Revolutionizing Prokaryotic Systematics Through Next-Generation Sequencing

Sangal, Vartul; Nieminen, Leena; Tucker, Nicholas P.; Hoskisson, Paul A.

doi:10.1016/bs.mim.2014.07.001

Cited by 8 publications

(11 citation statements)

References 116 publications

(142 reference statements)

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“…There is increasing evidence that current approaches to prokaryotic systematics will be enriched by the inclusion of whole genome sequencing data10121314151617. In particular, new metrics have been suggested for species delineation, as exemplified by an ANI cut-off of >94% and dDDH values of >70% to identify strains within a species439404142.…”

Section: Discussionmentioning

confidence: 99%

“…>98.7% identity between their 16S rRNA gene sequences and a high mutual phenetic similarity456. However, the value of phenotyping and DDH is limited, not least by a lack of reproducibility and compatibility of results between different laboratories78 while 16S rRNA gene sequences tend to provide insufficient resolution to distinguish between closely related species910. Moreover, it is not possible to apply the ‘polyphasic’ approach to unculturable bacteria311, the so called ‘microbial dark matter’.…”

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confidence: 99%

“…The limitations of current approaches to prokaryotic systematics have been addressed by several workers who have pressed the need to embrace the genome10121314151617. Indeed, the advent of inexpensive whole genome sequencing technologies and associated bioinformatic tools are promoting a step change in taxonomic practice, notably the availability of new metrics for delineating species101218.…”

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confidence: 99%

“…Indeed, the advent of inexpensive whole genome sequencing technologies and associated bioinformatic tools are promoting a step change in taxonomic practice, notably the availability of new metrics for delineating species101218. In contrast, prokaryotic genera remain loosely defined, typically based on monophyly of strains with an average sequence divergence <6% in16S rRNA gene phylogenies3.…”

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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

Sci Rep

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108

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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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Section: Discussionmentioning

confidence: 99%

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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

Sci Rep

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108

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“…Whole genome sequence analyses such as ANI [27,28] and AAI between orthologous genes [60] are powerful and reliable tools for species delineation [56]. Aerobic, Gram-stain-positive, non-motile actinobacteria which form short rods and coccoid-like elements and grow especially well on ISP 2 agar as black mucoid colonies.…”

Section: Discussionmentioning

confidence: 99%

Modestobacter caceresii sp. nov., novel actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyper-arid Atacama Desert soils

Busarakam

Bull

Trujillo

et al. 2016

Systematic and Applied Microbiology

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Michael (2016) Modestobacter caceresii sp. nov., novel actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyperarid Atacama Desert soils. Systematic and Applied Microbiology, 39 (4 Northumbria University has developed Northumbria Research Link (NRL) to enable users to access the University's research output. Copyright © and moral rights for items on NRL are retained by the individual author(s) and/or other copyright owners. Single copies of full items can be reproduced, displayed or performed, and given to third parties in any format or medium for personal research or study, educational, or not-for-profit purposes without prior permission or charge, provided the authors, title and full bibliographic details are given, as well as a hyperlink and/or URL to the original metadata page. The content must not be changed in any way. Full items must not be sold commercially in any format or medium without formal permission of the copyright holder. The full policy is available online: http://nrl.northumbria.ac.uk/policies.html This document may differ from the final, published version of the research and has been made available online in accordance with publisher policies. To read and/or cite from the published version of the research, please visit the publisher's website (a subscription may be required.)

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Current taxonomy of Rhodococcus species and their role in infections

Majidzadeh

Bafghi

2018

Eur J Clin Microbiol Infect Dis

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Rhodococcus is a genus of obligate aerobic, Gram-positive, partially acid-fast, catalase-positive, non-motile, and none-endospore bacteria. The genus Rhodococcus was first introduced by Zopf. This bacterium can be isolated from various sources of the environment and can grow well in non-selective medium. A large number of phenotypic characterizations are used to compare different species of the genus Rhodococcus, and these tests are not suitable for accurate identification at the genus and species level. Among nucleic acid-based methods, the most powerful target gene for revealing reliable phylogenetic relationships is 16S ribosomal RNA gene (16S rRNA gene) sequence analysis, but this gene is unable to differentiation some of Rhodococcus species. To date, whole genome sequencing analysis has solved taxonomic complexities in this genus. Rhodococcus equi is the major cause of foal pneumonia, and its implication in human health is related to cases in immunocompromised patients. Macrolide family together with rifampicin is one of the most effective antibiotic agents for treatment rhodococcal infections.

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Revolutionizing Prokaryotic Systematics Through Next-Generation Sequencing

Cited by 8 publications

References 116 publications

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

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

Modestobacter caceresii sp. nov., novel actinobacteria with an insight into their adaptive mechanisms for survival in extreme hyper-arid Atacama Desert soils

Current taxonomy of Rhodococcus species and their role in infections

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