Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and well-being1,2. Intestinal colonisation begins at birth and climaxes with the acquisition of two dominant groups of strict anaerobic bacteria belonging to the Firmicutes and Bacteroidetes phyla2. Culture independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases1. However, due to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown3. Here we describe a novel workflow based on targeted phenotypic culturing linked to large-scale whole genome sequencing, phylogenetic analysis and computational modeling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. Applying this approach to healthy individuals, we isolated 137 bacterial species from characterised and candidate novel families, genera and species that were archived as pure cultures. 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, specialised for host-to-host transmission. Our approach unlocks the human intestinal microbiota for phenotypic analysis and reveals how a significant proportion of oxygen-sensitive intestinal bacteria can transmit between individuals, impacting microbiota heritability.

The treatment of cancer patients near death is becoming increasingly aggressive over time.