Genome-Based Taxonomic Classification of the Phylum Actinobacteria

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 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 recognized 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.

Commentary: Genome-Based Taxonomic Classification of the Phylum Actinobacteria

“…Nouioui et al (2018) commend our work for identifying molecular synapomorphies for the five mycobacterial clades and their phylogenetic analysis and those by Tortoli et al (2017), also support the existence of these clades. However, while not questioning any aspects of our results, Nouioui et al (2018) question our division of the genus Mycobacterium into five genera for two reasons.…”

“…However, while not questioning any aspects of our results, Nouioui et al (2018) question our division of the genus Mycobacterium into five genera for two reasons. First, they indicate that our identification of several synapomorphies for all mycobacteria makes further division of this group into multiple genera arbitrary.…”

“…Nouioui et al (2018) are also critical of our proposal on the grounds that some Mycobacteriales genera viz. Rhodococcus, Gordonia, Nocardia , and Corynebacterium are more divergent than Mycobacterium .…”

“…Nouioui et al (2018) have recently reported comprehensive phylogeny and taxonomy of members from the phylum Actinobacteria. Based on genomic-scale analyses, this study makes proposals for many new taxa of Actinobacteria.…”

“…Thus, according to Rules 23a and 24a of the International Code of Nomenclature of Prokaryotes (Parker et al, 2015), the order name Mycobacteriales Janke 1924 has priority over the name Corynebacteriales Goodfellow and Jones 2015 and all of the families which are part of the order Corynebacteriales should be embedded within the order Mycobacteriales . To correct this anomaly, an emended description of the order Mycobacteriales , based partially on the description of the Corynebacteriales by Goodfellow and Jones (2012) and Nouioui et al (2018), is provided below.…”