The six most advanced microbiome players aiming for the gut

Image/Elena Resko
Microbiome bacteria health

This article was originally published in July 2022 and has since been updated by Willow Shah-Neville, on May 15, 2023.

After decades of research, gut microbiome therapies are beginning to reach the market. Here are six 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 reaching the market. 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 to the regulatory finish line. With the help of experts in the field, we’ve listed six of the front-running companies that are developing microbiome-based therapies.

Table of contents

    Rebiotix Inc.

    Headquarters: Roseville, Minnesota, U.S.

    Rebiotix was acquired by Swiss company Ferring Pharmaceuticals in 2018 and has developed a treatment for infections by Clostridium difficile, a type of bacteria that is commonly found in the healthy gut microbiome. When someone takes antibiotics, this can change the balance of microbes in the gut and lead to life-threatening C. diff infections (CDI). Even if they are cleared, the infections can return multiple times due to the imbalance in the gut flora. 

    Rebiotix’s therapy – Rebyota – was the first fecal microbiota product to be approved by the U.S. Food and Drug Administration (FDA), in November 2022. It is designed to prevent recurrent CDI by delivering a cocktail of gut microbiota to return the gut microbiome to a healthy state. The treatment involves taking stool from healthy donors, industrially processing it and rectally administering it to patients with recurrent CDI.

    In a statistical analysis that took into account two efficacy studies, the overall estimated rate of success in preventing recurrent CDI within a time frame of eight weeks was significantly higher in the group that received a dose of Rebyota (70.6%) than in the group that only received a dose of placebo (57.5%).

    Infant Bacterial Therapeutics AB

    Headquarters: Stockholm, Sweden

    Known as IBT for short, Infant Bacterial Therapeutics aims to help infants with necrotizing enterocolitis. This serious infection often occurs in premature babies and can result in the gut getting inflamed and breaking down, allowing bacteria to leak into the rest of the body.

    IBT’s lead candidate therapy consists of a type of bacteria called Lactobacillus reuteri, which is naturally present in breast milk and can improve gut health and reduce inflammation. The medicine is being tested in a phase 3 trial with an expected end date of December 2023.

    Additionally, IBT is developing three other new candidates, including a gut microbiome therapeutic to improve the care of gastroschisis: a rare, life-threatening and debilitating birth abnormality where a baby is born with its intestines outside of the body. Once surgery repairs the abnormality, IBT plans to deliver an undisclosed bacterial strain to improve the recovery of the gut.

    MaaT Pharma SA

    Headquarters: Lyon, France

    MaaT Pharma is a front-running microbiome company aiming to tackle graft-versus-host-disease (GvHD). This condition occurs when patients with cancer receive a bone marrow transplant and their grafted immune system starts to attack healthy tissue including the gut.

    MaaT Pharma’s most advanced therapy is in a phase 3 trial to treat patients with acute graft-versus-host-disease with gastrointestinal involvement (GI-aGvHD) that can’t be controlled with current treatments such as steroids. The candidate consists of an enema of stool bacteria taken from healthy donors and industrially screened and processed. The bacteria are designed to calm inflammation in the gut and blunt further immune attacks.

    MaaT Pharma’s lead drug is also in an investigator-sponsored phase 2a trial to see if the gut microbiome therapy can enhance the response of patients with melanoma to immune checkpoint inhibitor drugs. Another of the company’s programs include an oral donor-derived microbiome therapeutic and a custom-designed bacterial therapy for improving the response of patients with cancer to checkpoint inhibitors.

    Seres Therapeutics Inc.

    Headquarters: Cambridge, Massachusetts, U.S.

    Seres Therapeutics is another microbiome heavyweight company in the treatment of recurrent CDI. The company’s lead therapy, Vowst – co-developed with Nestlé Health Sciences – was recently approved by the FDA in April 2023, and is an oral capsule containing a type of beneficial gut bacteria called Firmicutes. By adding more of these bacteria to the patient’s gut, the company aims to make it harder for C. diff to build up and break out.

    According to a phase 3 trial, Vowst prevented CDI from recurring in 88% of patients for eight weeks, while just 60% of patients in the placebo group were free of recurrences.

    Seres’ second candidate is currently in a phase 1b trial for the treatment of GvHD in patients receiving a bone marrow transplant. The therapy is made up of a selection of gut bacteria designed to prevent the establishment of antibiotic-resistant bacteria in the gut and dampen harmful immune activity.

    Seres’ clinical program in treating the inflammatory condition ulcerative colitis hit a snag in 2021 when one of its candidates failed a phase 2b trial. The microbiome company is now researching on how to proceed with the program.


    Headquarters: Paris, France

    Enterome uses its Mimicry biocomputational platform to identify small proteins or peptides derived from gut bacteria for the treatment of cancer and immune diseases. In particular, the company is currently focusing on OncoMimics, which are bacterial peptides that closely mimic overexpressed tumor-associated antigens (TAAs) or markers in different cancer types.

    The company’s lead OncoMimic candidate is being evaluated in phase 1/2 clinical trials for the treatment of glioblastoma and adrenal tumors, in combination with the checkpoint inhibitor nivolumab. It combines three peptides that mimic three human tumor antigens found in glioblastoma and adrenal tumors.

    In addition to its four OncoMimic candidates, Enterome is also developing EndoMimics, which are oral bioactives drugs based on proteins secreted by the gut bacteria that act like human hormones or cytokines, targeting conditions such as inflammatory bowel disease (IBS) and food allergies.

    Vedanta Biosciences

    Headquarters: Cambridge, Massachusetts, U.S.

    Another company whose lead candidate focuses on treating high-risk CDI, Vedanta Biosciences is developing defined bacterial consortia as oral therapies to modulate the human microbiome. Its lead candidate consists of eight types of human commensal bacteria strains selected for their ability to provide colonization resistance to C.diff.

    In a phase 2 trial, the therapy achieved a greater than 80% reduction in recurrence risk compared with placebo at eight weeks, meeting its primary endpoint, and the company now has plans for a phase 3 trial to initiate in 2023, after recently raising $106.5 million in funding.

    Additionally, Vedanta has three other earlier-stage candidates aimed at treating IBS, solid tumors and gram-negative infections, as well as two investigator sponsored trials for food allergies and hepatic encephalopathy – a neurological disorder due to chronic, severe liver disease.

    Thanks to feedback from eureKARE and Isabelle de Cremoux at Seventure Partners.

    July 7 2022: Corrected mispellings of Rebiotix

    Explore other topics: EnteromeMaat PharmaMicrobiome

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