To mark World Microbiome Day, the France 2030 research program “Food Systems, Microbiomes, and Health” (PEPR SAMS) highlights the major advances made in its projects.
Found in our intestines, on our skin, and even in our mouths, the microbiome is central to our health and to many recent scientific advances. The balance of the microbiome is influenced by multiple factors: diet, the environment, lifestyle, certain medications, including repeated courses of antibiotics, and pollution. Gaining a better understanding of these invisible systems, how they evolve over the course of a lifetime and their links to disease, is one of the major challenges in biomedical research.
To advance in this field, one possible approach is to study the microbiome of groups of people, both healthy and/or sick, known as “cohorts” over a given period, in order to better understand the links between microbiomes, lifestyle habits, environmental exposures, and health status.
The PEPR SAMS has placed cohort studies at the heart of its research strategy to better understand how the microbiota influences our health and to find ways to preserve it in order to reduce the risk of certain diseases. As such, it supported the scientific event titled “Connecting Cohorts and Microbiomes”, held on June 26 in Paris (Necker University). The goal of this event, organized by the COHORTES-MICROBIOMES project, was to assess scientific and biomedical advances related to human microbiomes studied within cohorts, whether general population cohorts or patient cohorts.
Over the past few months, French research teams have published several major findings thanks to funding provided by the PEPR SAMS. Researchers have developed an innovative tool, the only one of its kind in the world, that improves the reliability of sequencing-based microbiome analyses [1]. Teams have, for the first time, characterized the changes in the microbiota associated with the small intestine mucosa in people with Crohn’s disease, a condition that most often affects this part of the intestine, in the context of postoperative recurrence [2]. Teams have also elucidated the spatial organization of the cells and molecules that make up the intestinal barrier and provided new insights into the function of this barrier [3, 4, 5, 6]. Converging research has also highlighted the influence of dietary habits and food additives on the gut microbiota in patients with chronic metabolic or inflammatory conditions [7, 8, 9, 10].
Ultimately, these advances, combined with those from other ongoing projects or those set to begin in 2027, should make it possible to identify new indicators of the state of our microbiomes (biomarkers) and pave the way for more personalized strategies for the prevention, diagnosis, and monitoring of chronic diseases.
For more information on these French scientific and medical advances:
[1] Ghassemi Nedjad et al. 2025 Seed2LP: seed inference in metabolic networks for reverse ecology applications. Bioinformatics. doi: 10.1093/bioinformatics/btaf140. (Cultissimo)
[2] Dubois et al. 2026 Uncovering the Dynamics of Mucosa-Associated Microbiota in Postoperative Recurrence of Crohn’s Disease. Gastroenterology. doi: 10.1053/j.gastro.2026.01.043. (SIM-IBD)
[3] Ranson et al. 2025 Moderate increase in dietary fat induces alterations of microbiota and metabolome along the digestive tract prior to systemic metabolic changes: insights from a pig model. Gut Microbes. doi: 10.1080/19490976.2025.2587964. (JEMINI)
[4] Duquesnoy & Chassaing 2026 MBRA 3.0: integrating the mucus environment for advanced high-throughput in vitro intestinal microbiome modeling. Gut Microbes. doi: 10.1080/19490976.2026.2612804. (AddiMapping)
[5] Simpson et al. 2026 Disruption of IgA-mediated aggregation at weaning favors mucus encroachment by commensal bacteria. NPJ Biofilms Microbiomes. doi: 10.1038/s41522-026-00946-4. (JEMINI)
[6] Bonazzi E et al. 2025 Microbiota modulation by a human Paneth cell α-defensin fragment protects against DSS-induced colitis. iScience. doi: 10.1016/j.isci.2025.114310 (AddiMapping)
[7] Delaroque C et al. 2025 Maternal emulsifier consumption alters the offspring early-life microbiota and goblet cell function leading to long-lasting diseases susceptibility. Nat Commun. doi: 10.1038/s41467-025-62397-3. (AddiMapping)
[8] Lamy-Besnier et al. 2026 Gut trialogue: How diet influences mucosal immune system-microbiota interactions. Mucosal Immunol. doi: 10.1016/j.mucimm.2026.01.009 (AddiMapping)
[9] Sanz et al. 2025 The gut microbiome connects nutrition and human health. Nat Rev Gastroenterol Hepatol. doi: 10.1038/s41575-025-01077-5. (COHORTES-MICROBIOMES)
[10] Hiol et al. 2025 From the laboratory to the plate: How gut microbiome science is reshaping our diet. J Nutrition. doi: 10.1016/j.tjnut.2025.08.032 (COHORTES-MICROBIOMES)