Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders ‘Frankiales’ and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov.

Abstract

Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. nov. and Nakamurellales ord. nov. The phylogeny of the class Actinobacteria remains controversial, essentially because it is very sensitive to the choice of dataset and phylogenetic methods. We used a test proposed recently, based on complete genome data, which chooses among candidate species phylogenies based on the number of lateral gene transfers (LGT) needed to explain the diversity of histories among gene trees for a set of genomes. We used 100 completely sequenced genomes representing 35 families and 17 orders of the class Actinobacteria and evaluated eight different hypotheses for their phylogeny, including one based on a concatenate of 54 conserved proteins present in single copy in all these genomes, trees based on 16S and 23S rRNA gene sequences or their concatenation, and a tree based on the concatenation of MLSA genes (encoding AtpI, GyrA, FtsZ, SecA and DnaK). We used Prunier to infer the number of LGT in 579 proteins (different from those used to build the concatenated tree) present in at least 70 species, using the different hypothetical species trees as references. The best tree, with the lowest number of lateral transfers, was the one based on the concatenation of 54 proteins. In that tree, the orders Bifidobacteriales, Coriobacteriales, 'Corynebacteriales', 'Micromonosporales', 'Propionibacteriales', 'Pseudonocardiales', Streptomycetales and 'Streptosporangiales' were recovered while the orders 'Frankiales' and Micrococcales were not. It is thus proposed that the order 'Frankiales', which has an effectively but not validly published name, be split into Frankiales ord. nov. (type family Frankiaceae), Geodermatophilales ord. nov. (Geodermatophilaceae), Acidothermales ord. nov. (Acidothermaceae) and Nakamurellales ord. nov. (Nakamurellaceae). The order Micrococcales should also be split into Micrococcales (genera Kocuria, Rothia, Micrococcus, Arthrobacter, Tropheryma, Microbacterium, Leifsonia and Clavibacter), Cellulomonales (Beutenbergia, Cellulomonas, Xylanimonas, Jonesia and Sanguibacter) and Brachybacteriales (Brachybacterium) but the formal proposal for this will have to wait until more genomes become available for a significant proportion of strains in this order.

Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes

“…These proteomic results are a further support for the presence of the monophyletic group composed of Bs and Go, which has been confirmed in silico by bioinformatics (Sen et al, 2014) as well as in vitro by microbiological and biochemical markers .…”

“…Geodermatophilaceae are an actinobacterial family (Normand, 2006) in the order Geodermatophiliales (Sen et al, 2014) that comprises three genera: Geodermatophilus, Blastococcus and Modestobacter initially isolated from desert soils (Luedemann, 1968), sea water (Ahrens and Moll, 1970) and Antarctic regolith (Mevs et al, 2000), respectively. These three genera have a complex life cycle and produce remarkably resistant enzymes such as esterases (Essoussi et al, 2010;Jaouani et al, 2012;Normand et al, 2014).…”

Microbial taxonomy in the post-genomic era: Rebuilding from scratch?

“…• Specialized journals, e.g., IJSEM and SAM are starting to get involved in an open scientific discussion on Microbial genomic taxonomy and offer a tribune for it (Sen et al 2014;Chun and Rainey 2014;Ramasamy et al 2014). This will attract bright young scientists, needed for the remolding the theory and practice of genomic microbial taxonomy.…”

Blastococcus capsensis sp. nov., isolated from an archaeological Roman pool and emended description of the genus Blastococcus, B. aggregatus, B. saxobsidens, B. jejuensis and B. endophyticus

“…The genus Blastococcus is classified together with Geodermatophilus and Modestobacter in the family Geodermatophilaceae (Normand, 2006;Normand et al, 2014) of the order Geodermatophilales (Sen et al, 2014). There are four species of the genus Blastococcus with validly published names: Blastococcus aggregatus (Ahrens & Moll, 1970;Urzì et al, 2004), Blastococcus saxobsidens (Urzì et al, 2004), Blastococcus jejuensis (Lee, 2006) and Blastococcus endophyticus (Zhu et al, 2013).…”