To help understanding the specific role of intestinal microbiota in host physiology, it is essential to characterize microbial diversity and functions at both the community and single strain level.

Molecular techniques have allowed in-depth assessment of intestinal microbiota in various environments. The main advantage of molecular techniques relies on the possibility to assess both cultivable and yet uncultured bacteria. However, there is still a lack of: (1) gold standards in metagenomics with respect to sample collection and processing as well as data analysis; and (2) tools for global assessment of microbial diversity and profile comparisons. Hence, we work on the development of pipelines and new tools for high-throughput analysis of sequencing datasets. For instance, we created the platform IMNGS (Integrated Microbial Next Generation Sequencing) to make use of the accumulated sequence knowledge in public repositories.

Yet uncultured bacteria can be considered as a pool of functions that remain to be discovered, and the isolation of novel bacteria gives the opportunity to study in detail some of their potentially important functions. Hence, we have established the mouse intestinal Bacterial Collection (miBC) and thereby provide the first exhaustive repository of bacterial strains and associated genomes from the mouse intestine to the scientific community. This new resource is a foundation for future research on diet-microbiome-host interactions in health and diseases, opening the way to novel molecular and targeted colonization approaches.


Zantow J, Just S, Lagkouvardos I, Lepage P, Clavel T*, Hust M* (2016) Mining gut microbiome oligopeptides by functional metaproteome display. Sci Rep 6:34337.

Lagkouvardos I, Joseph D, Kapfhammer M, Giritli S, Horn M, Haller D, Clavel T (2016) IMNGS: A massive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies. Sci Rep 6:33721.

Clavel T, Lagkouvardos I (2016) Microbiome sequencing: challenges and opportunities for molecular medicine. Expert Rev Mol Diagn 16:795.

Lagkouvardos I, Pukall R, Abt B, Foesel B, Meier-Kolthoff J, Kumar N, Bresciani A, Martinez I, Just S, Ziegler C, Brugiroux S, Garzetti D, Wenning M, Bui NTP, Wang J, Hugenholtz E, Plugge CM, Peterson D, Hornef M, Baines J, Smidt H, Walter J, Kristiansen K, Nielsen HB, Haller D, Overmann J, Stecher B, Clavel T (2016) The mouse intestinal Bacterial Collection (miBC) provides host-specific insight into cultured diversity and functional potential of the gut microbiota. Nat Microbiol 1:16131.

Clavel T, Lagkouvardos I, Blaut M, Stecher B (2016) The mouse gut microbiome revisited: From complex diversity to model ecosystems. Int J Med Microbiol 306:316.

Bui NTP, Shetty S, Lagkouvardos I, Ritari J, Chamlagain B, Douillard F, Paulin L, Clavel T, Plugge CM, de Vos WM (2016) Comparative genomics and physiology in Intestinimonas butyriciproducens from human and mouse. Environ Microbiol Rep doi: 10.1111/1758-2229.12483.

Hiergeist A, Reischl U, Priority Program 1656 Consortium, Gessner A (2016) Multicenter quality assessment of 16S ribosomal DNA-sequencing for microbiome analyses reveals high inter-center variability. Int J Med Microbiol 306:33.

Rausch P, Basic M, Priority Program 1656 Consortium, Bleich A, Baines J (2016) Analysis of factors contributing to variation in the C57BL/6J fecal microbiota across German animal facilities. Int J Med Microbiol 306:343.

Kläring K, Just S, Lagkouvardos I, Hanske L, Haller D, Blaut M, Wenning M, Clavel T (2015) Murimonas intestini gen. nov., sp. nov., an acetate-producing bacterium of the family Lachnospiraceae isolated from the mouse gut, Int J Syst Evol Microbiol 65:870.

Clavel T, Lepage P, Charrier C (2013) Family Coriobacteriaceae, In The Prokaryotes, 4th Edition, E Rosenberg, EF DeLong, F Thompson, S Lory, E Stackebrand (Eds), Springer.

Kläring K, Hanske L, Bui N, Charrier C, Blaut M, Haller D, Plugge CM, Clavel T (2013) Intestinimonas butyriciproducens gen. nov., sp. nov., a novel butyrate-producing bacterium from the mouse intestine. Int J Syst Evol Microbiol 63:4606.

Clavel T, Charrier C, Wenning M, Haller D (2013) Parvibacter caecicola gen. nov., sp. nov., a new bacterium of the family Coriobacteriaceae isolated from the caecum of a mouse. Int J Syst Evol Microbiol 63:2642.

Clavel T, Charrier C, Haller D (2013) Streptococcus danieliae sp. nov., a novel bacterium from the caecum of a mouse. Arch Microbiol 195:43.

Pfeiffer N, Desmarchelier C, Blaut M, Daniel H, Haller D and Clavel T (2012) Acetatifactor muris gen. nov., sp. nov., a novel acetate- and butyrate-producing bacterium isolated from the intestine of an obese mouse. Arch Microbiol 194:901.

Clavel T, Saalfrank A, Charrier C, Haller D (2010) Isolation of bacteria from mouse caecal samples and description of Bacteroides sartorii sp. nov. Arch Microbiol 192:427.

Clavel T, Duck W, Charrier C, Wenning M, Elson C, Haller D (2010) Enterorhabdus caecimuris sp. nov., a member of the family Coriobacteriaceae isolated from a mouse model of spontaneous colitis, and emended description of the genus Enterorhabdus. Int J Syst Evol Microbiol 60:1527.

Clavel T, Charrier C, Braune A, Wenning M, Blaut M, Haller D (2009) Isolation of bacteria from the ileal mucosa of TNFdeltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov. Int J Syst Evol Microbiol 59:1805.

Mueller S, Saunier K, Hanisch C, Norin E, Alm L, Midtvedt T, Cresci A, Silvi S, Orpianesi C, Verdenelli MC, Clavel T, Koebnick C, Zunft HJ, Doré J, Blaut M (2006) Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol 72:1027.

Universal 16S analysis

The mouse intestinal Bacterial Collection