Mikrobiom Core Facility

The intestinale microbiome is composed of all microorganisms (microbiota), inhabiting the gastro-intestinale-tract, and their collective genomes (metagenome). The microbiome is affected by numerous host intrinsic (age, genome) and environmental factors such as nutrition, life style, health status and medication. The composition of the intestinal microbiota is dominated by few phyla including Firmicutes and Bacteroidetes, Actinobacteria, as well as Proteobacteria. The diversity at the species level is high.

In total, 16S rRNA gene and shotgun metagenomic analyses identified more than 1000 distinct molecular species called operational taxonomic units (OTU). Diversity indices including alpha-diversity (e.g. Shannon and Simpson) and beta-diversity, describe the species richness and eveness within an ecosystem as well as the phylogenetic difference between ecosystems.

The Microbiome Core Facility at ZIEL established a platform for high-throughput analyses of microbial ecosystems using 16S rRNA gene amplicon and shotgun metagenomic sequencing. Novel bioinformatic tools for data analysis are available on-line using the IMNGS pipeline.

Link to IMNGS platform

In addition to the compositional analysis, the Microbiome Core Facility isolates and archives gut bacteria and implements the modern germfree mouse house for the functional analysis of microbiota-host interactions in gnotobiotic experiments.