Culturing_454_16S
Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice
16S and metagenomic survey of culturable and non-culturable microbiota
The proportion of the human gut bacterial community that is recalcitrant to culture remains poorly defined. In this report, we combine high-throughput anaerobic culturing techniques with gnotobiotic animal husbandry and metagenomics to show that the human fecal microbiota consists largely of taxa and predicted functions that are represented in its readily cultured members. When transplanted into gnotobiotic mice, complete and cultured communities exhibit similar colonization dynamics, biogeographical distribution, and responses to dietary perturbations. Moreover, gnotobiotic mice can be used to shape these personalized culture collections to enrich for taxa suited to specific diets. We also demonstrate that thousands of isolates from a single donor can be clonally archived and taxonomically mapped in multi-well format to create personalized microbiota collections. Retrieving components of a microbiota that have co-existed in single donors who have physiologic or disease phenotypes of interest and reuniting them in various combinations in gnotobiotic mice should facilitate pre-clinical studies designed to determine the degree to which tractable bacterial taxa are able to transmit donor traits or influence host biology.