © 2023 Source: GI and ID survey (n=300), 2021

HCP Enthusiasm for VOWST Driven by Desire to Prevent Recurrences and Limitations of Current Options Top 5 rCDI Treatment Goals Top 5 Unmet Needs % Ranked in Top 3 % Ranked in Top 3 Prevention of Preventing subsequent 59% 66% • Prevention of recurrences is recurrences recurrences seen as a top treatment goal for rCDI patients Prevention of Sustained efficacy / 48% 57% morbidity / mortality durability • Despite it being the top goal, physicians perceive standard Restoring 38% 40% More affordable Tx of care as lacking efficacy at patient QoL preventing recurrences Restore gut Symptom • As a result, preventing 35% 34% microbiome relief recurrences is also the biggest unmet need leading to Restoration of gut More rapidly address 25% 29% heightened appetite for a microbiome symptoms product like VOWST 11 Seres Therapeutics, Inc. © 2023 Source: Seres physician survey data (2022)

Co-commercializing VOWST in the United States with 50/50 profit sharing per July 2021 agreement, extending global strategic collaboration Combined Field Teams to Cover Highest Potential rCDI Prescribers Prioritize top volume and early adopting HCPs: Prioritize ~300 top HCOs: 20-person hospital team 150-person GI sales force • Includes ID engagement; ~1500 ID specialists see > 2 rCDI • GI sales force covers 85% of GI practices for current patients/year inline Nestle product, ZENPEP • Deployed Q1 ‘23; profiled top institutions • Average 10 years industry experience & 5 years in GI • Drove ZENPEP® acceleration over last 3 years 12 Seres Therapeutics, Inc. © 2023

Engaging with Key Commercial and Medicare Part D Plans to Initiate Broad Coverage Path to coverage for VOWST Payer mix Up to Launch + 12 months Launch + 18 months Payers utilize NTMBs* to limit Medicare coverage 37% Medicare demand begins 54% Commercial Launch + 12 months 6% Medicaid VOWST Medicaid coverage Launch begins 13 Seres Therapeutics, Inc. © 2023 * New To Market Block (NTMB) deny insurance coverage of a new therapy until it can be reviewed and covered by the health plan.

VOWST Delivers Compelling Value Proposition We Are Committed to Broad Patient Access Uniquely addresses #1 unmet need of preventing Addresses costly burden of rCDI: $43,000 cost / 1 recurrence, with robust efficacy, an established patient safety profile, and an orally administered regimen Innovative product; first and only FDA- Commitment to patient access and affordability approved orally administered microbiota-based therapeutic Providing financial and treatment support for eligible patients* *Subject to specific eligibility and financial criteria 14 Seres Therapeutics, Inc. © 2023 Sources: 1. Rodrigues et al Infect Control Hosp Epidemiol. 2017 Feb;38(2):196-202. ; inflation adjusted from $34K in 2016 dollars to 2023 dollars

Laying the Foundations to Ultimately Transform Standard of Care Initial Focus Expanded Focus • Increase HCP awareness and • Drive repeat use among higher- trial of an entirely new modality volume HCPs • Provide positive experience • Increase reach to lower-volume HCPs • Enhance hospital outflow • Optimize payer coverage with a • Engage payers to build coverage focus on commercial plans 15 Seres Therapeutics, Inc. © 2023

Well Positioned to Supply Commercial Demand at Launch and Beyond 10+ years of Seres technology & facility investment for anaerobic bacterial therapeutics Seres in-house GMP Manufacturing and Quality Control High-quality CMO support TM VOWST commercial supply + Bacthera collaboration provides redundancy and expands upon existing commercial supply capacity Joint venture between Chr. Hansen and Lonza with offices in Switzerland and Denmark Launch batches manufactured; anticipate Bacthera commercial drug production in 2024 for release in 2025, as the expected number of patients treated expands 16 Seres Therapeutics, Inc. © 2023 Note: Seres and Bacthera collaboration press release issued Nov. 10, 2021

SER-155 and Infection Protection Franchise 17 Seres Therapeutics, Inc. © 2023

Antimicrobial Resistant Infections - Urgent Public Health Threat Major burden to society Many high-risk patient populations Declared “one of the • Allogeneic HSCT recipients at risk for world’s most urgent bloodstream infections threats” • Additional patients with suppressed immune systems (e.g., transplant $20 billion excess recipients, cancer patients) direct healthcare costs • Patients with chronic diseases 35,000 deaths (e.g., cirrhosis) per year in US Limited innovation despite substantial and growing impact 18 Seres Therapeutics, Inc. © 2023

SER-155 Designed to Modulate Targets that Address Leading Causes of Mortality Following Allogeneic HSCT (allo-HSCT) Investigational 16-strain cultivated bacterial Specifically designed to reduce infections and consortium optimized using MbTx platform GvHD in allo-HSCT recipients Organ Second failure Malignancy 1% 7-9% Infection 17-21% Primary Causes of allo-HSCT disease mortality at 1 year** GVHD 46-60% • Consortium of unique, human commensal bacterial strains 19-23% • Cultivated and encapsulated for oral delivery • Strain selection based on broad pre-clinical screening for defined functions and insights from microbiome clinical data • Preclinical data show SER-155 leads to multi-log reductions of • Allo-HSCT recipients are medically vulnerable; Enterococcus (including VRE) and Enterobacteriaceae 50% 3 year mortality (including CRE) linked to GvHD in allo-HSCT patients* * Seres data shared in Jan 2022 Infection Protection Investor Event; VRE = vancomycin-resistant Enterococci; CRE = carbapenem-resistant Enterobacterales; VRE and CRE both included in US CDC Antibiotic Resistance Threats 19 Se Seres T res The herap rapeu eutics, tics, Inc. Inc. © © 20 2023 23 ** CIBMTR 2020

SER-155 May Represent a Novel Solution to Reduce GI Pathogen Abundance and Infection & GvHD in Allogeneic HSCT • Oral, cultivated consortium, designed to reduce abundance of pathogens linked to infections and GvHD in allogeneic HSCT recipients* Enrollment ongoing in • SER-155 Phase 1b study Cohort 1 SER-155 Phase 1b • SER-155 well-tolerated through 100 Days post HSCT Cohort 2, a randomized, double-blind, placebo- • SER-155 bacterial strain engraftment was as expected controlled study • GI pathogen domination was rare and transient in patients after SER-155 treatment compared to expected rates from prior cohort studies Expect Phase 1b Cohort 2 Topline Results in Mid-2024 *Note: SER-155 is an investigational therapeutic and has not been approved by any regulatory authority, including the US Food & Drug Administration 20 Se Seres T res The herap rapeu eutics, tics, Inc. Inc. © © 20 2023 23

ESKAPE Pathogen Domination was Rare and Transient in Cohort 1 ESKAPE pathogen domination* in SER-155 administered subjects observed at rates substantially lower than reference cohort SER-155 Cohort 1 Fig.1 Cumulative Domination Incidence • From HSCT Day 0-30, 11% of patients (1 subject, Fig.1 blue line) • From HSCT day 0-100, 22% of patients (2 subjects, Reference Cohort Incidence 64% not shown) (459 subjects) • All instances of pathogen domination were transient Reference Patient Cohort (MSKCC; Peled et al. 2020) • Day 0 through 30, 64% of patients (Fig.1 black line) Pathogen domination has been shown to be SER-155 Cohort-1 Incidence 11% associated with risk of blood stream infections (9 subjects) (Taur, CID 2012) and GvHD (Jenq Bio BMT 2015; Stein-Thoeringer Science 2019) * i.e., the families: Enterococcaceae, Enterobacteriaceae, Streptococcaceae & Staphylococcaceae HSCT Day 21 Se Seres T res The herap rapeu eutics, tics, Inc. Inc. © © 20 2023 23 Cumulative Incidence

SER-155 Potential Integration into Allogeneic HSCT Treatment Regimen Unique potential clinical and economic value for allogeneic HSCT patients Substantial impact for patients: Favorable safety profile based on almost 30,000 transplants / year across Cohort 1 data suggests appropriate for US and Europe use across HSCT population Avoids costs of post-transplant Double benefit of reducing infections and complications: $181K average additional GvHD, 2 of 3 leading causes of mortality costs for US patients with complications at 1 year Sources: CIBMTR 2020; Passweg et al Bone Marrow Transplantation 57 (2022) 742-752; Perales et al Biol Blood Marrow Transplant 23 (2017) 1788–1794; Broder, et al. “The Cost of Hematopoietic Stem-Cell Transplantation in the United States” Am Health and Drug Benefits 10 (2017) 366–374; 22 Se Seres T res The herap rapeu eutics, tics, Inc. Inc. © © 20 2023 23 https://data.cms.gov/provider-summary-by-type-of-service/medicare-inpatient-hospitals/medicare-inpatient-hospitals-by-geography-and-service/data/2019; Seres physician interviews

Seres’ Path Forward 23 Seres Therapeutics, Inc. © 2023

Maximizing the Opportunity in Infection Protection Broadly Target Antimicrobial Resistant • Broad preclinical Additional Opportunities Infections portfolio • Driving to an additional clinical development program in 2023 Autologous HSCT • Potentially 2+ Cancer Neutropenia Pre-clinical Portfolio additional programs Solid Organ Transplant within 3 years Cirrhosis SER-155 Active Clinical SER-155: Development BSI & GvHD in allogeneic HSCT recipients • Therapeutic adjacency to VOWST • Phase 1b study ongoing in cohort 2 Now Approved VOWST rCDI 24 Seres Therapeutics, Inc. © 2023

Well Positioned to Commercialize VOWST and Advance Infection Protection Franchise, Including SER-155 $125 million milestone 3/31/2023 cash balance: received following VOWST $106.5 million approval Secured up to $250 million debt facility; $110 million 3/31/2023 pro-forma cash balance: 1 funded at closing and 2 $282 million replaces existing debt facility Company continues to seek to drive operational efficiencies and opportunities to optimize its cost structure 1. $90 million of additional commitments (Tranche B and C) may be borrowed if certain conditions are satisfied, including net sales targets of VOWST, and an additional $50 million is available at Oaktree's discretion (Tranche D). Tranche B ($45 million) may be drawn by the Company until September 30, 2024, if net sales for the trailing 6 consecutive months are at least $35.0 million and at least 4.5% greater in the calendar quarter prior to the Applicable Funding Date (as defined in the Credit Facility) over the calendar quarter immediately preceding it. Tranche C ($45 million) may be drawn until September 30, 2025, if net sales for the trailing 12 consecutive months are at least $120 million and at least 4.5% greater in each of the two calendar quarters prior to the Applicable Funding Date relative, in each case, to the calendar quarter immediately preceding it. See recent SEC filings for additional information. 2. Includes $125 million VOWST approval milestone and net proceeds received at closing from Oaktree. 25 Seres Therapeutics, Inc. © 2023

Continued Microbiome Therapeutic Leadership, Anticipated Compelling Growth and Value Creation 2023 2025 TM • VOWST transforming standard of care for a TM VOWST approved; broad population of rCDI patients commercialization underway in rCDI • SER-155 in late-stage clinical development • 2+ additional Infection Protection candidates Advancing opportunities in in clinical development Infection Protection and • Extend industry-leading microbiome other therapeutic areas therapeutic platform 26 Seres Therapeutics, Inc. © 2023

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