title: Capturing prokaryotic dark matter genomes.
abstract: Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches.
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France. Electronic address: cyrielle.gasc@udamail.fr.
authors.forename: Cyrielle
authors.initials: C
authors.lastname: Gasc
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France. Electronic address: celine.ribiere1@udamail.fr.
authors.forename: Céline
authors.initials: C
authors.lastname: Ribière
authors.affiliation: Biologie Fonctionnelle Insectes et Interactions, UMR203 BF2I, INRA, INSA-Lyon, Université de Lyon, Villeurbanne, France. Electronic address: nicolas.parisot@insa-lyon.fr.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Parisot
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France. Electronic address: rejane.beugnot@udamail.fr.
authors.forename: Réjane
authors.initials: R
authors.lastname: Beugnot
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France. Electronic address: clemence.defois@udamail.fr.
authors.forename: Clémence
authors.initials: C
authors.lastname: Defois
authors.affiliation: Université Blaise Pascal, Laboratoire Microorganismes, Génome et Environnement, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 6023, F-63171 Aubière, France. Electronic address: corinne.PETIT@univ-bpclermont.fr.
authors.forename: Corinne
authors.initials: C
authors.lastname: Petit-Biderre
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France. Electronic address: delphine.boucher@udamail.fr.
authors.forename: Delphine
authors.initials: D
authors.lastname: Boucher
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France. Electronic address: eric.peyretaillade@udamail.fr.
authors.forename: Eric
authors.initials: E
authors.lastname: Peyretaillade
authors.affiliation: Clermont Université, Université d'Auvergne, EA 4678 CIDAM, BP 10448, F-63001 Clermont-Ferrand, France. Electronic address: pierre.peyret@udamail.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Peyret
mesh_terms: D001105:Archaea / Q000235:genetics / Q000378:metabolism*; D001419:Bacteria / Q000235:genetics / Q000378:metabolism*; D017753:Ecosystem; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D056186:Metagenomics / Q000379:methods; D011387:Prokaryotic Cells; D059010:Single-Cell Analysis
keywords: Complete genome reconstruction; Dark matter; Metagenomics; Single-cell genomics