Towards the human intestinal microbiota phylogenetic core
Abstract
Summary: The paradox of a host specificity of the human faecal microbiota otherwise acknowledged as characterized by global functionalities conserved between humans led us to explore the existence of a phylogenetic core. We investigated the presence of a set of bacterial molecular species that would be altogether dominant and prevalent within the faecal microbiota of healthy humans. A total of 10 456 non‐chimeric bacterial 16S rRNA sequences were obtained after cloning of PCR‐amplified rDNA from 17 human faecal DNA samples. Using alignment or tetranucleotide frequency‐based methods, 3180 operational taxonomic units (OTUs) were detected. The 16S rRNA sequences mainly belonged to the phyla Firmicutes (79.4%), Bacteroidetes (16.9%), Actinobacteria (2.5%), Proteobacteria (1%) and Verrumicrobia (0.1%). Interestingly, while most of OTUs appeared individual‐specific, 2.1% were present in more than 50% of the samples and accounted for 35.8% of the total sequences. These 66 dominant and prevalent OTUs included members of the genera Faecalibacterium , Ruminococcus , Eubacterium , Dorea , Bacteroides , Alistipes and Bifidobacterium . Furthermore, 24 OTUs had cultured type strains representatives which should be subjected to genome sequence with a high degree of priority. Strikingly, 52 of these 66 OTUs were detected in at least three out of four recently published human faecal microbiota data sets, obtained with very different experimental procedures. A statistical model confirmed these OTUs prevalence. Despite the species richness and a high individual specificity, a limited number of OTUs is shared among individuals and might represent the phylogenetic core of the human intestinal microbiota. Its role in human health deserves further study.
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Most human adult gut microbiota belong to the genera Faecalibacterium, Bacteroides, Roseburia, Ruminococcus, Eubacterium, Coprabacillus, and Bifidobacterium.
“Most belong to the genera Faecalibacterium, Bacteroides, Roseburia, Ruminococcus, Eubacterium, Coprabacillus, and Bifidobacterium.147”
From The Gut Microbiome and the Brain (2014) · cites this paper as [147]
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Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymesPreprint
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Self-citation
- Authors
- Tap, J., Mondot, S., Levenez, F., Pelletier, E., Caron, C., Furet, J., Ugarte, E., Muñoz‐Tamayo, R., Paslier, D. L. E., Nalin, R., Dore, J., & Leclerc, M.
- Affiliations
- Institut National de la Recherche Agronomique (FR)
- Centre National de la Recherche Scientifique (FR)
- Supélec (FR)
- Corresponding author
- Leclerc, Marion
- Venue
- Environmental Microbiology
- Publisher
- Wiley
- Published
- 2009-10
- Volume
- 11
- Issue
- 10
- Pages
- 2574-2584
- ISSN
- 1462-2912 (ISSN-L)
- 1462-2920
- OpenAlex
- W2029943794
- Cited by
- 927
- References
- 49
- Citations by year
- 2026: 19 · 2025: 20 · 2024: 46 · 2023: 56 · 2022: 61 · 2021: 59 · 2020: 70 · 2019: 53 · 2018: 53 · 2017: 52 · 2016: 62 · 2015: 55 · 2014: 56 · 2013: 76 · 2012: 58
- FWCI
- 25.20
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Environmental Microbiology (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- Agence Nationale de la Recherche (ANR-06-PNRA-0024)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
- Health Sciences › Dentistry › Periodontics › Oral microbiology and periodontitis research
- Keywords
- human gut microbiome, fecal microbiota, 16S rRNA sequences, operational taxonomic units, Firmicutes, Bacteroidetes, Faecalibacterium, Ruminococcus, Bifidobacterium, Bacteroides, Alistipes, species richness, host specificity, cross-study comparison
- MeSH terms
- Bacteroides, Bifidobacterium, DNA, Bacterial, Eubacterium, Feces, Gram-Positive Bacteria, Humans, Intestines, Phylogeny, RNA, Ribosomal, 16S, Species Specificity, Genome, Bacterial, Sequence Analysis, DNA, Biodiversity, Ruminococcus
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