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

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

doi:10.3389/fmicb.2018.02281

Abstract

Strains belonging to the genus Amycolatopsis 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 Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains. The study found a number of strains, particularly those identified as Amycolatopsis orientalis, 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.

Highlights

The genus Amycolatopsis is well known for the commercial production of multiple antibiotics, including the important broad spectrum antibiotics rifamycin and, vancomycin (Xu et al, 2014; Chen et al, 2016)
These strains were recovered as singletons in the multilocus sequence analysis (MLSA) analysis of SanchezHidalgo et al (2018), except for A. xylanica which was located at the periphery of the strains in our cluster A
Amycolatopsis is a homogeneous genus where most strains conform to the phylogenomic and taxogenomic indices defined for intra-generic boundaries

Summary

Introduction

The genus Amycolatopsis is well known for the commercial production of multiple antibiotics, including the important broad spectrum antibiotics rifamycin and, vancomycin (Xu et al, 2014; Chen et al, 2016). These strains have the potential to produce a number of other secondary metabolites and bioactive molecules (Adamek et al, 2018) and, can be exploited for a range of biotechnological applications (Davila Costa and Amoroso, 2014). They can form branching substrate hyphae that fragment into square, or rod-shaped elements and carry aerial hyphae (Saintpierre-Bonaccio et al, 2005; Tan and Goodfellow, 2015)

Methods

Results

Discussion

Conclusion