Revealing microbial species diversity using sequence capture by hybridization

Abstract

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.

RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties

“…As indicated by EMIRGE developers, occasional presence of small indel errors in the reconstructed sequence could occur but in practice, these rare indels have little effect on taxonomic classification. Accuracy of 16S sequence reconstruction can be controlled as recently demonstrated by Marre et al ( 85 ). The authors designed specific primers targeting nearly full-length reconstructed 16S rRNA genes using the KASpOD algorithm ( 86 ) and tested them on biological samples through PCR experiments coupled with Sanger sequencing.…”