A new genomic blueprint of the human gut microbiota
Open accessAbstract
The composition of the human gut microbiota is linked to health and disease, but knowledge of individual microbial species is needed to decipher their biological roles. Despite extensive culturing and sequencing efforts, the complete bacterial repertoire of the human gut microbiota remains undefined. Here we identify 1,952 uncultured candidate bacterial species by reconstructing 92,143 metagenome-assembled genomes from 11,850 human gut microbiomes. These uncultured genomes substantially expand the known species repertoire of the collective human gut microbiota, with a 281% increase in phylogenetic diversity. Although the newly identified species are less prevalent in well-studied populations compared to reference isolate genomes, they improve classification of understudied African and South American samples by more than 200%. These candidate species encode hundreds of newly identified biosynthetic gene clusters and possess a distinctive functional capacity that might explain their elusive nature. Our work expands the known diversity of uncultured gut bacteria, which provides unprecedented resolution for taxonomic and functional characterization of the intestinal microbiota.
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Metagenomic assembly can partially mitigate the underrepresentation of non-westernized microbiome members in genomic catalogs.
“Recent efforts showed that metagenomic assembly can partially mitigate this problem,23,25,33,34”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [33]
Microbiome members of individuals from non-westernized populations are underrepresented by current cultivation-based genomic catalogs, causing metagenomic profiling to miss large fractions of microbial diversity.
“Microbiome members of individuals from non-westernized populations are particularly underrepresented by current cultivation-based genomic catalogs causing metagenomic profiling approaches to miss large fractions of the microbial diversity in the samples.”
From Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population (2023) · cites this paper as [33]
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- Authors
- Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D.
- Affiliations
- European Bioinformatics Institute (GB)
- Wellcome Sanger Institute (GB)
- Western University (CA)
- Corresponding author
- Almeida, Alexandre
- Finn, Robert D.
- ORCID
- Venue
- Nature
- Published
- 2019-02-11
- Volume
- 568
- Issue
- 7753
- Pages
- 499-504
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC6784870
- OpenAlex
- W2913972921
- Cited by
- 1,314
- References
- 82
- Citations by year
- 2026: 96 · 2025: 144 · 2024: 169 · 2023: 164 · 2022: 215 · 2021: 253 · 2020: 200 · 2019: 67 · 2017: 1 · 2013: 1
- FWCI
- 62.28
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Monash University Research Portal (Monash University) (submittedVersion, other-oa)
- RePEc: Research Papers in Economics (submittedVersion)
- Funders
- Wellcome Trust (098051)
- European Molecular Biology Laboratory
- European Commission (HORIZON2020, 676559)
- State Government of Victoria
- Directorate for Biological Sciences
- Medical Research Council (098051)
- Biotechnology and Biological Sciences Research Council (BB/N018354/1)
- National Health and Medical Research Council (1141564, 1091097)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Keywords
- human gut microbiome, metagenome-assembled genomes, bacterial diversity, phylogenetic diversity, biosynthetic gene clusters, microbial taxonomy
- MeSH terms
- Gastrointestinal Microbiome, Bacteria, Multigene Family, Humans, Phylogeny, Species Specificity, Genome, Bacterial, Genomics, Metagenome
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