Towards the human intestinal microbiota phylogenetic core

Environ Microbiol. 2009 Oct;11(10):2574-84. doi: 10.1111/j.1462-2920.2009.01982.x. Epub 2009 Jul 6.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteroides / genetics*
  • Bacteroides / isolation & purification
  • Bifidobacterium / genetics
  • Bifidobacterium / isolation & purification
  • Biodiversity*
  • DNA, Bacterial / genetics
  • DNA, Bacterial / isolation & purification
  • Eubacterium / genetics
  • Eubacterium / isolation & purification
  • Feces / microbiology
  • Genome, Bacterial
  • Gram-Positive Bacteria / genetics*
  • Gram-Positive Bacteria / isolation & purification
  • Humans
  • Intestines / microbiology*
  • Phylogeny*
  • RNA, Ribosomal, 16S / analysis
  • RNA, Ribosomal, 16S / genetics
  • Ruminococcus / genetics
  • Ruminococcus / isolation & purification
  • Sequence Analysis, DNA
  • Species Specificity


  • DNA, Bacterial
  • RNA, Ribosomal, 16S