Our Research

Gut microbiomes via cultivation

The diversity of bacteria on earth is tremendous. In the intestine of mammals, one to two thirds of prokaryotic diversity remain to be described (i.e., strains of many taxa have never been isolated and described). This pool of unknown diversity represents a substantial phylogenetic hole and most of all an opportunity to discover novel bacterial functions. A substantial part of our work is dedicated to the cultivation and description of new taxa from the intestine of humans, pigs, and mice. In particular, because intestinal microbiomes have co-evolved with their host species, we put effort in establishing comprehensive collections of bacterial strains in a host-specific manner (in collaboration with the Leibniz-Institute DSMZ). These collections serve as a foundation for experimental studies that aim at studying the ecology of gut microbes as well as microbe-host interactions using in vitro (continuous culture) and in vivo (gnotobiology) systems.

The mouse intestinal bacterial collection

The pig intestinal bacterial collection

Microbe-host interactions

Because intestinal bacteria constantly interact with dietary factors and host cells and because they produce a myriad of bioactive molecules, they are known to influence the physiology of their host and can be implicated in the development of chronic diseases. The last decade of microbiome research has generated many descriptive data demonstrating shifts in gut microbiome structure and functions associated with diseases. Effort is now required to strengthen our knowledge about molecular mechanisms underlying microbe-host interactions. We are particularly interested in studying the impact microbiota members on the metabolism of cholesterol-derived compounds, with primary focus on bile acids. Models species within the family Coriobacteriaceae but also other secondary bile acid-producing taxa and their impact on liver physiology, metabolic disturbances, and the development of colorectal cancer are under investigation.



Intestinal microbes, diet & health

As gut bacteria are known to metabolize compounds from the diet and thereby modulate their bioavailabiltiy and bioactivities, we have investigated the conversion of dietary polyphenols and identified several bacteria responsible for the production of bioactive metabolites. Our current research focuses on the conversion of dietary and host-derived lipids.

Diet can modulate the gut microbial ecosystem and the use of molecular techniques has been really helpful in dissecting diet-microbiota interactions in a culture-independent manner and assessing their importance for health regulation. We have been using high-throughput sequencing to identify microbiome signatures associated with specific dietary components and host pathologies. The culture resources aforementioned allow us to test the generated hypotheses in experimental models.

Further reading

  • Clavel, Fricke, Gessner, Hiergeist (2019) Aus dem Labor: Wie vermisst man das Mikrobiom (in German), In Trillium Immunologie, Heft 1/2019, Haller D. et al. (Eds.) Deutsche Gesellschaft für Immunologie
  • Clavel, Ecker (2018) Microbiome and diseases – Metabolic disorders, In The Gut Microbiome in Health and Disease, Haller D (Ed.), Springer, ISBN 978-3-319-90544-0
  • Clavel, Lagkouvardos, Stecher (2017) From complex gut microbial communities to model bacterial consortia via cultivation. Curr Opin Microbiol 38:148
  • Clavel, Gomes-Neto, Lagkouvardos, Ramer-Tait (2017) Deciphering interactions between the gut microbiota and the immune system via microbial cultivation and minimal microbiomes. Immunol Reviews 279:8
  • Clavel, Lagkouvardos, Hiergeist (2016) Microbiome sequencing: challenges and opportunities for molecular medicine. Expert Rev Mol Diagn 16:795
  • Clavel, Lagkouvardos, Blaut, Stecher (2016) The mouse gut microbiome revisited: from complex diversity to model ecosystems. Int J Med Microbiol 306:316
  • Hörmannsperger,* Clavel,* Haller (2012) Gut matters: intestinal microbial ecology in allergic diseases. J Allergy Clin Immunol 129:1452 (* shared 1st authorship)
  • Clavel, Doré, Blaut (2007) Bioavailability of lignans in human subjects. Nutr Res Rev 19:187
  • Blaut, Clavel (2007) Metabolic diversity of the intestinal microbiota: Implications for health and disease. J Nutr 137:751S