Functionality of the Intestinal Ecosystem / Nicolas Lapaque

Functionality of the Intestinal Ecosystem



Funtionality of the Intestinal Ecosystem


Head of the lab : Nicolas Lapaque

The FInE/Blottière Team


Team members and alumni

We are hiring an Assistant Ingénieur to supervize the cell biology workshop.

All the information here :


The human intestinal microbiota, as we know it today, appears to be very complex. In order to move towards a holistic understanding of the gut microbiota, including its non-cultivable component, which is still in the majority to date, we have contributed to the development of a new and powerful approach, metagenomics, which has enabled rapid progress in the characterisation of the genomic and genetic diversity of the gut microbiota. For example, the microbial genome (microbiome) of each individual contains ~28 times more genes than the human genome. The microbiota is, moreover, considered to be a host organ in its own right.
The FInE team aims to deepen the current understanding of the fundamental role played by the microbiota in human health. Our objective is to better understand the mechanisms of the human-microbe symbiosis and the influence of our diet, in particular the importance of fibre, polyphenols and probiotics, in order to define strategies for its modulation.
FInE is a joint team linked to the MICA and AlimH departments of INRAE. It is closely linked to MetaGenoPolis since it contributed to the emergence of two of its platforms (SAMBO and MétaFun).
Our theme is based on several themes carried out by the team's researchers and supported by 4 technical workshops and a fermenter platform in collaboration with MGP


Ongoing Research Projects :

ANR Gut-Alpk1 (2022-2025) : Nicolas Lapaque

ANR IMAT (2021-2024) : Coordinator Maude LeGall (INSERM)

PLBIO-INCA (2021-2024) : Nicolas Lapaque

ERC Advanced Homo-Symbosius (2019-2023) : Joël Doré

EU FP7 Microb-Predict (2019-2026) Coordinator : Jonel Trebicka (EF CLIF, Barcelone)

ANR LUMI (2019-2022) Coordinator : Sylvia Cohen-Kaminsky (INSERM)

Several projects in collaboration with industrial partners including Maat Pharma, DuPont, Sanofi & Roquette are also going on.

Important projects in which we participated :

EU FP7 MetaCardis (2012-2018) Coordinator : K Clément (ICAN)

ANR FunAMetaGen (2015-2019) Coordinator : Laurent Chene (Entérome)

ANR PigletBiota (2014-2018) Coodinator : J Estellé (INRA - Gabi)

ANR ProteoCardis (2016-2020) Coordinator : Catherine Juste

EU FP7 IHMS (2011-2015) Coordinator : SD Ehrlich (MGP)
EU FP7 METAHIT (2008-2012) Coordinator : SD Ehrlich (MGP)
EU FP7 Cross-Talk (2008-2012) Coordinators : E Maguin (Ife - Micalis) & HM Blottière (FInE - Micalis)

ANR SUSFLORA (2011-2014) Coordinator : C Rogel-Gaillard (INRA - Gabi)
ANR Surfing (2011-2014) Coordinators : G Jan (STLO - INRA) & M van de Guchte (Ife - Micalis) 
ANR SFBIMPRO (2010-2013) Coordinator : V Gaboriau-Routhiau (INSERM - Necker)

ANR EPIFLORE (2013-2016) Coordinator : MJ Butel (Université Paris Descartes)

ANR FunMetaGen (2012-2014) Coordinator : HM Blottière (FInE - Micalis)
ANR MicroObes (2008-2012) Coordinator : J Doré (FInE - Micalis)

Risk OGM CRYMUC (2012-2016) Coordinator : C. Nielsen-Leroux (GME - Micalis)

INRA MEM MetaScreen (2011-2013) Coordinator: G Veronese (LISBP – INRA
INRA MEM OBOMICS (2012-2014) Coordinator : C Juste (FInE - Micalis)

Key publications

(List of all publications since 2017)

1.           Martin-Gallausiaux C, Garcia-Weber D, Lashermes A, Larraufie P, Marinelli L, Teixeira V, Rolland A, Béguet-Crespel F, Brochard V, Quatremare T, Jamet A, Doré J, Gray-Owen SD, Blottière HM, Arrieumerlou C, Lapaque N. Akkermansia muciniphila upregulates genes involved in maintaining the intestinal barrier function via ADP-heptose-dependent activation of the ALPK1/TIFA pathway. Gut Microbes 2022;14(1). doi:10.1080/19490976.2022.2110639.

2.           Mondot S, Lachkar L, Doré J, Blottière HM, Hanachi M. Roseburia, a decreased bacterial taxon in the gut microbiota of patients suffering from anorexia nervosa. Eur. J. Clin. Nutr. 2022;76(10):1486–1489. doi:10.1038/S41430-022-01116-3

3.           Di Lodovico L, Mondot S, Doré J, Mack I, Hanachi M, Gorwood P. Anorexia nervosa and gut microbiota: A systematic review and quantitative synthesis of pooled microbiological data. Prog. Neuro-Psychopharmacology Biol. Psychiatry 2021;106. doi:10.1016/j.pnpbp.2020.110114.

4.           van de Guchte M, Mondot S, Doré J. Dynamic Properties of the Intestinal Ecosystem Call for Combination Therapies, Targeting Inflammation and Microbiota, in Ulcerative Colitis. Gastroenterology 2021;161(6):1969-1981.e12. doi:10.1053/J.GASTRO.2021.08.057

5.           Martin-Gallausiaux C, Marinelli L, Blottière HM, Larraufie P, Lapaque N. SCFA: Mechanisms and functional importance in the gut. Proc. Nutr. Soc. 2020:1–13. doi:10.1017/S0029665120006916

6.           Van de Guchte M, Burz SD, Cadiou J, Wu J, Mondot S, Blottière HM, Doré J. Alternative stable states in the intestinal ecosystem: proof of concept in a rat model and a perspective of therapeutic implications. Microbiome 2020;8(1):153. doi:10.1186/S40168-020-00933-7

7.           Patrascu O, Béguet-Crespel F, Marinelli L, Le Chatelier E, Abraham AL, Leclerc M, Klopp C, Terrapon N, Henrissat B, Blottière HM, Doré J, Béra-Maillet C. A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic. Sci. Reports 2017 71 2017;7(1):1–15. doi:10.1038/srep40248


Nicolas Lapaque

Institut Micalis Institute (UMR1319)/Université Paris Saclay - INRAE-AgroParisTech-
INRAE, Domaine de Vilvert
78352 Jouy-en-Josas cedex, France

Modification date : 30 January 2024 | Publication date : 14 April 2011 | Redactor : Micalis