title: Microbial taxonomy in the post-genomic era: rebuilding from scratch?
abstract: Microbial taxonomy should provide adequate descriptions of bacterial, archaeal, and eukaryotic microbial diversity in ecological, clinical, and industrial environments. Its cornerstone, the prokaryote species has been re-evaluated twice. It is time to revisit polyphasic taxonomy, its principles, and its practice, including its underlying pragmatic species concept. Ultimately, we will be able to realize an old dream of our predecessor taxonomists and build a genomic-based microbial taxonomy, using standardized and automated curation of high-quality complete genome sequences as the new gold standard.
authors.affiliation: Laboratory of Microbiology, 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: Gilda R
authors.initials: GR
authors.lastname: Amaral
authors.forename: Mariana
authors.initials: M
authors.lastname: Campeão
authors.forename: Robert A
authors.initials: RA
authors.lastname: Edwards
authors.forename: Martin F
authors.initials: MF
authors.lastname: Polz
authors.forename: Bas E
authors.initials: BE
authors.lastname: Dutilh
authors.forename: David W
authors.initials: DW
authors.lastname: Ussery
authors.forename: Tomoo
authors.initials: T
authors.lastname: Sawabe
authors.forename: Jean
authors.initials: J
authors.lastname: Swings
authors.forename: Fabiano L
authors.initials: FL
authors.lastname: Thompson
mesh_terms: D001105:Archaea / Q000145:classification* / Q000235:genetics*; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D002965:Classification / Q000379:methods*; D003198:Computer Simulation; D023281:Genomics; D008829:Microbiology / Q000639:trends*