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.

Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes

“…It can be differentiated from a similar method called multilocus sequence analysis (MLSA) [19,20] by applying a substantially higher number of orthologous genes that were rationally selected using large scale comparative genomics [21][22][23]. The combination of phylogenomic treeing and highly conserved phenotypes, including chemotaxonomic markers, should play a significant role in the classification of genera and higher taxa.…”

Aequorivita sinensis sp. nov., isolated from sediment of the East China Sea, and reclassification of Vitellibacter todarodis as Aequorivita todarodis comb. nov. and Vitellibacter aquimaris as Aequorivita aquimaris comb. nov.

“…The description of the genus Aequorivita was later modified by Park et al [2]. Recently, Hahnke et al [3] proposed to place Vitellibacter into Aequorivita and to emend the description of Aequorivita accordingly. This genus Aequorivita accommodates bacteria that are aerobic, Gram-negative, non-sporeforming and are characterized chemotaxonomically by having MK-6 and iso-C 15 : 0 and anteiso-C 15 : 0 as the predominant menaquinone and branched-chain saturated fatty acids, respectively [1].…”

Aequorivita lutea sp. nov., a novel bacterium isolated from the estuarine sediment of the Pearl River in China, and transfer of Vitellibacter todarodis and Vitellibacter aquimaris to the genus Aequorivita as Aequorivita todarodis comb. nov. and Aequorivita aquimaris comb. nov.

“…Recently, different novel species belong to the genus Aequorivita were successfully isolated from various habits, including Aequorivita capsosiphonis A71 T isolated from marine algae collected from the South Sea of the Republic of Korea [2] and Aequorivita viscosa 8-1b T isolated from an intertidal zone [3]. Additionally, bacteria in the genus of Vitellibacter were recently moved to the genus Aequorivita in 2016 [4]. The proposed names of type species Vitellibacter vladivostokensis KMN 3516 T [5], Vitellibacter aestuarii JC2436 T [6], Vitellibacter soesokkakensis RSSK-12 T [7], Vitellibacter nionensis VBW088 T [8] and Vitellibacter echinoideorum CC-CZW007 T [9], were amended as Aequorivita vladivostokensis KMN 3516 T , Aequorivita aestuarii JC2436 T , Aequorivita soesokkakensis RSSK-12 T , Aequorivita nionensis VBW088 T and Aequorivita echinoideorum CC-CZW007 T , respectively [4].…”

“…Additionally, bacteria in the genus of Vitellibacter were recently moved to the genus Aequorivita in 2016 [4]. The proposed names of type species Vitellibacter vladivostokensis KMN 3516 T [5], Vitellibacter aestuarii JC2436 T [6], Vitellibacter soesokkakensis RSSK-12 T [7], Vitellibacter nionensis VBW088 T [8] and Vitellibacter echinoideorum CC-CZW007 T [9], were amended as Aequorivita vladivostokensis KMN 3516 T , Aequorivita aestuarii JC2436 T , Aequorivita soesokkakensis RSSK-12 T , Aequorivita nionensis VBW088 T and Aequorivita echinoideorum CC-CZW007 T , respectively [4]. Two recently identified species in the genus of Vitellibacter, Vitellibacter aquimaris [10] and Vitellibacter todarodis [11], were not classified into the genus Aequorivita, even though they phylogenetically grouped with those type strains being moved to the genus Aequorivita from the genus Vitellibacter.…”

“…Temperature, pH and salinity suitable for the growth of strain q18 T and the reference strain A. echinoideorum CC-CZW007 T were measured as described previously [20,21]. Growth at different temperatures (4,10,15,20,25,30,35,40,45 and 50 °C) of strain q18 T was determined in 2216E marine broth medium. The test of salinity requirements was based on different NaCl concentrations adjusted from 0 to 15 % (w/v) with intervals of 1 % at 25 °C.…”