title: Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning.
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.
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France. celine.ribiere1@udamail.fr.
authors.forename: Céline
authors.initials: C
authors.lastname: Ribière
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France. rejane.beugnot@udamail.fr.
authors.forename: Réjane
authors.initials: R
authors.lastname: Beugnot
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France. nico.parisot@gmail.com.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Parisot
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France. cyrielle.gasc@sfr.fr.
authors.forename: Cyrielle
authors.initials: C
authors.lastname: Gasc
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France. clemence.defois@udamail.fr.
authors.forename: Clémence
authors.initials: C
authors.lastname: Defois
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France. jdenonfoux@yahoo.fr.|Genoscreen, Campus de l'Institut Pasteur de Lille, 59000, Lille, France. jdenonfoux@yahoo.fr.
authors.forename: Jérémie
authors.initials: J
authors.lastname: Denonfoux
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, BP 10448, 63000, Clermont-Ferrand, France. delphine.boucher@udamail.fr.
authors.forename: Delphine
authors.initials: D
authors.lastname: Boucher
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France. eric.peyretaillade@udamail.fr.
authors.forename: Eric
authors.initials: E
authors.lastname: Peyretaillade
authors.affiliation: EA 4678, CIDAM, Clermont Université, Université d'Auvergne, 28 place Henri Dunant, 63001, Clermont-Ferrand, France. pierre.peyret@udamail.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Peyret
mesh_terms: D015415:Biomarkers; D019295:Computational Biology; D004269:DNA, Bacterial / Q000235:genetics*; D017753:Ecosystem; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D054892:Metagenome / Q000235:genetics; D056186:Metagenomics / Q000379:methods*; D009693:Nucleic Acid Hybridization / Q000379:methods; D015347:RNA Probes; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D015415:Biomarkers; D004269:DNA, Bacterial; D015347:RNA Probes
keywords: Metagenomics; Metatranscriptomics; Microbial diversity; Next-generation sequencing; RNA probes; Solution hybrid selection