TechBio and Microbiome (I)

MetaphysicalCells: A newsletter about Science, Technology and AI Drug Discovery

Feb 27, 2025

📌 In 2021, microbiome companies collectively raised $1.6B in capital in just 2 years, mostly from VC funds: 5 Best Microbiome Companies (February 2025).

📌 The Top 🔝 🎩 5 Microbiome Biology Companies List has been created to highlight companies following the criteria below:

Publicly traded.
Actively exclusively or mostly on the microbiome, which excludes large companies active in the field but without a central focus on the topic.
Have a good track record of innovation in the field.
Good successful product development track record, either already commercialized/licensed or supported by reputable partners.
Reasonable expectations are that it could commercialize a product from its current R&D efforts.

1️⃣ *Finch Therapeutics Group, Inc. (FNCH +0.32%), 2️⃣ Synlogic, Inc. (SYBX -4.9%), 3️⃣ Maat Pharma, 4️⃣ **Evelo Biosciences, Inc. (EVLO +0%) and 5️⃣ Seres Therapeutics, Inc. (MCRB -1%)

*In 2024 Finch Announces Delisting from Nasdaq and SEC Deregistration

**In 2023 Flagship-backed microbiome biotech Evelo to shut down.

TechBio and Microbiome (I)

🥁 Axial Biotherapeutics Inc

Axial Biotherapeutics (Boston, 2016) is a biopharmaceutical company harnessing the link between the human gut microbiome and Central Nervous System (CNS) to develop a new class of therapeutics to improve the quality of life for people with CNS diseases and disorders, leveraging its Microbial Inspired Therapeutics® Discovery Platform.

Axial’s lead product candidate, AB-2004, is a gut-restricted molecular therapy being developed as a treatment for irritability associated with autism. The company has shown that bacterial metabolites produced in the gut can enter the bloodstream and reach the brain where they impact development of certain brain cells in regions of the brain associated with emotional control and behavior.

AB-2004 has the unique mechanism of action of selectively adsorbing these metabolites in the gut before they enter the bloodstream and reach the brain. In a Phase 1b/2a clinical trial in adolescents with autism, AB-2004 was safe and well-tolerated and exhibited no drug-related serious adverse events (ACTRN12618001956291). Based on this strong body of evidence, Axial undertook and recently completed enrollment in a global Phase 2b randomized placebo-controlled clinical study to further evaluate AB-2004 as a potential treatment for irritability associated with autism.

On September 26, 2023, Axial Therapeutics Announced Completion of Enrollment in Global Phase 2b Clinical Trial for AB-2004 for Irritability Associated with Autism. The TAPESTRY Autism Study is a Phase 2b clinical trial of Axial’s lead product candidate AB-2004, and the global, randomized clinical trial enrolled 156 children and adolescents with autism.

Axial’s pipeline also includes AX-5006, a gut-selective, small molecule therapy aimed at slowing disease progression and improving the quality of life of people with Parkinson’s disease (PD). In preclinical research, Axial has established that certain gut bacteria, specifically through the production of bacterial amyloids, contribute to gastrointestinal symptoms, motor symptoms, and brain pathology in PD. AX-5006 is designed to reduce bacterial amyloid aggregation in the gut, thereby alleviating symptoms and attenuating disease progression. Being gut-targeted, it is anticipated to have a favorable safety profile.

🥁 BiomeSense Inc

Biomesense (Chicago, 2018) is leveraging the power of big data and AI to unlock microbiome precision medicine. BiomeSense is developing the first integrated hardware, software and data platform to massively scale microbiome data collection and analysis during clinical research. Their groundbreaking GutLab and Al-driven MetaBiome platform generates and analyzes unprecedented volumes of dense longitudinal microbiome data at a fraction of the cost. This data-rich approach unlocks insights that were previously unattainable, paving the way for personalized medicine that is more precise and effective.

On August 26, 2024, BiomeSense decided to Test Microbiome GutLab Technology with Pendulum. In particular, a new study will test BiomeSense’s at-home gut microbiome monitoring technology in a collaboration with probiotic developer Pendulum Therapeutics (developing targeted formulations of natural bacterial strains to rebalance the microbiome which restores and improves one’s health). BiomeSense’s GutLab technology will allow regular gut microbiome monitoring in the participants’ homes, something that could allow a precision medicine approach to microbiome monitoring and treatment in the future, if successful, on a large scale. The study will specifically look at levels of Akkermansia muciniphila, a bacterial 🦠 species thought to play a key role in gut health. People with lower-than-normal levels of this bacteria in their gut have higher than average rates of obesity, diabetes, and inflammation, as well as higher gut permeability ↔️, which can lead to health problems.

On May 18, 2023, BiomeSense Closed 🔒 Oversubscribed $3 Million Funding Round. More specifically, BiomeSense, the biotech company offering the novel “smart bathroom” hardware technology and advanced bioinformatics, announced the close of its oversubscribed $3M funding round, led by Bluestein Ventures. The financing included new investor Harvest Ridge Capital along with participation from existing investors SOSV and Seerave Foundation.

🥁 Folium Science, Folium Food Science Limited

British startup Folium Science (2016) offers Guided Biotics, a proprietary technology that uses biotics to control the microbiome in soils, plants and animals. Highly specific biotics, based on clustered regularly interspaced short palindromic repeats (CRISPR)-associated technology, identify and target unique DNA sequences present in the targeted pathogenic and spoilage bacteria. The startup is currently developing poultry feed additives targeting all serotypes of salmonella.

On July 9, 2024, FOLIUM Science was awarded a grant 🏆 through Department for Environment, Food and Rural Affairs Farming Innovation Programme (FIP), delivered by Innovate UK (Folium Science using Guided Biotics® to reduce Campylobacter in farming systems for sustainable agriculture). This will allow FOLIUM Science to continue to showcase the utility of its Guided Biotics® technology to sustainably address major challenges within farming practices and to boost environmental resilience.

On December 10, 2024, FOLIUM Science announced that the innovative component for its new product, BiomElix® One, has been approved by Brazil’s Ministry of Agriculture (MAPA) for use as an animal feed additive and included in their Positive List of Feed Ingredients. This approval comes after extensive review of efficacy data in poultry and detailed evaluation by Brazilian authorities (Innovative feed ingredient harnessing CRISPR in its natural microbiome setting gains approval). BiomElix® One was developed using FOLIUM Science’s proprietary CRISPR-Cas based technology platform Guided Biotics® and utilizes natural biological systems to modulate the microbiome, improving productivity by removing unwanted microbes and bacteria, while preserving the beneficial ones, resulting in a healthier animal gut.

🥁 REM Analytics, REM Analytics SA

Swiss startup REM Analytics (2017) provides a complete development service from proof of concept to production-ready prototype (ATGC), and they develop new microbiome-based therapeutics for different health conditions, including new personalized probiotics, cosmetics containing live bacteria, and prebiotics nourishing the skin.

🥁 Vedanta Biosciences Inc

Founded in 2010, Vedanta spun out of Cambridge, Massachusetts, is an affiliate of PureTech Health, a company traded on the London Stock Exchange that focuses on developing therapies caused by dysfunctions in the gut-brain axis. Vedanta isolates specific bacterial strains that have a specific biological effect on the microbiome that would restore balance to this internal ecosystem. Their proven proprietary product engine interrogates human interventional Fecal Microbiota Transplantation (FMT) data to identify bacteria that correlate with clinical response. They evaluate the role of microbiome in driving desired phenotype by screening one of the world’s largest microbiome strain libraries in proprietary assays to select strains with desired pharmacology. They assemble and optimize customized consortia using computational tools, co-culture systems, and animal models. They manufacture CGMP-grade drug supplies from clonal cell banks at in-house, state-of-the-art facilities. To conclude, they test defined consortia in humans to evaluate engraftment, safety, & efficacy.

The company has about a dozen patents related to its bacterial-based therapies. Its leading candidate is VE303 (is a live biotherapeutic product containing 8 clonal human commensal bacterial strains manufactured under GMP conditions), is orally-administered and consists of live bacteria designed to restore gut balance and provide resistance against gut pathogens, including a type of bacteria called Clostridium difficile, that can cause serious inflammation of the colon, killing about 15,000 people per year. Right now, the best treatment for C. diff is a fecal transplant.

On January 23, 2025, Vedanta Biosciences announced the publication of additional results from the Phase 2 CONSORTIUM study for its lead candidate, VE303, which is being evaluated for prevention of recurrent Clostridioides difficile infection (rCDI) (Vedanta Biosciences Publishes Additional Phase 2 VE303 Results in Nature Medicine). The new 🆕 analyses published in Nature Medicine can be viewed here: Multi-omic profiling a defined bacterial consortium for treatment of recurrent Clostridioides difficile infection.

The initial clinical results from Vedanta’s successful Phase 2 CONSORTIUM study, published in the Journal of the American Medical Association (JAMA), demonstrated that the higher dose of VE303 studied was well tolerated and reduced the odds of CDI recurrence by more than 80% compared with placebo. Moreover, VE303 rapidly and robustly colonized the gut in a dose-dependent manner. This colonization predicted greater recurrence-free probability, establishing a direct connection between exposure and clinical response.

Vedanta is currently enrolling participants into a Phase 3 study of VE303 for patients with recurrent Clostridioides difficile infection (rCDI) (RESTORATiVE303 is a double-blind, placebo-controlled, Phase 3 study).

Additionally, Vedata is developing a second candidate, VE202, a wholly-owned, orally-administered defined bacterial consortium candidate consisting of 16 strains of live commensal bacteria 🧫 🦠 for the treatment of IBD. So far, VE202 was well tolerated in a completed Phase 1 study and observed to be non-immunosuppressive. Adverse events were generally mild, gastrointestinal in nature, and transient; a very limited number of adverse events, none of which were serious, were related to VE202. They are currently conducting COLLECTiVE202, a randomized, double-blind, placebo-controlled, multinational Phase 2 study of VE202 in individuals with mild-to-moderate UC. The FDA has granted VE202 Fast Track designation for the treatment of adults with UC (Vedanta is currently enrolling participants into a Phase 2 study of VE202 for patients with IBD).

Finally, Vedata is developing a third candidate, VE707, that is their preclinical candidate for the prevention of Gram-negative infections, including those caused by AMR strains, that affect a wide range of vulnerable populations in areas such as oncology, urology, transplantation, and critical care (VE707 for prevention of Gram-negative antimicrobial-resistant (AMR) infections). VE707 is designed to be administered orally and consists of a defined consortium of commensal bacteria designed to decolonize Gram-negative Enterobacteriaceae, including carbapenem-resistant and extended- spectrum beta-lactamase-producing Klebsiella pneumoniae (Kpn) and Escherichia coli (Eco). Vedata believes that among the populations that could potentially benefit from VE707 are patients at high risk for developing life-threatening infections, including those in an intensive care unit, afflicted with blood cancers, with frequent infections such as recurring urinary tract infection (rUTI), and who have received a solid organ transplant or a hematopoietic stem cell transplant, among others. This program is being advanced with up to $16.6M of grant funding from CARB-X.

🥁 Microbiota Limited

Microbiotica (UK, 2016) is a leading, clinical stage biopharmaceutical company specializing in the development of precision live biotherapeutic products (LBPs) with lead products in immuno-oncology and inflammatory bowel 🧻 disease. Microbiotica’s platform includes the world’s leading Reference Genome Database and Culture Collection of gut bacteria, and an unrivalled capability to culture and characterize all gut bacteria from patients at scale. This is complemented by a suite of bioinformatic and ML tools that enable the identification of previously undetectable gut bacterial signatures linked to patient phenotype. The company also has capabilities to develop and take such products to the clinic.

On February 21, 2025, Microbiotica presented new data on the mechanism of action of MB310, a product in development as a treatment for ulcerative colitis (UC) 🚽, at the Keystone Symposia ‘Human Microbiome: Diversity, Selection and Adaptation’ held February 18-21 in Banff, Canada and at the European Crohn’s and Colitis Organisation (ECCO) meeting held February 19-22 in Berlin (Microbiotica unveiled data on the mechanism of action of MB310, a clinical-stage drug candidate in development for the treatment of ulcerative colitis). In particular 🔎

MB310 has been developed as an oral capsule, dosed once daily, containing a defined consortium of eight live gut commensal bacterial strains.
MB310 acts via at least three independent mechanisms that are central to the pathology of UC: promoting the healing of the damaged gut epithelial barrier, regulating the balance of cytokines that are inflammatory (TNF) and immune-modulatory (IL-10); and inducing a regulatory T-cell response.
Phase 1b data (NCT06582264; 2023-507376-50) anticipated in 2025.
On November 13, 2024, Microbiotica Announced First Patient Dosed in its Phase 1b Trial (COMPOSER-1) of MB310, a Precision Microbiome Medicine, in Ulcerative Colitis Patients.

Back 🔙 on October 7, 2024, Microbiotica announced that the first patient has been dosed in its advanced melanoma (MELODY-1) trial of MB097. This international trial is due to recruit up to 40 patients at clinical centres in the UK, France, Italy and Spain. Initial data readouts are expected by the end of 2025 (Microbiotica Announces First Patient Dosed in its International Phase 1b Trial, MELODY-1 of MB097 Precision Microbiome Co-Therapy in Advanced Melanoma).

MB097 is a once daily, orally administered LBP consisting of a defined consortium of nine strains of commensal bacteria designed to enhance the efficacy of immune checkpoint inhibitors (ICIs). The MELODY-1 study (NCT06540391) will investigate the safety, tolerability, and initial signals of efficacy of MB097 in advanced (metastatic) melanoma, in combination with KEYTRUDA^® (pembrolizumab), MSD’s (Merck & Co., Inc., Rahway, NJ, USA) anti-PD-1 therapy, in patients with cutaneous melanoma who have failed to respond to immunotherapies.

🥁 Seres Therapeutics Inc

Seres Therapeutics (2010) is a microbiome therapeutics platform company operating in the US developing biological drugs which are referred as ecobiotic microbiome therapeutics designed to restore health ⚖️ by repairing the function of a dysbiotic microbiome and treat dysbiosis in the colonic microbiome. Over the past decade, Seres has pioneered the translation of microbiome insights into an entirely new class of potential new medicines. This includes the development and commercialization of the first-ever FDA-approved oral live biotherapeutic, VOWST™, which was sold to Nestlé Health Science in September 2024 (namely, SER-155 that is Seres' first commercialized product, having received FDA approval in April 2023 to prevent the recurrence of C. difficile infection in adults). On January 16, 2025, Seres Therapeutics Announced Receipt of Expected $50 Million Installment Payment Related to VOWST Sale.

Moreover, the company’s product SER-109 (a consortium of purified bacterial spores of multiple Firmicute species, manufactured by fractionating targeted bacteria from stool of healthy human donors, with further steps to inactivate and remove potential pathogens) is designed to prevent further recurrences of Clostridium difficile infection (CDI), a debilitating infection of the colon.

More specifically, on November 10, 2021 Bacthera, a specialized contract development and manufacturing organization, and Seres Therapeutics announced a collaboration to manufacture SER-109 (Bacthera and Seres Therapeutics Collaborate for Commercial Manufacturing of SER-109, a Potential Treatment Against Recurrent C. difficile Infection). Under the terms of the agreement, Bacthera established a dedicated facility for commercial manufacturing in its new Microbiome Center of Excellence, a manufacturing site dedicated to the production of LBPs located on Lonza’s Ibex^® campus in Visp, Switzerland.

Additionally ➕ the company is developing:

SER-301: an investigational, oral, rationally-designed, fermented microbiome therapeutic (multiple bacterial strains) for the treatment of mild-to-moderate ulcerative colitis (UC). Seres partnered on IBD/SER-301 program with CCF (Crohn’s and Colitis Foundation) which is a non-profit, volunteer-fueled organization dedicated to finding cures for Crohn’s disease and ulcerative colitis 🧻🚽 and improving the quality of life of children and adults affected by these diseases.
SER-147 for chronic liver disease.
And SER-155 Allo-HSCT. On January 09, 2025, Seres Therapeutics Announced New Translational Biomarker Results from SER-155 Phase 1b Clinical Study and Provides Corporate Updates. New SER-155 Phase 1b study biomarker data in allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients demonstrated that SER-155 promoted epithelial barrier integrity and decreased systemic inflammatory biomarkers compared to placebo; and data supported the broader potential of Seres’ live biotherapeutics to target inflammatory and immune diseases.

To conclude, in recent transactions disclosed by Seres Therapeutics, Inc (NASDAQ:MCRB), a $141M market cap biotech company currently trading near its 52-week low, Lisa von Moltke, the Executive Vice President and Chief Medical Officer, sold shares of the company (Seres Therapeutics executive sells shares worth $3,579). According to a Form 4 filing with the Securities and Exchange Commission, von Moltke sold 4,416 shares on February 18, 2025, at a weighted average price of $0.8105 per share, totaling approximately $3,579.

For more: TechBio and Microbiome (II).