title: Culturing of 'unculturable' human microbiota reveals novel taxa and extensive sporulation.
abstract: Our intestinal microbiota harbours a diverse bacterial community required for our health, sustenance and wellbeing. 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. Culture-independent, genomic approaches have transformed our understanding of the role of the human microbiome in health and many diseases. However, owing to the prevailing perception that our indigenous bacteria are largely recalcitrant to culture, many of their functions and phenotypes remain unknown. 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.
authors.affiliation: Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Hilary P
authors.initials: HP
authors.lastname: Browne
authors.affiliation: Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.|Centre for Innate Immunity and Infectious Diseases, Hudson Institute of Medical Research, Clayton, Victoria, Australia.|Department of Molecular and Translational Sciences, Monash University, Clayton, Victoria, Australia.
authors.forename: Samuel C
authors.initials: SC
authors.lastname: Forster
authors.affiliation: Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Blessing O
authors.initials: BO
authors.lastname: Anonye
authors.affiliation: Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Nitin
authors.initials: N
authors.lastname: Kumar
authors.affiliation: Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: B Anne
authors.initials: BA
authors.lastname: Neville
authors.affiliation: Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Stares
authors.affiliation: Microbial Pathogenesis Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: David
authors.initials: D
authors.lastname: Goulding
authors.affiliation: Host-Microbiota Interactions Laboratory, Wellcome Trust Sanger Institute, Hinxton, UK.
authors.forename: Trevor D
authors.initials: TD
authors.lastname: Lawley
mesh_terms: D000693:Anaerobiosis; D001419:Bacteria / Q000145:classification* / Q000187:drug effects / Q000235:genetics / Q000254:growth & development* / Q000302:isolation & purification; D015373:Bacterial Typing Techniques; D018929:Cell Culture Techniques; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome / Q000187:drug effects / Q000235:genetics / Q000502:physiology*; D016680:Genome, Bacterial / Q000235:genetics; D006262:Health; D006801:Humans; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics; D010100:Oxygen / Q000378:metabolism / Q000494:pharmacology; D010641:Phenotype; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013171:Spores, Bacterial / Q000145:classification / Q000187:drug effects / Q000254:growth & development
chemical_list: D010100:Oxygen