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Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
Open accessAbstract
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.
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“Many more species continue to be cultured as laboratory-based efforts have become more high-throughput 43,44 .”
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Metadata
- Authors
- Browne, H. P., Forster, S. C., Anonye, B. O., Kumar, N., Neville, B. A., Stares, M. D., Goulding, D., & Lawley, T. D.
- Affiliations
- Wellcome Sanger Institute (GB)
- Corresponding author
- Lawley, Trevor D.
- ORCID
- Venue
- Nature
- Published
- 2016-05-04
- Volume
- 533
- Issue
- 7604
- Pages
- 543-546
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC4890681
- OpenAlex
- W2345813655
- Cited by
- 1,299
- References
- 41
- Citations by year
- 2026: 60 · 2025: 90 · 2024: 119 · 2023: 102 · 2022: 131 · 2021: 164 · 2020: 170 · 2019: 180 · 2018: 119 · 2017: 120 · 2016: 41
- FWCI
- 79.72
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- CLOK (University of Central Lancashire) (acceptedVersion)
- Monash University Research Portal (Monash University) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Wellcome Trust (098051)
- State Government of Victoria
- Medical Research Council (098051, PF451, MR/K000551/1)
- National Health and Medical Research Council (1091097)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- uncultured bacteria, human gut microbiome, bacterial sporulation, spore-forming bacteria, host-to-host transmission, novel bacterial taxa, Firmicutes, Bacteroidetes, anaerobic bacteria, metagenomics, whole genome sequencing
- MeSH terms
- Gastrointestinal Microbiome, Anaerobiosis, Bacteria, Feces, Health, Humans, Oxygen, Phenotype, Phylogeny, Species Specificity, Spores, Bacterial, Bacterial Typing Techniques, Genome, Bacterial, Sequence Analysis, DNA, Cell Culture Techniques, Metagenome, Metagenomics
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