For a few years now, we are told that the future of medicine relies on the health of our gut microbiome. But beyond the classic probiotics and prebiotics that your doctor has probably already recommended to you, can we really speak of curative effects? The answer is yes! And as proof, health industry players are increasingly turning towards the development of therapies based on the microbiome to treat numerous pathologies, ranging from chronic infections to cancers, including Charcot’s disease. In this article, Alcimed highlights the challenges associated with these therapies, while exploring the main advances and the future of this field.
The microbiome refers to the genomes of all microorganisms such as parasites, bacteria, fungi and viruses located on or in many organs of the human body, in particular our skin, our eyes and our intestines. These microorganisms are generally harmless, 80% are even beneficial to health.
The human microbiome can ensure metabolic and synthetic functions essential to human health, notably the regulation of the immune system and assistance with digestion. In order to obtain a complete characterization of the human microbiome and analyze its role in human health and disease, the Human Microbiome Project (HMP) was supported by the common fund of the National Institutes of Health from 2007 to 2016.
The initial phase of the project, HMP1, established in 2008, enabled the characterization of microbial communities of 300 healthy individuals, on five major body sites: the nasal passages, the oral cavity, the skin, the gastrointestinal tract and the urogenital tract. The second phase iHMP aims to create integrated longitudinal datasets from both the microbiome and the host. This phase will exploit data from different “omics” approaches from three different cohort studies studying microbiome-associated pathologies.
One of the studies concerns inflammatory bowel diseases and aims to understand how the human gut microbiome evolves over time in adults and children affected by these pathologies.
Why does the gut microbiome arouse the interest of researchers? To understand this point, we must review together some facts concerning the gut microbiome:
Microbiome therapies (MBT) are currently in development to prevent recurrent Clostridium difficile (C. Diff) infections, which are mainly contracted in hospitals and cause diarrhea, dehydration, fever and weight loss. These MBT should improve the quality of life of patients and reduce the burden on the healthcare system.
A first major challenge in the development of therapies based on the microbiome lies in understanding the complex interactions between the gut microbiome and various pathologies, which hinders the development of these therapies. It is essential to highlight that these treatments must take into account the interindividual variability of the gut microbiome, influenced both by genetic and environmental characteristics of the patient, which leads to a personalized medical approach.
When addressing the issue of manufacturing, a major challenge lies in quality control and production processes, which require specialized skills and infrastructure. To date, CDMOs (Contract Development and Manufacturing Organizations) have limited expertise in this field, which leads to difficulties, particularly in ensuring the viability of microorganisms throughout the manufacturing process.
Finally, a key issue lies at the regulatory level. Until 2022, the European Commission had not defined a clear position on the status of these new therapies. That year, a report was published, leaving each EU country the possibility to classify them according to their own regulations. Thus, France, Spain and Germany have classified these therapies as biological products for medicinal use, while Belgium and Italy have integrated them into their regulations related to the use of tissues and cells. It should also be noted that this regulatory vagueness goes beyond the borders of the European Union: in the United Kingdom, Canada, Australia and the United States, these therapies are generally considered as biological drugs, although exceptions exist.
Despite the various constraints associated with these therapies, the FDA has approved, since 2022, the commercialization of two treatments based on the gut microbiome. In November 2022, Ferring Pharmaceuticals obtained the authorization to market REBYOTA, a treatment intended for the prevention of recurrent Clostridioides difficile infections (CDI) in adults aged 18 and over, after antibiotic treatment for a recurrent CDI. Six months later, Seres Therapeutics also received the authorization to market VOWST, a treatment aiming to address exactly the same issue.1Research, C. F. B. E. A. (2022, December 19). REBYOTA. U.S. Food And Drug Administration. https://www.fda.gov/vaccines-blood-biologics/vaccines/rebyota2VOWSTTM | Official patient website. (n.d.). https://www.vowst.com/
In April 2023, Maat Pharma obtained FDA approval to launch phase III clinical trials of its MaaT013 treatment. The positive results of these trials were published in February 2025. It is important to note that the MaaT013 treatment targets acute graft-versus-host disease (aGvHD), a rare but serious complication that occurs after allogeneic hematopoietic stem cell transplantation, used to treat various blood pathologies. This treatment received orphan drug designation from both the EMA and the FDA for patients suffering from steroid-refractory aGvHD (first-line treatment) and resistant to Ruxolitinib (second-line treatment).Moreover, MaaT Pharma is developing other therapies based on the gut microbiome, such as MaaT033, currently in phase IIb clinical trials, aiming to rebalance the gut microbiota in patients affected by Charcot’s disease, a currently incurable disease.
It is also worth mentioning Siolta Therapeutics and Vedanta Biosciences, both engaged in the development of therapies based on the microbiome. Siolta Therapeutics currently has a candidate in phase I clinical study for the prevention of atopic diseases, as well as two other candidates in preclinical phase for the prevention of recurrent bacterial vaginosis and necrotizing enterocolitis. For its part, Vedanta Biosciences is conducting three clinical studies with its candidates: VE202, intended for inflammatory bowel diseases, VE303, for the treatment of Clostridioides difficile infections (CDI), and V707, which targets the prevention of antimicrobial-resistant (AMR) Gram-negative infections.
Find out how our team can help you with your microbiome projects >
The therapies currently developed or in development target only a tiny portion of the pathologies potentially treatable by the microbiome. Indeed, numerous conditions cause dysbiosis, that is to say an imbalance in the composition, abundance and diversity of the gut microbiome, thus disrupting the balance between the host and its microbiome. Among these pathologies are intestinal infections, inflammatory bowel diseases, irritable bowel syndrome, type 2 diabetes, obesity, liver diseases, certain cancers, as well as neurological disorders, such as autism spectrum disorders (ASD).
Another development axis of these therapies lies in the different usable approaches. Indeed, three types of approaches are conceivable: non-targeted approaches, such as prebiotics, classic probiotics and fecal microbiome transplants; targeted approaches, like single-strain biotherapies, phage therapies and microorganism engineering; and finally, microbial consortia, which are situated at the intersection of these two categories of approaches. It should be noted that today, the only approaches significantly explored are non-targeted approaches, leaving open the field of possibilities regarding the exploration of the other two treatment categories.
Therapies based on the microbiome, which rely on understanding the complex interactions between the gut microbiome and pathologies, are part of a strong growing trend and are beginning to find their place in the pharmaceutical market. However, they must still overcome several challenges, notably in terms of production quality and regulation, both at European and global levels. Alcimed is ready to support you on these challenges, whether to identify your future partners, help you position yourself on the market, or guide you in complying with the appropriate regulatory standards. Don’t hesitate to contact our team!
About the authors,
Jessica, Consultant in Alcimed’s Healthcare team in France.
Chaoyue & Christelle, Project Managers in Alcimed’s Healthcare in France.
Healthcare
Microbiome-cancer studies aim at developing drugs to mitigate chemotherapy side effects or identifying microbial biomarkers for early diagnosis or disease progression monitoring. The most promising ...
Healthcare
What are the possible strategies to ensure the proper development of the infant microbiota following a caesarean section? How does the biopharmaceutical market respond to these major challenges? At ...
Cross-sector
Since the 2000s, scientific interest in the microbiota has been growing steadily, particularly in the United States and Europe. After the intestinal microbiota success, bacteria and other ...