title: Genome-Based Taxonomic Classification ofBacteroidetes.
abstract: The bacterial phylumBacteroidetes, characterized by a distinct gliding motility, occurs in a broad variety of ecosystems, habitats, life styles, and physiologies. Accordingly, taxonomic classification of the phylum, based on a limited number of features, proved difficult and controversial in the past, for example, when decisions were based on unresolved phylogenetic trees of the 16S rRNA gene sequence. Here we use a large collection of type-strain genomes fromBacteroidetesand closely related phyla for assessing their taxonomy based on the principles of phylogenetic classification and trees inferred from genome-scale data. No significant conflict between 16S rRNA gene and whole-genome phylogenetic analysis is found, whereas many but not all of the involved taxa are supported as monophyletic groups, particularly in the genome-scale trees. Phenotypic and phylogenomic features support the separation ofBalneolaceaeas new phylumBalneolaeotafromRhodothermaeotaand ofSaprospiraceaeas new classSaprospiriafromChitinophagia.Epilithonimonasis nested within the older genusChryseobacteriumand without significant phenotypic differences; thus merging the two genera is proposed. Similarly,Vitellibacteris proposed to be included inAequorivita.Flexibacteris confirmed as being heterogeneous and dissected, yielding six distinct genera.Hallella seregensis a later heterotypic synonym ofPrevotella dentalis. Compared to values directly calculated from genome sequences, the G+C content mentioned in many species descriptions is too imprecise; moreover, corrected G+C content values have a significantly better fit to the phylogeny. Corresponding emendations of species descriptions are provided where necessary. Whereas most observed conflict with the current classification ofBacteroidetesis already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.
authors.affiliation: Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany.
authors.forename: Richard L
authors.initials: RL
authors.lastname: Hahnke
authors.affiliation: Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany.
authors.forename: Jan P
authors.initials: JP
authors.lastname: Meier-Kolthoff
authors.affiliation: Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany.
authors.forename: Marina
authors.initials: M
authors.lastname: García-López
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI) Walnut Creek, CA, USA.
authors.forename: Supratim
authors.initials: S
authors.lastname: Mukherjee
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI) Walnut Creek, CA, USA.
authors.forename: Marcel
authors.initials: M
authors.lastname: Huntemann
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI) Walnut Creek, CA, USA.
authors.forename: Natalia N
authors.initials: NN
authors.lastname: Ivanova
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI) Walnut Creek, CA, USA.
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.affiliation: Department of Energy Joint Genome Institute (DOE JGI)Walnut Creek, CA, USA; Department of Biological Sciences, Faculty of Science, King Abdulaziz UniversityJeddah, Saudi Arabia.
authors.forename: Nikos C
authors.initials: NC
authors.lastname: Kyrpides
authors.affiliation: School of Biology, Newcastle University Newcastle upon Tyne, UK.
authors.forename: Hans-Peter
authors.initials: HP
authors.lastname: Klenk
authors.affiliation: Department of Microorganisms, Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Braunschweig, Germany.
authors.forename: Markus
authors.initials: M
authors.lastname: Göker
keywords: Bacteroidaeota-Rhodothermaeota-Balneolaeota-Chlorobaeota superphylum; G+C content; genome BLAST distance phylogeny; gliding motility; gut microbiome; marine microbiology; one thousand microbial genomes project; phylogenetic classification