The five most advanced microbiome players aiming for the gut

After decades of research, gut microbiome therapies are on the cusp of reaching the market. Here are five of the companies that are closest to hitting this historic milestone.

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 edging closer to 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 racing to take these treatments to the regulatory finish line. With the help of experts in the field, we’ve listed five of the front-running players that could develop the first marketed microbiome-based therapy.

Rebiotix Inc.

Headquarters: Roseville, Minnesota, U.S.

Rebiotix is developing 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 lead candidate therapy 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 delivering it as an enema to patients with CDI. According to a recent analysis, the therapy allowed almost 79% of patients across multiple clinical trials with recurrent CDI to go eight weeks without another recurrence.

Rebiotix was acquired by the Swiss company Ferring Pharmaceuticals in 2018. The team has filed for U.S. approval of its lead candidate and is developing an orally administered microbiome therapeutic for the same indication in phase 3.   

Finch Therapeutics Group Inc.

Headquarters: Somerville, Massachusetts, U.S.

Finch Therapeutics is also taking aim at recurrent CDI with its lead candidate therapy: oral pills made of freeze-dried gut microbiota-derived from healthy donors. The therapy reduced the risk of a recurring infection by about a third compared to placebo in a phase 3 trial, and is being tested in a second phase 3 trial.

Fearing the risk of transmitting COVID-19 via stool transplants, the U.S. Food and Drug Administration (FDA) placed a temporary hold on the clinical testing of Finch’s lead candidate therapy in March 2022. The hold was lifted in late April as Finch updated its manufacturing and quality systems to address the FDA’s concerns. However, enrollment into the ongoing phase 3 trial has been delayed until late 2022.

Earlier this year, Finch also cut the development of its lead candidate for the treatment of hepatitis B infections. Instead, the company expects to redouble its focus on its lead program in CDI, inflammatory bowel disease treatments partnered with Takeda, and a preclinical-stage microbiome-derived treatment for autism spectrum disorder.

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 a preclinical-stage 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 the frontrunning microbiome player 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 GvHD 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. The trial is expected to finish in late 2024.

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. Other MaaT Pharma programs include an oral donor-derived microbiome therapeutic in phase 1b testing and a preclinical-stage 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 in the treatment of recurrent CDI. The company’s lead therapy — co-developed with Nestlé Health Sciences — 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 recent phase 3 trial, Seres’ lead therapy prevented CDI from recurring in 88% of patients for eight weeks, while just 60% of patients in the placebo group were free of recurrences. Following promising results in an open-label study in June 2022, Seres is gunning to apply for approval in the U.S. later this year.

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 company is now researching on how to proceed with the program.