Genome-Based Taxonomic Classification of the Phylum Actinobacteria

TLDR

Phylogenetic taxonomy has improved Actinobacteria classification, yet relationships remain unclear because of limited features and poorly resolved 16S rRNA trees. The authors constructed genome‑based phylogenies from draft genomes of numerous actinobacterial type strains using phylogenetic systematics principles. The genome‑based trees revealed most taxa to be monophyletic but identified many taxa needing revision, prompting proposals for 2 new orders, 10 families, 17 genera, and over 100 species transfers, while also showing that genome size and GC content are valuable markers and that whole‑genome phylogenies resolve incongruities better than single‑gene trees.

Abstract

The application of phylogenetic taxonomic procedures led to improvements in the classification of bacteria assigned to the phylum Actinobacteria but even so there remains a need to further clarify relationships within a taxon that encompasses organisms of agricultural, biotechnological, clinical and ecological importance. Classification of the morphologically diverse bacteria belonging to this large phylum based on a limited number of features has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees. Here, draft genome sequences of a large collection of actinobacterial 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, as well as many species and a few subspecies were shown to be in need of revision leading to proposals for the recognition of 2 orders, 10 families and 17 genera, as well as the transfer of over 100 species to other genera. In addition, emended descriptions are given for many species mainly involving the addition of data on genome size and DNA G+C content, the former can be considered to be a valuable taxonomic marker in actinobacterial systematics. Many of the incongruities detected when the results of the present study were compared with existing classifications had been recognised from 16S rRNA gene trees though whole-genome phylogenies proved to be much better resolved. The few significant incongruities found between 16S/23S rRNA and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences. Similarly good congruence was found between the discontinuous distribution of phenotypic properties and taxa delineated in the phylogenetic trees though diverse non-monophyletic taxa appeared to be based on the use of plesiomorphic character states as diagnostic features.