Bacteria living on and in the human body play an essential role in maintaining human health. Compared to other body sites, the human gastrointestinal tract harbors the largest community of microbes. Gut bacteria are responsible for the production of energy, e.g. fermentation of undigested carbohydrates, the biosynthesis of amino acids and vitamins; they are involved in bile acid metabolism and play a role in the development of the immune system as well as in immunomodulation. Alterations of a stable gut bacterial community can result in metabolic and complex autoimmune diseases such as inflammatory bowel disease. It has been shown that gut microbiota can be altered by numerous aspects such as host genetic variation, antibiotic usage, dietary habits and other environmental factors (smoking, geography, infections, etc.).
The current focus of our study group is to identify genetic and non-genetic factors that shape the microbiome. Multi-OMICs studies that integrate microbial profiles, metabolic, genetic, phenotypic, and nutritional data are ongoing to identify relevant factors and mechanisms.
Our laboratory has established methods to determine bacterial richness and OTUs in a given sample (Who is there? 16S rDNA high-throughput sequencing). In addition, whole-metagenome (Who is there and what are they doing?) and whole-metatranscriptome (What are they doing and who is alive?) sequencing have been established on Illumina MiSeq and HiSeq 2000 instruments. We have further established a pipeline to whole-genome sequence thousands of bacteria and detect their genetic variation. Our sequencing and analysis infrastructure is open to scientific collaboration partners.