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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples
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Revealing microbial species diversity using sequence capture by hybridization.

Sophie Marre1, Cyrielle Gasc1,2, Camille Forest1

  • 1Université Clermont Auvergne, INRAE, MEDIS, F-63000, Clermont-Ferrand, France.

Microbial Genomics
|December 9, 2021
PubMed
Summary

Metabarcoding using 16S rDNA can miss species-level identification. A new gene capture method reveals high bacterial diversity in the human gut, identifying novel taxa and potential polyphenol degraders.

Keywords:
16S rRNA genegene capture by hybridizationhuman gut microbiotamicrobial diversitypolyphenol degradationrare biospherespecies identification

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Area of Science:

  • Microbiology
  • Genomics
  • Bioinformatics

Background:

  • Metabarcoding of 16S rDNA offers microbial insights but lacks species-level resolution.
  • Operational Taxonomic Units (OTUs) can obscure significant diversity within the rare biosphere.
  • Precise characterization of gut microbiota is crucial for understanding its functions.

Purpose of the Study:

  • To develop a novel strategy for identifying species within rare biosphere OTUs.
  • To enhance taxonomic resolution beyond traditional metabarcoding limitations.
  • To explore bacterial diversity and function in the human gut microbiota, particularly after polyphenol supplementation.

Main Methods:

  • Gene capture by hybridization targeting 16S rRNA genes.
  • Analysis of three specific OTUs from the rare biosphere of human gut microbiota.
  • Genome mining to identify bacteria with potential polyphenol degradation capabilities.

Main Results:

  • Successfully retrieved 59 nearly full-length 16S rRNA genes from three rare biosphere OTUs.
  • Revealed substantial hidden bacterial diversity, with intra-OTU sequence similarities as low as 85%.
  • Identified one new family (Clostridiales), 39 new genera, and 52 novel species.

Conclusions:

  • The developed gene capture strategy significantly enhances the identification of novel taxa and species in the human gut microbiota.
  • The human gut harbors greater bacterial diversity than previously recognized, including novel species potentially involved in polyphenol metabolism.
  • This approach enables precise characterization of microorganisms, advancing our understanding of gut microbiome functions.