title: Microbial genomic taxonomy.
abstract: A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.
authors.affiliation: Institute of Biology, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil. thompsoncristiane@gmail.com.
authors.forename: Cristiane C
authors.initials: CC
authors.lastname: Thompson
authors.forename: Luciane
authors.initials: L
authors.lastname: Chimetto
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Jean
authors.initials: J
authors.lastname: Swings
authors.forename: Erko
authors.initials: E
authors.lastname: Stackebrandt
authors.forename: Fabiano L
authors.initials: FL
authors.lastname: Thompson
mesh_terms: D001419:Bacteria / Q000145:classification*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D058885:Multilocus Sequence Typing; D009693:Nucleic Acid Hybridization; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D012336:RNA, Ribosomal, 16S