Open AccessRevealing microbial species diversity using sequence capture by hybridization
Author(s) -
Sophie Marre,
Cyrielle Gasc,
Camille Forest,
Yacine Lebbaoui,
Pascale Mosoni,
Pierre Peyret
Publication year - 2021
Publication title -
microbial genomics
Language(s) - English
Resource type - Journals
ISSN - 2057-5858
DOI - 10.1099/mgen.0.000714
Subject(s) - biology , phylogenetic tree , 16s ribosomal rna , clostridiales , operational taxonomic unit , phylogenetics , evolutionary biology , phylogenetic diversity , metagenomics , microbiome , taxonomic rank , human microbiome project , taxon , human microbiome , biodiversity , genetics , gene , ecology
Targeting small parts of the 16S rDNA phylogenetic marker by metabarcoding reveals microorganisms of interest but cannot achieve a taxonomic resolution at the species level, precluding further precise characterizations. To identify species behind operational taxonomic units (OTUs) of interest, even in the rare biosphere, we developed an innovative strategy using gene capture by hybridization. From three OTU sequences detected upon polyphenol supplementation and belonging to the rare biosphere of the human gut microbiota, we revealed 59 nearly full-length 16S rRNA genes, highlighting high bacterial diversity hidden behind OTUs while evidencing novel taxa. Inside each OTU, revealed 16S rDNA sequences could be highly distant from each other with similarities down to 85 %. We identified one new family belonging to the order Clostridiales , 39 new genera and 52 novel species. Related bacteria potentially involved in polyphenol degradation have also been identified through genome mining and our results suggest that the human gut microbiota could be much more diverse than previously thought.