Genome-Based Taxonomic Classification of Bacteroidetes

Abstract

The bacterial phylum <i>Bacteroidetes</i>, 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 from <i>Bacteroidetes</i> and 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 of <i>Balneolaceae</i> as new phylum <i>Balneolaeota</i> from <i>Rhodothermaeota</i> and of <i>Saprospiraceae</i> as new class <i>Saprospiria</i> from <i>Chitinophagia</i>. <i>Epilithonimonas</i> is nested within the older genus <i>Chryseobacterium</i> and without significant phenotypic differences; thus merging the two genera is proposed. Similarly, <i>Vitellibacter</i> is proposed to be included in <i>Aequorivita</i>. <i>Flexibacter</i> is confirmed as being heterogeneous and dissected, yielding six distinct genera. <i>Hallella seregens</i> is a later heterotypic synonym of <i>Prevotella dentalis</i>. 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 of <i>Bacteroidetes</i> is already visible in 16S rRNA gene trees, as expected whole-genome phylogenies are much better resolved.