This overlap was 72% after de novo assembly ( Extended Data Fig. When sequenced, the original faecal sample and the cultured bacterial community shared an average of 93% of raw reads across the six donors. Importantly, we observed a strong correlation between the two samples at the species level (Spearman’s ρ = 0.75, P < 0.01) ( Fig. Applying shotgun metagenomic sequencing, we profiled and compared the bacterial species present in the original faecal samples to those that grew as distinct colonies on agar plates containing the complex, broad-range bacteriological medium, YCFA 7. Accordingly, we collected fresh faecal samples from six healthy humans and defined the resident bacterial communities with a combined metagenomic sequencing and bacterial culturing approach. We sought to establish a genomic-based workflow that could be used as a platform for targeted culturing of specific bacterial phenotypes ( Extended Data Fig. This formidable challenge to validate and decipher the functional attributes of the microbiota has been hindered because the majority of intestinal bacteria are widely considered to be ‘unculturable’ and have never been isolated in the laboratory 3, 6. However, many basic microbiota functions related to homeostasis, immune system development, digestion, pathogen resistance and microbiota inheritance have yet to be discovered 5. ![]() Despite the taxonomic diversity, metagenomic sequencing has highlighted that a health-associated intestinal microbiome codes for highly conserved gene families and pathways associated with basic bacterial physiology and growth 2. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a marked proportion of oxygen-sensitive intestinal bacteria can be transmitted between individuals, affecting microbiota heritability.Ī typical human intestinal microbiota contains 100–1,000 bacterial species with tremendous compositional diversity between individuals, such that each individual’s microbiota is as unique as a fingerprint 1, 4. Whole-genome and metagenomic sequencing, combined with computational and phenotypic analysis, suggests that at least 50–60% of the bacterial genera from the intestinal microbiota of a healthy individual produce resilient spores, specialized for host-to-host transmission. ![]() Applying this approach to healthy individuals, we isolated 137 bacterial species from characterized and candidate novel families, genera and species that were archived as pure cultures. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole-genome sequencing, phylogenetic analysis and computational modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown 3. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases 1. Intestinal colonization begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla 2. ![]() Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing 1, 2.
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