Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We have recently presented the Human Gastrointestinal Bacteria Culture Collection (HBC) (Nature Biotechnology, 2019), a comprehensive set of 737 whole-genome-sequenced bacterial isolates, representing 273 species (105 novel species) from 31 families found in the human gastrointestinal microbiota. This resource increased the number of bacterial genomes derived from human gastrointestinal microbiota by 37% and allows metagenomic classification rates of 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, representing a 61% improvement on the Human Microbiome Project (HMP) genome collection alone. Importantly this collection enables sub-species level classification of over 50% of metagenomic reads.
We have now combined detailed functional analysis with high throughput computational investigation of 13,490 shotgun sequenced metagenomic samples from around the world to investigate the diversity of functions and define core, keystone species, essential capacity and functional redundancy. Taken together, this knowledge provides the capacity to develop standardised live biotherapeutic (bacteriotherapy) compositions that provide the necessary functional capacity to restore health in patients with dysbiosis associated conditions including gastrointestinal infections and chronic inflammatory bowel diseases.