Launched in March 2025 by PEPR SAMS management team as part of its COHORTES-MICROBIOMES focus project and operated by Inserm, the call for projects was designed to support research focused on characterizing human microbiomes and studying host-microbiome interactions in healthy individuals and patients.
With funding of up to €250,000 (including administrative costs) for projects lasting up to 3 years, this call targeted studies based on meta-omic approaches, primarily metagenomic and metabolomic. The research was required to draw on human microbiome samples that had already been collected, or were currently being collected, from subjects who had been finely phenotyped and were participating in clinical studies or included in existing cohorts.
Ultimately, this call aims to contribute to the establishment of a national reference for the microbiomes of the French population — and potentially even at the international level — and to strengthen the international influence of French research in this field. The identification and characterization of microbiomic signatures, as well as the discovery of predictive and diagnostic biomarkers, remain major challenges for research on human microbiomes today.
Following the application submission period, 68 proposals were evaluated according to the following process:
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- An initial selection phase, conducted by a national jury, aimed to determine the project’s technical eligibility and scientific relevance.
- A second selection phase, conducted by an independent international jury (Germany, Spain, Italy, Luxembourg, the Netherlands, Sweden), was based on an analysis of the research proposals submitted following a consolidation phase alongside the pilot team of the COHORTES-MICROBIOMES project.
At the conclusion of these selection stages, 12 projects were selected, including 3 in collaboration with Le French Gut project.
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- AIMISEP – Analysis of the Interactions Between the Gut Microbiome, the Progression of Multiple Sclerosis, and Associated Treatments in the OFSEP HD Cohort
In collaboration with Le French Gut
Project coordinator: Éric Thouvenot
Coordinating institution: Centre Hospitalier Universitaire de Nîmes
Duration: 3 years
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- BACSSPA – Bacterial strain-level involvement of gut microbiota in spondyloarthritis
In collaboration with Le French Gut
Project coordinator: Maxime Breban
Coordinating institution: Université Versailles Saint-Quentin-en-Yvelines
Duration: 3 years
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- BioHPV – Impact of the vaginal, intestinal, oral microbiota and cutaneous Human Papillomavirus (HPV) reservoir on the prognosis of high-grade squamous intraepithelial lesions associated with HPV: A prospective multicenter study of prognostic biomarkers
In collaboration with Le French Gut
Project coordinator: Judith Michels
Coordinating institution: Institut Gustave Roussy
Duration: 3 years
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- ClinicObiome – The Oncology Clinic of Microbiome
Project coordinator: Lisa Derosa
Coordinating institution: Institut Gustave Roussy
Duration: 3 years
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- INTERACT – Diet Modulation of Phage–Bacteria–Host Interactions in Cardiometabolic Diseases
Project coordinator: Lejla Imamovic
Coordinating institution: Sorbonne Université
Duration: 3 years
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- KIDS-ALLERGUT – Microbiota in children with emergent and increasing digestive atopic diseases
Project coordinator: Anaïs Lemoine
Coordinating institution: Sorbonne Université
Duration: 1.5 years
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- MicMetALD – Microbial metabolomics and proteomics signatures in alcoholic liver disease
Project coordinator: Dragos Ciocan
Coordinating institution: Inserm – Délégation Régionale Paris Sud
Duration: 3 years
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- MIDAS – Longitudinal Analysis of Anal microbiote Dynamics in men who have sex with men in Togo According to HIV Status And Its Association with Sexually Transmitted Infections and Anal Lesions
Project coordinator: Valentine Ferré
Coordinating institution: Inserm – Délégation Régionale Paris Centre & Nord
Duration: 1.5 years
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- MIRACLE-CKD – Microbiome and metabolomic features along the spectrum of chronic kidney disease and its progression
Project coordinator: Laetitia Koppe
Coordinating institution: Lyon 1 Université Claude Bernard
Duration: 3 years
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- MUCKY – Impact of the microbiome on the risk of acute rejection following a kidney transplant
Project coordinator: Antoine Durrbach
Coordinating institution: Inserm – Délégation Régionale Paris Sud
Duration: 3 years
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- NutriGut-Santé – Nutrition, gut microbiota and health : stool sample collection among participants from the NutriNet-Santé cohort
Project coordinator: Mélanie Deschasaux-Tanguy
Coordinating institution: Inserm – Délégation Régionale Paris Centre & Nord
Duration: 3 years
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- RENEGADE-IBD – Role of Enteric NEurons, Glia, And Dysbiosis in pErsistent functional symptoms of quiescent Inflammatory Bowel Disease
Project coordinator: Catherine Le Berre
Coordinating institution: Centre Hospitalier Universitaire de Nantes
Duration: 3 years
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- Mathilde Poyet – Kiel University, Germany
- Ingo Autenrieth – Heidelberg University, Germany
- Francesco Asnicar – University of Trento, Italy
- Corinna Bang – Kiel University, Germany
- Robert Jan Brummer – örebro University, Sweden
- Flavio Caprioli – University of Milan, Italy
- Francesca De Filippis – University of Naples Federico II, Italy
- Mahesh Desai – Luxembourg Institute of Health, Luxembourg
- Rochellys Diaz Heijtz – Karolinska Institutet, Sweden
- Mathieu Groussin – Kiel University, Germany
- Amira Metwaly – Technical University of Munich, Germany
- Francisco Javier Moreno – Instituto de Investigación en Ciencias de la Alimentación of Spain, Spain
- Simone Rampelli – University of Bologna, Italy
- Urvish Trivedi – University of Copenhagen, Sweden
- Silvia Turroni – University of Bologna, Italy
- Luisa Warchavchik Hugerth – Uppsala University, Sweden
- Sasha Alexandra Zhernakova – University Medical Centre Groningen, Netherlands