The 11 most advanced microbiome players aiming for the gut

After decades of research, gut microbiome therapies are beginning to reach the market. Here are 11 of the companies harnessing the power of the microbiome to develop treatments derived from the gut. 

Over the years, gastrointestinal research has increasingly focused on the role of the microbe communities residing in our gut, known collectively as the gut microbiome.  

One major advance in the last decade was the growing use of so-called fecal microbiota transplants to treat gut infections that are resistant to antibiotics. These transplants typically involve getting a stool sample from a healthy donor, screening it for harmful pathogens, blending it, and then giving it to the patient. However, it is tough to ensure consistent quality and safety when producing the treatments for patients. 

Another generation of gut microbiome therapies is now in the pipeline. Though many involve sampling gut microbes from healthy donors, these therapies differ from traditional fecal microbiota transplants because the manufacturer implements a more controlled and centralized process to ensure consistency in the bacterial therapeutic.  

There are now many companies working on taking these treatments across the regulatory finish line.  

BiomeBank 

• Headquarters: Adelaide, Australia 
• Founded: 2018 
• Lead candidate: BB265 

BiomeBank is a clinical-stage biotech developing microbiome therapeutics that restore gut microbial ecology. The company combines a first-generation donor-derived product with a second-generation, co-cultured approach built on its CONSORTIOME platform.  

Its approved donor-derived therapy Biomictra is authorized by Australia’s Therapeutic Goods Administration (TGA) for the prevention of recurrent Clostridioides difficile infection, one of the first regulated approvals for a donor-derived microbiome product globally. The firm has since expanded GMP (good manufacturing practice) manufacturing capacity to support the supply and development of next-gen therapies. 

Pipeline-wise, BB265 targets ulcerative colitis using a designed, co-cultured microbial community. The platform aims to reproduce over 90% of the gene families of a healthy gut community, enabling emergent functions that single strains can’t deliver. The company has also discussed reformulating products as oral, freeze-dried capsules to ease administration. 

Eligo Bioscience 

• Headquarters: Paris, France 
• Founded: 2014 
• Lead candidate: EB005 

Eligo Bioscience is a biotech company that takes a novel route to the microbiome: rather than simply adding or transplanting microbes, it develops technologies to edit the genes of bacteria within the microbiome. Its proprietary “Eligobiotics” platform uses phage‐derived delivery systems carrying CRISPR or base‐editor payloads to specifically target problematic bacterial strains or genes in the gut or skin microbiome. It’s more of a genetic medicine company rather than a microbiome therapeutic company, but its approach is worth mentioning. 

In a 2024 study that Eligo published in Nature, it achieved near-100% base-editing efficiency on target gut bacteria in vivo (in mice), modifying antibiotic-resistance or virulence genes without broadly disrupting the microbial ecosystem. 

The company completed $30 million series B in late 2023 to drive its microbiome gene-editing pipeline forward. In May 2025, Eligo was awarded $5 million to advance its gene‐editing platform in immuno-dermatology. 

Enterome 

• Headquarters: Paris, France 
• Founded: 2012 
• Lead candidate: EO2463 

Enterome uses a proprietary “Mimicry” platform built on the gut microbiome to develop immunomodulatory drugs primarily in oncology, but also targeting gut-immune disorders. 

Through its Mimicry approach, Enterome identifies bacterial proteins from its gut-microbiome-derived database that mimic human tumor antigens, OncoMimics, or human cytokines/hormones, EndoMimics. The goal is to activate or modulate immune responses by leveraging pre-existing gut-microbiome-trained immunity, rather than relying solely on traditional biologics. For example, EO2463 comprises four synthetic peptides derived from gut-bacterial sequences that mimic B-cell lineage markers plus a helper peptide; it’s being tested in a phase 1/2 trial in indolent non-Hodgkin lymphoma. 

Enterome recently secured Fast Track designation from the U.S. Food & Drug Administration (FDA) for EO2463 in follicular lymphoma and reported encouraging interim phase 2 data at ICML 2025.  

EnteroBiotix 

• Headquarters: Glasgow, Scotland 
• Founded: 2017  
• Lead candidate: EBX-102-02 

EnteroBiotix is developing orally administered gut-microbiome therapeutics based on “full-spectrum” microbial ecosystems rather than single-strain or narrow consortia. Its proprietary platform emphasizes high-diversity donor-derived microbial communities. 

Its lead product, EBX-102-02, was tested in a phase 2a trial involving 122 adult irritable bowel syndrome (IBS)-C patients. The company reported clinically meaningful improvements in IBS symptom severity, stool consistency, abdominal pain, and bowel-movement frequency, with engraftment of the product microbiota into patient guts; the data were selected for a late-breaker oral session at DDW 2025. Simultaneously, earlier phase 1b data in liver cirrhosis showed translational biomarker shifts and good safety, supporting expansion into hepatic indications. 

Exeliom Biosciences 

• Headquarters: Paris, France 
• Founded: 2016 
• Lead candidate: EXL01 

Exeliom Biosciences is a clinical-stage company built around one of the gut’s most important commensal bacteria, Faecalibacterium prausnitzii, a species strongly associated with anti-inflammatory immune effects and epithelial barrier repair. Unlike companies developing complex microbial consortia, Exeliom focuses on a single-strain, enabling defined pharmacology and simpler manufacturing.  

Its lead candidate, EXL01, is an anaerobically manufactured, freeze-dried formulation of F. prausnitzii designed to restore immune balance and enhance responses to checkpoint inhibitors. The therapy is currently being tested in multiple phase 2 studies in combination with PD-1/PD-L1 immunotherapy in advanced solid tumours, as well as in an early trial for inflammatory bowel disease.  

In October 2025, the French biotech raised an additional €2.85 million ($3.3 million), bringing its total funding to about €30 million ($35 million).  

Infant Bacterial Therapeutics (IBT) 

• Headquarters: Stockholm, Sweden 
• Founded: 2013 
• Lead candidate: IBP‑9414 

IBT is focused on developing therapies for the most vulnerable neonatal gut disorders. Its flagship product, IBP-9414, leverages a strain naturally found in human breast milk to support gut maturation and reduce the risk of necrotizing enterocolitis (NEC), a severe, often fatal inflammation that causes portions of the intestinal tissue in premature infants to die. 

In its large phase 3 program involving 2,158 premature infants in 10 countries, IBT reported that while the trial did not meet its dual primary endpoints of NEC incidence reduction and improved time to sustained full enteral feeding (SFT), it did achieve a statistically significant 27% reduction in all-cause mortality in the treated group.  

And in March 2025, the FDA granted IBP-9414 Breakthrough Therapy Designation for its potential to reduce gastrointestinal-related mortality in this high-risk population.  

MaaT Pharma 

• Headquarters: Lyon, France 
• Founded: 2014 
• Lead candidate: Xervyteg (MaaT013) 

MaaT Pharma is a late-stage microbiome therapeutics company focused on oncology and immune modulation. Its “full-ecosystem” approach uses high-diversity, standardized microbial consortia to restore gut-immune homeostasis in patients undergoing hematologic cancer treatment. 

Xervyteg (MaaT013), MaaT Pharma’s lead product, recently delivered positive results in its pivotal phase 3 trial for patients with steroid-resistant gastrointestinal graft-versus-host disease, helping more than half of treated patients achieve a clinical response and showing encouraging one-year survival rates. 

MaaT also signed an exclusive European commercialization partnership with Clinigen for Xervyteg and continues advancing MaaT033 and MaaT034. 

Metagen Therapeutics 

• Headquarters: Tsuruoka, Japan  
• Founded: 2020 
• Lead focus: Oral FMT-style drug candidate for ulcerative colitis 

Metagen Therapeutics is a biotech company building a gut-microbiome drug platform from the ground up in Japan. Its approach is to transform what has historically been a donor stool and fecal microbiota transplant (FMT) niche into an orally delivered, regulated therapeutic for gut disorders such as ulcerative colitis, while also constructing the full ecosystem of stool donation, manufacturing, and donor screening locally. 

In June 2025, Metagen announced that its oral FMT drug program for ulcerative colitis was selected under a Japanese government “Drug Discovery Venture Ecosystem” support scheme. The month before, it opened Japan’s first stool-donation facility to collect screened donor material, as part of the pipeline manufacturing supply-chain build-out.  

Microbiotica 

• Headquarters: Cambridge, U.K. 
• Founded: 2016  
• Lead candidate: MB097 

Microbiotica is developing precision live biotherapeutic products (LBPs) based on defined bacterial consortia for gut-microbiome-driven therapy. Its proprietary platform leverages extensive gut microbiome genomics, machine-learning, and culturing capabilities to identify bacterial signatures linked to treatment outcomes, then manufactures defined multi-strain products for oral delivery. 

Its lead program, MB097, is designed to boost the effectiveness of immune checkpoint inhibitors in patients with advanced melanoma who have not responded well to prior immunotherapy. The six- to nine-strain consortium is delivered orally once-daily. The company also has MB310 in parallel for ulcerative colitis. 

In late 2024, Microbiotica announced dosing of the first patient in its phase 1b trial of MB097 in melanoma. In August 2025, it reported that recruitment is complete for its phase 1b trial of MB310 in ulcerative colitis. 

MRM Health 

• Headquarters: Ghent, Belgium 
• Founded: 2020  
• Lead candidate: MH002 

MRM Health is a clinical-stage biotech company developing microbiome-based therapies for chronic inflammatory diseases. Its proprietary CORAL platform designs and manufactures live consortia of commensal bacterial strains, optimized for immune-modulation, mucosal healing, and scalability. 

The lead program MH002 comprises six optimized commensal strains selected for their butyrate-producing and barrier-restoring properties; early clinical data in patients with mild-to-moderate ulcerative colitis and in pouchitis demonstrated good safety and initial signals of efficacy. The recent €55 million ($64 million) series B funding round in September 2025 is expected to help advance MH002 into phase 2b, and to push two additional microbial consortia programs toward investigational new drug (IND) stage. 

Vedanta Biosciences 

• Headquarters: Cambridge, Massachusetts, U.S. 
• Founded: 2010 
• Lead candidate: VE303 

Vedanta Biosciences develops defined bacterial consortia, oral live biotherapeutic products composed of selected, cultured strains, to restore a balanced gut microbiome. Unlike donor-derived products, Vedanta’s therapies are built from characterized species grown from pure cultures, enabling standardized manufacturing and reproducible dosing. 

Its lead candidate, VE303, consists of eight human commensal bacterial strains designed to rebuild gut microbial diversity after antibiotic treatment. In a phase 2 clinical trial, VE303 achieved an 80% reduction in C. difficile recurrence risk compared with placebo, meeting its primary endpoint. Based on these results, the company is preparing a pivotal phase 3 trial. 

Vedanta raised $106 million in 2023 to advance VE303 and its broader pipeline, including VE707, targeting antibiotic-resistant infections, and VE800, an immuno-oncology program in combination with checkpoint inhibitors. 

Microbiome drugs becoming mainstream? 

The approval of donor-derived microbiome therapies such as Rebyota from Rebiotix and Vowst brought by Seres Therapeutics has proven that live bacterial treatments can meet regulatory standards. The next challenge lies in transforming those early proofs of concept into scalable, precisely defined medicines. 

Companies like Vedanta Biosciences and MRM Health are leading the charge toward standardized, culture-based consortia, while innovators such as Eligo Bioscience and Promakhos Therapeutics are exploring how to modulate or even reprogram the microbiome at the molecular level. 

Meanwhile, infrastructure-driven efforts in regions like Japan (Metagen Therapeutics) and Australia (BiomeBank) show how governments are starting to support this emerging therapeutic class with dedicated manufacturing and regulatory frameworks.