Genome-Based Taxonomic Classification of Bacteroidetes

Abstract

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

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.

Figure 1

Relationship between G+C content values from species descriptions and those calculated from the genome sequences. (A) scatter plot showing the relationship between G+C content values calculated from the genome sequences and those found in the respective last revision in the literature, mostly calculated traditionally. The gray band indicates the boundary of 1% deviation, green color (when ranges were provided) and circles indicate values within that range, red color and triangles indicate values outside that range. (B) box plots showing the MP scores calculated with TNT from the rescaled G+C content values of distinct origin (pub, published; min, avg and max refer to whether the lower, average or upper value was used when a range was given) in conjunction with the 100 pseudo-bootstrapped GBDP trees. The values calculated from the genome sequences yield a significantly lower MP score (and thus a significantly better fit to the tree) than the ones from the respective last emendation in the literature.

Figure 2

First part of the phylogenomic tree inferred with GBDP. Tree inferred with FastME from GBDP distances calculated from whole proteomes. The numbers above branches are GBDP pseudo-bootstrap support values from 100 replications. Tip colors indicate the phylum, colors to the right of the ingroup tips indicate, from left to right, class, order and family (see the embedded legend for details). Gray scale on the very right indicates the exact G+C content as calculated from the genome sequences. The Bacteroidia and Flavobacteriia parts of the tree, which have been collapsed here, are shown in Figures 3, 4.

Figure 3

Second part of the phylogenomic tree inferred with GBDP. Tree inferred with FastME from GBDP distances calculated from whole proteomes. The numbers above branches are GBDP pseudo-bootstrap support values from 100 replications. Tip colors indicate the phylum, colors to the right of the ingroup tips indicate, from left to right, class, order and family (see the legend embedded in Figure 2 for details). Gray scale on the very right indicates the exact G+C content as calculated from the genome sequences. The non-Bacteroidia parts of the tree, which have been collapsed here, are shown in Figures 2, 4.

Figure 4

Third part of the phylogenomic tree inferred with GBDP. Tree inferred with FastME from GBDP distances calculated from whole proteomes. The numbers above branches are GBDP pseudo-bootstrap support values from 100 replications. Tip colors indicate the phylum, colors to the right of the ingroup tips indicate, from left to right, class, order and family (see the legend embedded in Figure 2 for details). Gray scale on the very right indicates the exact G+C content as calculated from the genome sequences. The non-Flavobacteriia parts of the tree, which have been collapsed here, are shown in Figures 2, 3.

Figure 5

Comparison of branch support. Shown are the negative or positive branch support values for each taxon inferred from whole genomes with GBDP in comparison to those inferred from 16S rRNA gene sequences with ML (A) and MP (B). The colors indicate the taxonomic rank. The upper right corner contains the taxa significantly supported by all methods, the lower left corner those significantly opposed by all methods. The other two corners, which would indicate a significant conflict between the methods, are empty. Jitter was used to avoid overplotting.