Whole genome sequence of "Genomic and metabolic profiling of commensal human gut bacteria"

Recent advances in culturomics have enabled the isolation of human gut commensal microbes. However, the genotype-phenotype association for cultivated human gut bacteria is still lacking. To this end, we established the Human Gut Bacteria Isolate Collection (GBIC), which comprises 1,319 strains isolated from healthy human volunteers. We performed whole genome sequencing for GBIC strains and obtained 442 high-quality draft genomes for 323 species. The GBIC strains include 70 novel species and 18 novel genera, and cover >80% of core species and genera of the human gut microbiome. Through metabolomics profiling of 54 GBIC strains, we found significant correlation between phylogenetic distance and metabolic capacity. Moreover, we performed comprehensive genomic annotation and phenotypic profiling for GBIC strains, including short-chain fatty acid (SCFA) production, inulin utilization, bile acid metabolism, xenobiotics metabolism, and antibiotic resistance. In particular, we found that the presence of SCFA pathways via genomic annotation can accurately predict the capacity of SCFA production in monoculture (e.g. sensitivity = 92.9% and specificity = 96.8% for butyrate). In summary, the establishment of genotype-phenotype association for human gut bacterial strains allows for genome-guided discovery of functional microbes and facilitates the development of probiotics and live biotherapeutic products.