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

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.

Comparative Genomic and Phylogenomic Analyses Clarify Relationships Within and Between Bacillus cereus and Bacillus thuringiensis: Proposal for the Recognition of Two Bacillus thuringiensis Genomovars

“…The outcome of the study together with those of previous phylogenomic analyses of species classified as B. cereus sensu lato (Liu et al, 2015, 2017b, 2018) is a timely reminder that advances in the classification, nomenclature, and identification of prokaryotes reflect the introduction of new metrics for the recognition of species and genera (Chun and Rainey, 2014; Chun et al, 2018) which are based on better quality taxonomic data drawn from the application of new technologies (Goodfellow et al, 2014). This study also provides further evidence that analyses of high-quality genome sequences provide a framework for the clarification of taxonomically complex groups of prokaryotes (Carro et al, 2018; Sangal et al, 2018). Further, genome-based taxonomic investigations have proved clarifying the status of taxa of biotechnological, ecological, and medical importance, as exemplified by work on the phylum Actinobacteria (Nouioui et al, 2018) and more specifically the genera Amycolatopsis (Sangal et al, 2018) and Mycobacterium (Gupta et al, 2018).…”

“…This study also provides further evidence that analyses of high-quality genome sequences provide a framework for the clarification of taxonomically complex groups of prokaryotes (Carro et al, 2018; Sangal et al, 2018). Further, genome-based taxonomic investigations have proved clarifying the status of taxa of biotechnological, ecological, and medical importance, as exemplified by work on the phylum Actinobacteria (Nouioui et al, 2018) and more specifically the genera Amycolatopsis (Sangal et al, 2018) and Mycobacterium (Gupta et al, 2018).…”

“…Classifications based on whole-genome sequences and associated bioinformatic tools are not only clarifying relationships between closely related bacteria that proved difficult to resolve using conventional taxonomic procedures (Carro et al, 2018; Gupta et al, 2018; Nouioui et al, 2018; Sangal et al, 2018) but are also providing improved metrics for recognizing species boundaries (Chun and Rainey, 2014; Chun et al, 2018), such as those based on average nucleotide identity (ANI; Goris et al, 2007; Arahal, 2014) and digital DNA–DNA hybridization (dDDH; Auch et al, 2010; Meier-Kolthoff et al, 2013). Similarly, dDDH values of 79–80% have been set for the recognition of sub-species (Meier-Kolthoff et al, 2014; Nouioui et al, 2018).…”

Actinobacteria as Promising Candidate for Polylactic Acid Type Bioplastic Degradation

“…SCM_MK2-4 (Penkhrue et al, 2015). Members of the genus Amycolatopsis are well known producers of secondary metabolites which can be exploited for biotechnological applications (Tan and Goodfellow, 2015;Sangal et al, 2018). Amycolatopsis species are commonly found in arid or hyper-arid soils (Tan and Goodfellow, 2015) as exemplified by the description of recent novel Amycolatopsis from desert soils (Busarakam et al, 2016;Idris et al, 2018).…”

Phylogenomic characterisation of a novel corynebacterial species pathogenic to animals

“…Genome-based matrices have been extensively used to define novel bacterial species (Nouioui et al 2018(Nouioui et al , 2019Sangal et al 2016Sangal et al , 2018. The dDDH and ANI cut-off values for defining new species are 70% and 95%, respectively (Auch et al 2010b;Tiedje 2005, 2007).…”