Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation
By H. Browne, S. C. Forster, Blessing O. Anonye, Nitin Kumar, B. Neville, Mark D. Stares, D. Goulding, T. Lawley. Nature, 2016
1,099 citations recorded by the source corpus.
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.
Subfields: Food Science, Infectious Diseases, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/f478b21fd5c02aae87b77625e0ce50cb7d1fd353
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Citations in the corpus
- Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies (2017, background): “in the human gut identified by DNA sequencing can be cultured, and that similar statistics can be obtained for soil and water samples (Browne et al., 2016).”
- Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle (2019, neutral): “Since physiological characterization of diverse, uncharacterized human-associated microbes by cultivation can be difficult in high throughput (Browne et al., 2016), additional approaches are needed that scale with the extent of populations that can now be surveyed using metagenomic sequencing.”
- Human gut microbiome: hopes, threats and promises (2018, background): “72 73 Moreover, when a putative candidate has been isolated and cultured, it is still necessary to culture it in quantities that are compatible with chronic in vivo testing.”
- Formation of propionate and butyrate by the human colonic microbiota. (2017, background): “A renewed interest in isolation and study of gut bacteria (Walker et al., 2014, Browne et al., 2016) together with novel systems for gene transfer and knockout on the horizon will enable a thorough understanding of the different members of the microbial community.”
- The First Microbial Colonizers of the Human Gut: Composition, Activities, and Health Implications of the Infant Gut Microbiota (2017, background): “Until the recent development of novel culturomics approaches (31), only a very small fraction of the human gut microbiota had been isolated and studied in pure culture (30).”
- Human gut microbiota in health and disease: Unveiling the relationship (2022, background): “The gut environment, sequentially, can help reproduce, grow, and survive the microbial community (Browne et al., 2016).”