Microbial Environmental Genomics (MEG) pp 167-182

Part of the Methods in Molecular Biology book series (MIMB, volume 1399)

| Cite as

Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning

  • Céline Ribière
  • Réjane Beugnot
  • Nicolas Parisot
  • Cyrielle Gasc
  • Clémence Defois
  • Jérémie Denonfoux
  • Delphine Boucher
  • Eric Peyretaillade
  • Pierre Peyret

Abstract

Microbial communities are extremely abundant and diverse on earth surface and play key role in the ecosystem functioning. Thus, although next-generation sequencing (NGS) technologies have greatly improved knowledge on microbial diversity, it is necessary to reduce the biological complexity to better understand the microorganism functions. To achieve this goal, we describe a promising approach, based on the solution hybrid selection (SHS) method for the selective enrichment in a target-specific biomarker from metagenomic and metatranscriptomic samples. The success of this method strongly depends on the determination of sensitive, specific, and explorative probes to assess the complete targeted gene repertoire. Indeed, in this method, RNA probes were used to capture large DNA or RNA fragments harboring biomarkers of interest that potentially allow to link structure and function of communities of interest.

Key words

Solution hybrid selection Metagenomics Metatranscriptomics Microbial diversity RNA probes Next-generation sequencing 

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Copyright information

© Springer Science+Business Media New York 2016

Authors and Affiliations

  • Céline Ribière
    • 1
  • Réjane Beugnot
    • 1
  • Nicolas Parisot
    • 1
  • Cyrielle Gasc
    • 1
  • Clémence Defois
    • 1
  • Jérémie Denonfoux
    • 1
    • 2
  • Delphine Boucher
    • 1
  • Eric Peyretaillade
    • 3
  • Pierre Peyret
    • 3
  1. 1.EA 4678, CIDAMClermont Université, Université d’AuvergneClermont-FerrandFrance
  2. 2.GenoscreenLilleFrance
  3. 3.EA 4678, CIDAMClermont Université, Université d’AuvergneClermont-FerrandFrance

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