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Goodfellow, Michael; Alderson, Grace; Chun, Jongsik

doi:10.1023/a:1001730725003

Cited by 119 publications

(34 citation statements)

References 140 publications

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“…Our new study provides insight into the core features, diversity, population structure and genome evolution of R. equi . It also clarifies the phylogenetic position of the species, repeatedly questioned based on equivocal 16S rDNA and numerical phenetic studies (Goodfellow et al 1998; Gurtler et al 2004; Jones and Goodfellow 2012; Jones et al 2013b), unambiguously confirming R. equi is a bona fide member of the genus Rhodococcus. …”

Section: Introductionmentioning

confidence: 63%

Pangenome and Phylogenomic Analysis of the Pathogenic ActinobacteriumRhodococcus equi

et al. 2016

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We report a comparative study of 29 representative genomes of the animal pathogen Rhodococcus equi. The analyses showed that R. equi is genetically homogeneous and clonal, with a large core genome accounting for ≈80% of an isolates’ gene content. An open pangenome, even distribution of accessory genes among the isolates, and absence of significant core–genome recombination, indicated that gene gain/loss is a main driver of R. equi genome evolution. Traits previously predicted to be important in R. equi physiology, virulence and niche adaptation were part of the core genome. This included the lack of a phosphoenolpyruvate:carbohydrate transport system (PTS), unique among the rhodococci except for the closely related Rhodococcus defluvii, reflecting selective PTS gene loss in the R. equi–R. defluvii sublineage. Thought to be asaccharolytic, rbsCB and glcP non-PTS sugar permease homologues were identified in the core genome and, albeit inefficiently, R. equi utilized their putative substrates, ribose and (irregularly) glucose. There was no correlation between R. equi whole-genome phylogeny and host or geographical source, with evidence of global spread of genomovars. The distribution of host-associated virulence plasmid types was consistent with the exchange of the plasmids (and corresponding host shifts) across the R. equi population, and human infection being zoonotically acquired. Phylogenomic analyses demonstrated that R. equi occupies a central position in the Rhodococcus phylogeny, not supporting the recently proposed transfer of the species to a new genus.

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Section: Introductionmentioning

confidence: 63%

Pangenome and Phylogenomic Analysis of the Pathogenic ActinobacteriumRhodococcus equi

et al. 2016

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“…Despite multiple calls to revisit complex rhodococcal taxonomy202122252729, a recent study based on the analyses of fewer rhodococcal genome sequences presented an alternative phylogenomic view even though similar species-groups were recovered49. In contrast, the present study is based on more extensive and comprehensive phylogenomic and taxogenomic analyses of a larger genomic dataset, including more type strains.…”

Section: Discussionmentioning

confidence: 88%

“…Here, we have built upon such studies by applying a comprehensive genomic approach to delineate species within the genus Rhodococcus that include strains of agricultural, industrial and medical/veterinary significance. The genetic heterogeneity within this genus has become increasingly clear, particularly in the light of a succession of 16S rRNA gene sequence analyses2122252744. However, the number and composition of distinct lineages varied between these studies thereby indicating the need to re-examine relationships within this genus using genomic methods.…”

Section: Discussionmentioning

confidence: 99%

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Next-generation systematics: An innovative approach to resolve the structure of complex prokaryotic taxa

Sangal

Goodfellow

Jones

et al. 2016

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106

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Prokaryotic systematics provides the fundamental framework for microbiological research but remains a discipline that relies on a labour- and time-intensive polyphasic taxonomic approach, including DNA-DNA hybridization, variation in 16S rRNA gene sequence and phenotypic characteristics. These techniques suffer from poor resolution in distinguishing between closely related species and often result in misclassification and misidentification of strains. Moreover, guidelines are unclear for the delineation of bacterial genera. Here, we have applied an innovative phylogenetic and taxogenomic approach to a heterogeneous actinobacterial taxon, Rhodococcus, to identify boundaries for intrageneric and supraspecific classification. Seven species-groups were identified within the genus Rhodococcus that are as distantly related to one another as they are to representatives of other mycolic acid containing actinobacteria and can thus be equated with the rank of genus. It was also evident that strains assigned to rhodococcal species-groups are underspeciated with many misclassified using conventional taxonomic criteria. The phylogenetic and taxogenomic methods used in this study provide data of theoretical value for the circumscription of generic and species boundaries and are also of practical significance as they provide a robust basis for the classification and identification of rhodococci of agricultural, industrial and medical/veterinary significance.

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“…DSM 13002 is a bacteria that is resistant to many chemicals that are considered toxic and has a strong wall structure. For an extensive discussion of this bacterium see Goodfellow and Alderson (1998) and successive papers in the same journal.…”

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confidence: 99%