A human gut bacterial genome and culture collection for improved metagenomic analyses

Abstract

Understanding gut microbiome functions requires cultivated bacteria for experimental validation and reference bacterial genome sequences to interpret metagenome datasets and guide functional analyses. We present the Human Gastrointestinal Bacteria Culture Collection (HBC), 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. The HBC increases the number of bacterial genomes derived from human gastrointestinal microbiota by 37%. The resulting global Human Gastrointestinal Bacteria Genome Collection (HGG) classifies 83% of genera by abundance across 13,490 shotgun-sequenced metagenomic samples, improves taxonomic classification by 61% compared to the Human Microbiome Project (HMP) genome collection and achieves subspecies-level classification for almost 50% of sequences. The improved resource of gastrointestinal bacterial reference sequences circumvents dependence on de novo assembly of metagenomes and enables accurate and cost-effective shotgun metagenomic analyses of human gastrointestinal microbiota.

High-throughput isolation and sorting of gut microbes reduce biases of traditional cultivation strategies

“…Despite large-scale cultivation efforts employing the manual picking of tens of thousands of colonies [7][8][9][10], a significant fraction of gut microbiota remains uncultured. In fact, recent large-scale analyses that reconstructed population genomes directly from gut metagenomes indicate that our current culture collections lack 40% to 50% of genera encompassing ~2,000 species [45][46][47].…”

“…However, inferring the taxonomic composition or functional potential of complex gut microbiomes does not reveal mechanistic underpinnings of observed associations [3][4][5]. Microbial cultivation is an essential first step to address some of these shortcomings as this strategy enables the recovery of complete reference genomes [6], accurate identification of taxonomy and functional potential of new strains [7,8], and validation of causality by perturbation experiments [5]. Microbial cultivation is currently experiencing a pronounced revival [7][8][9][10][11], yet the majority of cultivation efforts require arduous manual picking of thousands of colonies, impeding the efforts to harmonize discoveries that emerge from 'omics strategies with downstream mechanistic investigations in the rapidly advancing field of microbiome research.…”

Capturing the Complex Interplay Between Drugs and the Intestinal Microbiome

“…Using in vitro techniques, we have found that Escherichia coli ( E. coli ) is inhibited on media containing a concentration equivalent to tea brewed with 1 tea bag (~ 0.5 g/L catechins), whereas 1.5 tea bags are required to inhibit the growth of Enterococcus faecium . Nevertheless, culture‐based assays are laborious and limited by the fact that we do not yet know how to culture some microorganisms from the human intestine …”

“…Nevertheless, culture-based assays are laborious and limited by the fact that we do not yet know how to culture some microorganisms from the human intestine. 1 The most common approach for studying the intestinal microbiome is to perform sequencing of the 16S ribosomal RNA (rRNA) gene of fecal samples before and after treatment with a drug (Figure 1b). Sequencing the 16S rRNA has become popular due to the gene's ubiquity across all prokaryotes, ease of selective amplification with polymerase chain reaction primers targeting conserved regions, and variable regions that may provide genus-level resolution.…”

“…The intestinal microbiome is a complex community of microorganisms, typically containing hundreds of different species, many of which can be cultured in the laboratory. 1 The composition of individuals' microbiomes is remarkably resilient given that they reside in a transient environment with a continual flux of variable food sources. Microbiome composition varies considerably from person to person, and interindividual variation is often greater than day-to-day variation within the same individual.…”