Studies on the human microbiome indicate that an alteration in the relationship between humans and their microbiomes is one of the determining factors in the onset and persistence of chronic diseases, which have become a major public health problem.
France benefits from dynamic clinical and epidemiological research, enabling in-depth clinical, biological and nutritional phenotyping of a wide range of subjects and patients. However, financial and technical constraints limit the characterization of associated microbial ecosystems, particularly in terms of their composition, functions and metabolites, products of their activities and those of the host.
To meet these challenges, the COHORTES-MICROBIOMES project of PEPR SAMS aims to support analyses that will enable the characterization of human microbiomes or host-microbiome interactions of healthy subjects or highly phenotyped patients participating in clinical studies or included in existing cohorts. To ensure the comparability of data generated when studying the human microbiota, appropriate sample collection procedures and methods will need to be followed. In this context, a call for projects is organized by Inserm on behalf of the PEPR SAMS management as part of the targeted COHORTES-MICROBIOMES project.
Funding will be a maximum of €250,000 (including management costs).
Eligible projects will have a duration of 3 years, including the sample collection phases (where applicable), as well as the technical phases of data processing and analysis.
Selected projects will receive financial support for the characterization of microbiomes through meta-omics analyses, mainly shotgun metagenomics and metabolomics. Other requests for omics analyses will have to be justified in terms of scientific interest and data already collected. More specifically, the objectives are to take advantage of available data and biological samples already collected, or whose collection can be rapidly organized, in order to complete and enhance the studies. Projects must be in line with the priorities of the “microbiomes and health” pillar and the SAMS PEPR axes, which aim to i) identify associations between environmental factors and the state of the microbiome-host symbiosis, ii) mechanisms of host-microbiome interactions, or iii) biomarkers linked to human microbiome dysfunction, or iv) preventive or therapeutic approaches.
Depending on the study design, project leaders may request funding for metagenomic and/or metabolomic analyses, or for other omics analyses if justified (except for studies associated with Le French Gut). To reinforce the analyses, part of the funding may be dedicated to: i) completing the collection of information on the subjects’ dietary habits, concomitant with the biological samples to be studied and/or ii) financing human resources for the analysis and integration of multi-omic and clinical data.
There are two possible ways of participating in this call for proposals: i) In the general case, apply as an independent cohort for metagenomic and/or metabolomic analyses; ii) In the specific case, apply in association with the Le French Gut project for metagenomic analyses of human stool microbiota.
The call for projects is divided into two phases:
- the first, selective and compulsory, establishes the project’s technical eligibility and scientific relevance, assessed respectively by a questionnaire and a mini-resume;
- the second consists of submitting the consolidated project.
- Text of the call: here
- Application submission platform (prior account creation required): https://www.eva3.inserm.fr/login
- Contact us: equipe@pepr-sams.fr
- Phase 1 application submission dates: 11/03/2025 – 27/06/2025 [Closed]
- Phase 1 results announced: November 2025 – overall selection rate of 57%
- Phase 2 application submission dates: opens in January 2026
- Phase 2 results announced: second semester of 2026
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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: Karine Clément
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