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. Current activities embedded in the priority program SPP1656 of the DFG focus on the establishment, utilization, and distribution of standardized minimal microbiomes. 

Agar media showing growth of gut bacteria

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.


Coriobacteriaceae

 

Intestinal microbes, diet & health

On the one hand, gut bacteria are known to metabolize compounds from the diet, thereby modulating their bioavailabiltiy and bioactivities. In that context, we have been investigating the conversion of dietary polyphenols and thereby identified several bacterial strains or associations thereof responsible for the production of bioactive metabolites. On the other hand, 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 in health regulation. In collaboration with the ZIEL Institute for Food and Health of the Technical University of Munich (Prof. Dirk Haller), we currently analyze population-based fecal microbiota profiles in relation to diet and cardiometabolic health. 

Reviews for further information

  • Kong, Andersson, Clavel, Common, Jackson, Olson, Segre, Traidl-Hoffmann (2016) Performing skin microbiome research: A method to the madness. J Invest Dermatol doi: 10.1016/j.jid.2016.10.033
  • Clavel, Lagkouvardos, Hiergeist (2016) Microbiome sequencing: challenges and opportunities for molecular medicine. Expert Rev Mol Diagn 16:795
  • Bieber et al. (2016) Atopic dermatitis/Eczema: Challenges and opportunities towards precision medicine. Allergy 71:488
  • Clavel, Lagkouvardos, Blaut, Stecher (2016) The mouse gut microbiome revisited: from complex diversity to model ecosystems. Int J Med Microbiol 306:316
  • Clavel, Desmarchelier, Haller, Gérard, Rohn, Lepage, Daniel (2014) Intestinal microbiota in metabolic diseases: from bacterial community structure and functions to species of pathophysiological relevance. Gut Microbes 5:544
  • Hörmannsperger,* Clavel,* Haller (2012) Gut matters: intestinal microbial ecology in allergic diseases. J Allergy Clin Immunol 129:1452 (* shared 1st authorship)
  • Clavel, Haller (2007) Bacteria- and host-derived mechanisms to control intestinal epithelial cell homeostasis: implications for chronic intestinal inflammation. IBD 13:1153
  • Clavel, Haller (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
  • 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