Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Abstract

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Mesonia oceanica sp. nov., isolated from oceans during the Tara oceans expedition, with a preference for mesopelagic waters

“…maritima [11]. The genus is one of the many included in a recent phylogenomic study of the phylum Bacteroidetes [12] and has not been affected by the reclassifications therein proposed.…”

List of new names and new combinations previously effectively, but not validly, published

“…2 Priority number assigned according to the date the documentation and request for validation are received. 3 The journal in which the name was effectively published does not have continuous pages. 4 In the genus protologue, the name of the type species was misspelled Albibacterium bauzanensis.…”

Patiriisocius marinistellae gen. nov., sp. nov., isolated from the starfish Patiria pectinifera, and reclassification of Ulvibacter marinus as a member of the genus Patiriisocius comb. nov.

“…litoralis KMM 3912 T , phylogenetic placement based on both the 16S rRNA genes and the genomes indicated the independency of strain KK4 T from type species of the neighbouring genera Ulvibacter , Marixanthomonas , Marinirhabdus , Aureitalea and Aequorivita (Figs 1 and 2). A recent comprehensive survey of the genomic phylogeny of the family Flavobacteriacea also demonstrated that Ulvibacter , Marinirhabdus , Aureitalea and Aequorivita formed one phylogenetic cluster (UMA cluster) [52]; however, strain KK4 T formed a branch independent from the UMA cluster ( and S1). Moreover, AAI values also support the phylogenetic distinctiveness of strain KK4 T from type strains in the UMA cluster ().…”