AUTHOR=Sangal Vartul , Goodfellow Michael , Blom Jochen , Tan Geok Yuan Annie , Klenk Hans-Peter , Sutcliffe Iain C. 

TITLE=Revisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach

JOURNAL=Frontiers in Microbiology

VOLUME=9

YEAR=2018

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2018.02281

DOI=10.3389/fmicb.2018.02281

ISSN=1664-302X

ABSTRACT=<p>Strains belonging to the genus <italic>Amycolatopsis</italic> are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five <italic>Amycolatopsis</italic> strains including <italic>Amycolatopsis circi</italic> DSM 45561<sup>T</sup>, <italic>Amycolatopsis palatopharyngis</italic> DSM 44832<sup>T</sup> and <italic>Amycolatopsis thermalba</italic> NRRL B-24845<sup>T</sup>. The genome sequences were analyzed with 52 other publically available <italic>Amycolatopsis</italic> genomes, representing 34 species, and 12 representatives from related genera including <italic>Saccharomonospora</italic>, <italic>Saccharopolyspora</italic>, <italic>Saccharothrix</italic>, <italic>Pseudonocardia</italic> and <italic>Thermobispora</italic>. Based on the core genome phylogeny, <italic>Amycolatopsis</italic> strains were subdivided into four major clades and several singletons. The genus <italic>Amycolatopsis</italic> is homogeneous with only three strains noted to group with other genera. <italic>Amycolatopsis halophila</italic> YIM93223<sup>T</sup> is quite distinct from other <italic>Amycolatopsis</italic> strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, <italic>Amycolatopsis palatopharyngis</italic> DSM 44832<sup>T</sup> and <italic>Amycolatopsis marina</italic> CGMCC4 3568<sup>T</sup> grouped in a clade with <italic>Saccharomonospora</italic> strains and showed similar taxogenomic differences to this genus as well as other <italic>Amycolatopsis</italic> strains. The study found a number of strains, particularly those identified as <italic>Amycolatopsis orientalis</italic>, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99–100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.</p>