http://www.nature.com/nature/journal/vaop/ncurrent/full/nature17645.html
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
Hilary P. Browne,1, * Samuel C. Forster,1, 2, 3, * Blessing O. Anonye,1, Nitin Kumar,1, B. Anne Neville,1, Mark D. Stares,1, David Goulding4, & Trevor D. Lawley1,
Journal name Nature Year published: (2016)
DOI: doi:10.1038/nature17645 Received 25 September 2015 Accepted 08 March 2016
Published online 04 May 2016
Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
Hilary P. Browne,1, * Samuel C. Forster,1, 2, 3, * Blessing O. Anonye,1, Nitin Kumar,1, B. Anne Neville,1, Mark D. Stares,1, David Goulding4, & Trevor D. Lawley1,
Journal name Nature Year published: (2016)
DOI: doi:10.1038/nature17645 Received 25 September 2015 Accepted 08 March 2016
Published online 04 May 2016
Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing1, 2. Intestinal colonization 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, owing 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 modelling that demonstrates that a substantial proportion of the intestinal bacteria are culturable. 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. 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. 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.