Microbiome Studies

Facts & Details: 

Microorganisms 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 microbes 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 microbial 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 with a specific focus on the etiology of inflammatory autoimmune diseases.

Our laboratory has established methods to determine bacterial richness and ASVs in a given sample (Who is there? 16S rDNA or ITS2 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 NovaSeq 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.


Main research Projects: 

Microbial dysbiosis is often associated with chronic inflammatory diseases, thus the microbiome is considered a promising target for innovative and individualized therapies in human medicine.

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  • In project 1 of the CRU 306 Primary Sclerosing Cholangitis we investigate the the intestinal and biliary microbiome, as well as the relationship between genetics, metabolism, and nutrition with the microbiome in chronic liver diseases, which are often associated with gastrointestinal disorders.


  • Our research on the Microbiome-Immune-Brain-Axis within the Clinician Scientist Program Gut-Brain-Axis of the Else Kröner-Forschungskolleg (EKFK) encompasses cross-disease mechanisms of development and influencing factors within the reciprocal relationship between microbiome, inflammation and brain in neurological (multiple sclerosis, Parkinson's disease, Alzheimer's disease) and internal diseases (inflammatory bowel disease, obesity and diabetes).

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  • Evolutionary and/or ecological changes in the interaction with the microbiome appear to contribute to the development of chronic inflammatory diseases. In subproject A2 of the CRC Origin and function of metaorganisms, we aim to unravel the underlying mechanisms of functional changes of the microbiome to prevent etiology of chronic diseases.


  • To identify which genetic mechanisms are involved in reciprocal adaptation within the human metaorganism, we already created the so far largest German gut microbiota reference data set (MicrobiotaGWAS) from three geographically distinct cross-sectional cohorts and identified associations between the blood group system and human microbiota taxonomic composition. Currently, we expand this knowledge within the international consortium MiBioGen.

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Main Publications

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