16S rRNA gene amplicon sequencing of human gut microbiota cultivated under anaerobic conditions Raw sequence reads

Microbial consortia were collected from different compartments of the Simulator of Human Intestinal Microbial Ecology (SHIME) and cultivated under anaerobic conditions using different selective media. Metataxonomic (16S rRNA gene amplicon) profiles were analyzed before and after cultivation to assess the impact of growth conditions on taxonomic composition. Metataxonomic data were integrated with measurements of short-chain fatty acids (SCFAs). This study is a preliminary step toward developing stable cultivation conditions to enable testing of SHIME-derived microbial consortia in human intestinal cell culture models.