mkdoherty
commented
8 years ago All 16S rRNA pyrosequencing datasets have been deposited in the National Center for Biotechnology In- formation (NCBI) Sequence Read Archive (SRA) (accession no. SRA026269).
and all shotgun pyrosequencing datasets are available in the NCBI SRA under accession no. SRA026270
Contigs and unassembled reads were mapped by BLAST to the National Center for Biotechnology Information (NCBI) nonredundant database and to a custom database of 122 human gut microbial genomes. All sequence datasets have been deposited in the NCBI Sequence Read Archive (SRA) under accession no. SRA026271.
Goodman, A. L. Kallstrom, G. Faith, J. J. Reyes, A. Moore, A. Dantas, G. Gordon, J. I. 2011. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. http://dx.doi.org/10.1073/pnas.1102938108 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 multiwell format to create personalized microbiota collections. Retrieving components of a microbiota that have coexisted in single donors who have physiologic or disease phenotypes of interest and reuniting them in various combinations in gnotobiotic mice should facilitate preclinical studies designed to determine the degree to which tractable bacterial taxa are able to transmit donor traits or influence host biology.