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GRK 1482 Jahrbuch 2011-2014

Abstract In this project we intend to establish and improve methods for taxon- specific cell enrichment. In that process, the focus is on bacteria of relevance in the gut. Furthermore the project aims to evaluate if these methods are suited for the study of sub-metagenomes by sequencing. Introduction The microbiota of the gut consists of a huge number of different microbial species whose com- position has been shown to vary greatly between individuals. Despite the recent finding from large-scale- sequencing of fecal metagenomes that three robust “enterotypes”, which are defined mostly by species composition, exist among human gut microbiomes [1], the microbial compositions remain complex and their whole-scale analysis in individu- als is challenging. For certain scientific questions, however, it would suffice to examine in a targeted manner only a taxon-specific sub-metagenome, e.g. the species belonging to one genus of interest such as Entero- coccus or Escherichia/Shigella or Clostridium. Examples for study objectives along this line are (i) the in-depth analysis of the metagenomes of selected taxa with respect to variation in individuals including the functional genomic information, (ii) the analysis of changes in the composition and functionality in taxon-specific populations of microbes under different conditions (e.g. in re- sponse to diet or inflammation), or (iii) the analysis of changes in the composition and function- ality of taxon-specific populations under the influence of competing or probiotic strains, etc. The taxon of choice to start this project is Entero- coccus, representing only a subdominant popu- lation of the intestinal microbiome, with compara- tively few species members. The enterococci are Gram-positive, facultative anaerobic cocci with the ability to survive harsh conditions. Although the genus constitutes a small portion of the gut mi- crobiota, it includes some of the most important nosocomial multidrug-resistant organisms, caus- ing urinary tract infections (UTIs) and bloodstream infections [2]. ASSOCIATED FELLOWS Page 62 | GRK Progress Report 2011-2014 Lena Bruder (Mag.biol.) Microbiology PhD 3/2 Reducing the metagenomic sequence space for analysis of the gut microflora by taxon-specific cell enrichment