The intestinal microbiota (the communities of microorganisms in the mammalian gut) is highly diverse and influences host health and the development of chronic diseases. However, underlying mechanisms are still poorly understood.

The long-term objective of our work is to characterize intestinal bacterial communities and associated functions that play a role in the development of chronic disorders such as inflammatory bowel diseases, metabolic diseases, or colorectal cancer.

Explorative analysis is based on high-throughput sequencing approaches using samples from state-of-the-art human cohorts. Functional analysis of microorganisms of relevance relies on the use of in vitro screening systems and in vivo experiments using conventional and gnotobiotic mouse models.


Lee T,* Clavel T,* Smirnov K,* Schmidt A, Lagkouvardos I, Walker A, Lucio M, Michalke B, Schmitt-Kopplin P, Fedorak F, Haller D (2016) Oral versus intravenous iron replacement therapy distinctly alters the gut microbiota and metabolome in patients with inflammatory bowel diseases. Gut, doi: 10.1136/gutjnl-2015-309940.

Fugmann M, Breier M, Rottenkolber M, Banning F, Ferrari U, Sacco V, Grallert H, Parhofer K, Seissler J, Clavel T, Lechner A (2015) The stool microbiota of young women at high risk for type 2 diabetes. Sci Rep, doi: 10.1038/srep13212

Schaubeck M,* Clavel T,* Calasan J, Lagkouvardos I, Haange SB, Jehmlich N, Basic M, Dupont A, Hornef M, van Bergen M, Bleich A, Haller D (2015) Dysbiotic gut microbiota causes transmissive Crohn's disease-like ileitis independent of failure in antimicrobial defense, Gut. (* shared 1st authorship)

Wolf M, Adili A, Piotrowitz K, Abdullah Z, Boege Y, Stemmer K, Ringelhan M, Simonavicius N, Sigg M, Wohlleber D, Lorentzen A, Einer C, Schulz S, Clavel T, Protzer U, Thiele C, Zischka H, Moch H, Tschöp M, Tumanov AV, Haller D, Unger K, Karin M, Kopf M, Knolle P, Weber A, Heikenwalder M (2014) Metabolic activation of intrahepatic CD8+ and NKT-cells causes nonalcoholic steatohepatitis and hepatocellular carcinoma via cross-talk with hepatocytes, Cancer Cell 26:549.

Clavel T, Desmarchelier C, Haller D, Gérard P, Rohn S, Lepage P, Daniel H (2014) Intestinal microbiota in metabolic diseases: From bacterial community structure and functions to species of pathophysiological relevance. Gut Microbes 5.

Daniel H, Gholami AM, Berry D, Desmarchelier C, Hahne H, Loh G, Mondot S, Lepage P, Rothballer M, Walker A, Böhm C, Wenning M, Wagner M, Blaut M, Schmitt-Kopplin P, Kuster B, Haller D, Clavel T (2014) High-fat diet alters gut microbiota physiology in mice. ISME J 8:295.

Hemmerling J, Heller K, Hörmannsperger G, Bazanella M, Clavel T, Kollias G, Haller D (2014) Fetal exposure to maternal inflammation does not affect postnatal development of genetically-driven ileitis and colitis. PLoS One 9:e98237.

Perez-Munoz ME, Bergstrom K, Peng V, Schmaltz R, Jimenez-Cardona R, Marsteller N, McGee S, Clavel T, Ley R, Xia L, Peterson DA (2014) Discordance between changes in the gut microbiota and pathogenicity in a mouse model of spontaneous colitis. Gut Microbes 5.

Hörmannsperger G,* Clavel T,* Haller D (2012) Gut matters: Microbe-host interactions in allergic diseases. J Allergy Clin Immunol 129:1452.

Mabrok HB, Klopfleisch R, Ghanem KZ, Clavel T, Blaut M, Loh G (2011) Lignan transformation by gut bacteria lowers tumor burden in a gnotobiotic rat model of breast cancer. Carcinogenesis 33:203.

Werner T, Wagner S, Martinez I, Walter J, Chang J-S, Clavel T, Kisling S, Schümann K, Haller D (2011) Depletion of luminal iron alters the gut microbiota and prevents Crohn's disease-like ileitis. Gut 60:325.

Hörmannsperger G, Clavel T, Hoffmann M, Reiff C, Kelly D, Loh G, Blaut M, Hölzlwimmer G, Laschinger M, Haller D (2009) Post-translational inhibition of IP-10 secretion in IEC by probiotic bacteria: impact on chronic inflammation. PLoS One 4:e4365.

Clavel T, Haller D (2007) Molecular interactions between bacteria, the epithelium, and the mucosal immune system in the intestinal tract: implications for chronic inflammation. Curr Issues Intest Microbiol 8:25.

Blaut M, Clavel T (2007) Metabolic diversity of the intestinal microbiota: implications for health and disease. J Nutr 137:751S.

Clavel T, Haller D (2007) Bacteria- and host-derived mechanisms to control intestinal epithelial cell homeostasis: implications for chronic inflammation. Inflamm Bowel Dis 13:1153.