Top Microbiome Therapeutics Companies Shaping the Future of Precision Medicine

The microbiome is increasingly becoming the newest frontier in life sciences with scientists mining for potential discoveries. Microbiome therapy includes probiotics, Fecal Microbiota Transplant (FMT), prebiotics, or engineered microbes to cure diseases, such as C. difficile infection, inflammatory bowel disease and metabolic disorders. The increase in research initiatives and rising number of gut infections along with enhanced microbiome sequencing capabilities is resulting in the positive growth of the microbiome therapeutics industry. The main aim of microbiome therapeutic products is to restore and maintain the normal balance and healthy function of organisms or microbiota in the gut. Researchers, investors and business owners are closely observing the development of microbiome therapeutics.

Fueled by these factors, Fortune Business Insights states that the market for microbiome therapeutics reached USD 288.8 million in 2025. It is anticipated to hit USD 4,023.1 million in 2034, with a CAGR of 34.90% during the forecast period.

Fortune Business Insights Reveals Top 9 Microbiome Therapeutics Companies Shaping the Future of Biotech Partnerships

1. Seres Therapeutics

Headquartered in the U.S., Seres Therapeutics is a clinical stage biotech-company, manufacturing new therapies comprised of live selected bacteria consortia. The company is also working to treat a wide range of diseases by modulating the function of the human microbiome.

In May 2021, Seres Therapeutics, Inc. developed a new breed of multifunctional bacterial consortia capable of having a functional relationship with host cells and tissues to cure various illnesses. The result of the SER-109 program was the 1st positive pivotal clinical results achieved from a targeted microbiome drug candidate. It also received the Orphan Drug Designation from the FDA. Additionally, it was designated as a breakthrough therapy and accepted by the FDA of Biologics License Application for ser-109 as an investigational microbiome therapeutic to treat recurrent c. difficile infections (CDI).

2. Finch Therapeutics Group, Inc.

Finch Therapeutics Group, Inc. is a clinical-stage microbiome therapeutics organization, which specializes in the production of orally administered biological drugs. Its headquarters is located in the U.S. The company’s portfolio consists of a variety of product strategies and therapeutic areas.

In January 2023, Finch Therapeutics focused on maximizing the potential of its intellectual property portfolio and other available sources. The company has pre-clinical microbiome products in development that will treat ulcerative colitis, Crohn’s disease, and autism spectrum disorder.

3. Ferring

Headquartered in Switzerland, Ferring is an innovative and research-focused biopharmaceutical group, specializing in reproductive health, maternal health, gastroenterology, and urology. Established in 1950, the company’s mission is to aid every woman conceive children and maintain healthy pregnancy through its high-quality services.

In December 2023, Ferring Pharmaceuticals and Zürich-based microbiome company, PharmaBiome, announced a research & development collaboration to drive forward new microbiome-based bio-therapeutics in the field of gastroenterology. The deal offered Ferring with exclusive rights to develop, manufacture, and commercialize next generation microbiome-based therapeutics within the field of gastroenterology.

4. MaaT Pharma

Headquartered in France, MaaT Pharma, a biotech company, that develops microbiome ecosystem therapies that aims to improve cancer patient outcomes.

In July 2023, MaaT Pharma joined the Microbiome Therapeutics Innovation Group (MTIG). The MTIG is comprised of several companies working together to develop and research FDA approved drug and product candidates from the microbiome.

5. Vedanta Biosciences, Inc.

Vedanta Biosciences, headquartered in the U.S., is a clinical-stage biopharmaceutical company, among the top 9 microbiome therapeutics companies, which aims to develop a new category of oral microbiome therapeutics based on defined bacterial consortia. Unlike traditional fecal microbiota transplants (FMT) that depend on donor stool, Vedanta’s therapies are manufactured from pure, clonal bacterial cell banks. 

6. Nestlé Health Science

Nestle Health Science, headquarters in Switzerland, is a well-recognized global leader in the area of nutritional science. The company also provides the latest advances in nutrition through their extensive research team and healthcare staff.

In July 2017, Nestlé Health Science in collaboration with Enterome partnered to form Microbiome Diagnostics Partners (MDP) to play a leading role in creation and commercialization of novel microbiome based diagnostics. This joint venture is an extension of Nestlé Health Science's first monetary contribution made in April 2016.

7. Evelo Biosciences

Evelo Biosciences, headquartered in the U.S., is a bio-technology company which is developing a platform for orally deliverable medicines. The company’s therapies are effective, safe, and affordable to the consumers across the world.

In April 2016, Evelo Biosciences and the University of Chicago collaborated into an exclusive worldwide license agreement to develop and commercialize a microbiome-based cancer immunotherapy. The cancer therapy, developed in the laboratories of Thomas Gajewski, professor of medicine and pathology at UChicago, employs select gut microbes to boost the immune system’s attack on cancer cells and improve the efficiency of anti-cancer drugs.

8. Enterome

Enterome, headquartered in France, is a clinical-stage biopharmaceutical company which is heavily focused on manufacturing immunomodulatory drugs for cancer treatment.

In June 2025, French microbiome biotech Enterome raised USD 19 million in Series E funding to progress its cancer and inflammatory bowel disease therapies to phase I trials in a few weeks. Enterome is developing cancer immunotherapies based on proteins produced by the human gut microbiome, a collection of microorganisms that live in our intestines. These proteins are called ‘OncoMimic’ proteins that mimic those given off by cancer cells that can trigger the immune system to target specific tumors.

9. Synlogic

A clinical stage biopharmaceutical company located in Cambridge, U.S., Synlogic is dedicated to developing synthetic biotic drugs. They are used as live therapies for a variety of immunological and metabolic diseases by consuming or altering disease-causing substances (metabolites) found in the Gastrointestinal (GI) tract. They are specifically designed not to be absorbed systemically, so they can effectuate healing primarily by solely treating the underlying problem in the gut; thus, the medications provide local and acute healing benefits.

Will the Advancements in Microbiome Medicine Drive the Next Breakthrough in Treatments?

The future of microbiome medicine is moving towards smart treatments tailored for the body. Microbiome medicine is shifting away from standard treatments based primarily on the ingestion of probiotics to more sophisticated "design" medical treatments tailored specifically to an individual. As researchers utilize artificial intelligence, they are able to identify and map out the trillions of bacterial organisms in the gastrointestinal tract (GI tract), thereby allowing for the identification of the specific medication required for diseases such as cancer and diabetes or mental illnesses. The idea is to move beyond solely using the microorganisms found in the donated feces of healthy human donors. To that end, top 9 microbiome therapeutics companies are developing a new form of bacteria called "designer bacteria" that will act like mini factories inside the body, releasing the correct amount of medication only when it’s needed. Although this field is currently growing rapidly, the ultimate goal over the next 10 years will be to ensure that these 'living drugs' are safe, consistent and can survive in a person's unique internal environment.