The focus of our microbiome laboratory is the identification of genetic and non-genetic factors that shape the microbiome. Multi-OMICs studies integrating microbial profiles, metabolic, genetic, phenotypic and nutritional data are performed under standardized high-throughput methods to identify relevant factors and mechanisms. The Microbiome laboratory at the Institute of Clinical Molecular Biology of the Christian-Albrechts-University of Kiel and the University Medical Center Schleswig-Holstein has established methods to determine bacterial richness and ASVs in a given sample (Who's there? 16S rDNA high-throughput sequencing). In addition, we offer metagenome (Who is there and what are they doing?) and metatranscriptome sequencing (Who is there and what cellular processes are they performing?) on Illumina MiSeq and NovaSeq instruments. In addition, a pipeline has been established for genome sequencing of individual bacteria and detection of their genetic variation, e.g. for identification of resistance genes. We also offer a broad portfolio of extraction methods for different sample types (stool, swabs, soil) derived from different hosts and environments, and the analytical tools are scalable, partially automated, and applicable in experiments ranging from a few observation points to larger cohorts with thousands of patients.