1887

Abstract

Opinion 106 of the Judicial Commission has clarified the nomenclature of the taxon variously named , ’ and . As a consequence, we present here the genus name and that of its nomenclatural type species, comb. nov., for valid publication and propose the reclassification of four rhodococcal species as novel combinations in the genus, namely Guo et al. 2015 comb. nov., Kämpfer . 2014 comb. nov., Li . 2015 comb. nov. and Lee . 2019 comb. nov. In addition, we note that a clinical isolate, strain 86–07 (=W8901), likely represents an additional species within the genus . Nearly a century after the original description of the type strain of the type species as , we provide a stable home for and its relatives.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2022-09-14
2024-05-02
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References

  1. Sangal V, Goodfellow M, Jones AL, Sutcliffe IC. A stable home for an equine pathogen: valid publication of the binomial Prescottella equi gen. nov., comb. nov., and reclassification of four rhodococcal species into the genus Prescottella. Figshare 2022 [View Article]
    [Google Scholar]
  2. Magnusson H. Spezifische infecktiose Ppneumonie beim Ffohlen. Eein neuer Eeitererreger beim Ppferd. Arch Wiss Prakti Tierheilk 1923; 50:22–38
    [Google Scholar]
  3. Sly LI, Mutimer MD, Woolcock JB. Confusing Irregularities in the nomenclature of some Rhodococcus species. Int J Syst Bacteriol 1983; 33:658–659 [View Article]
    [Google Scholar]
  4. Goodfellow M. The taxonomic status of Rhodococcus equi. Vet Microbiol 1987; 14:205–209 [View Article] [PubMed]
    [Google Scholar]
  5. Vázquez-Boland JA, Meijer WG. The pathogenic actinobacterium Rhodococcus equi: what’s in a name?. Mol Microbiol 2019; 112:1–15 [View Article] [PubMed]
    [Google Scholar]
  6. Goodfellow M, Alderson G. The actinomycete-genus Rhodococcus: a home for the “rhodochrous” complex. J Gen Microbiol 1977; 100:99–122 [View Article] [PubMed]
    [Google Scholar]
  7. Jones AL, Sutcliffe IC, Goodfellow M. Proposal to replace the illegitimate genus name Prescottia Jones et al. 2013 with the genus name Prescottella gen. nov. and to replace the illegitimate combination Prescottia equi Jones et al. 2013 with Prescottella equi comb. nov. Antonie van Leeuwenhoek 2013; 103:1405–1407 [View Article]
    [Google Scholar]
  8. Kämpfer P, Dott W, Martin K, Glaeser SP. Rhodococcus defluvii sp. nov., isolated from wastewater of a bioreactor and formal proposal to reclassify [Corynebacterium hoagii] and Rhodococcus equi as Rhodococcus hoagii comb. nov. Int J Syst Evol Microbiol 2014; 64:755–761 [View Article]
    [Google Scholar]
  9. Tindall BJ. The correct name of the taxon that contains the type strain of Rhodococcus equi. Int J Syst Evol Microbiol 2014; 64:302–308 [View Article] [PubMed]
    [Google Scholar]
  10. Goodfellow M, Sangal V, Jones AL, Sutcliffe IC. Charting stormy waters: A commentary on the nomenclature of the equine pathogen variously named Prescottella equi, Rhodococcus equi and Rhodococcus hoagii. Equine Vet J 2015; 47:508–509 [View Article] [PubMed]
    [Google Scholar]
  11. Garrity GM. Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Corynebacterium hoagii (Morse 1912) Eberson 1918. Int J Syst Evol Microbiol 2014; 64:311–312 [View Article]
    [Google Scholar]
  12. Vázquez-Boland JA, Scortti M, Meijer WG. Conservation of Rhodococcus equi (Magnusson 1923) Goodfellow and Alderson 1977 and rejection of Rhodococcus hoagii (Morse 1912) Kämpfer et al. 2014. Int J Syst Evol Microbiol 2020; 70:3572–3576
    [Google Scholar]
  13. Arahal DR, Busse H-J, Bull CT, Christensen H, Chuvochina M et al. Judicial Opinions 103-111. Int J Syst Evol Microbiol 2022; 72:005197 [View Article] [PubMed]
    [Google Scholar]
  14. Jones AL, Sutcliffe IC, Goodfellow M. Prescottia equi gen. nov., comb. nov.: a new home for an old pathogen. Antonie van Leeuwenhoek 2013; 103:655–671 [View Article] [PubMed]
    [Google Scholar]
  15. Sangal V, Goodfellow M, Jones AL, Schwalbe EC, Blom J et al. Next-generation systematics: an innovative approach to resolve the structure of complex prokaryotic taxa. Sci Rep 2016; 6:38392 [View Article]
    [Google Scholar]
  16. Sangal V, Goodfellow M, Jones AL, Seviour RJ, Sutcliffe IC. Refined systematics of the genus Rhodococcus based on whole genome analyses. In Biology of Rhodococcus Springer Cham; 2019
    [Google Scholar]
  17. Anastasi E, MacArthur I, Scortti M, Alvarez S, Giguère S et al. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol 2016; 8:3140–3148 [View Article]
    [Google Scholar]
  18. Tindall BJ. Rule 27 of the International Code of Nomenclature of Prokaryotes: the basonym is not enough. Int J Syst Evol Microbiol 2016; 66:4897–4899 [View Article]
    [Google Scholar]
  19. Sangal V, Jones AL, Goodfellow M, Hoskisson PA, Kämpfer P et al. Genomic analyses confirm close relatedness between Rhodococcus defluvii and Rhodococcus equi (Rhodococcus hoagii). Arch Microbiol 2015; 197:113–116 [View Article] [PubMed]
    [Google Scholar]
  20. Li S-H, Yu X-Y, Park D-J, Hozzein WN, Kim C-J et al. Rhodococcus soli sp. nov., an actinobacterium isolated from soil using a resuscitative technique. Antonie van Leeuwenhoek 2015; 107:357–366 [View Article] [PubMed]
    [Google Scholar]
  21. Guo Q-Q, Ming H, Meng X-L, Duan Y-Y, Gao R et al. Rhodococcus agglutinans sp. nov., an actinobacterium isolated from a soil sample. Antonie van Leeuwenhoek 2015; 107:1271–1280 [View Article] [PubMed]
    [Google Scholar]
  22. Lee SD, Kim YJ, Kim IS. Rhodococcus subtropicus sp. nov., a new actinobacterium isolated from a cave. Int J Syst Evol Microbiol 2019; 69:3128–3134 [View Article] [PubMed]
    [Google Scholar]
  23. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article] [PubMed]
    [Google Scholar]
  24. Asnicar F, Thomas AM, Beghini F, Mengoni C, Manara S et al. Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0. Nat Commun 2020; 11:2500 [View Article]
    [Google Scholar]
  25. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article]
    [Google Scholar]
  26. Nguyen TM, Kim J. Rhodococcus pedocola sp. nov. and Rhodococcus humicola sp. nov., two antibiotic-producing actinomycetes isolated from soil. Int J Syst Evol Microbiol 2016; 66:2362–2369 [View Article] [PubMed]
    [Google Scholar]
  27. Táncsics A, Máthé I, Benedek T, Tóth EM, Atasayar E et al. Rhodococcus sovatensis sp. nov., an actinomycete isolated from the hypersaline and heliothermal Lake Ursu. Int J Syst Evol Microbiol 2017; 67:190–196 [View Article] [PubMed]
    [Google Scholar]
  28. Li C, Cao P, Jiang M, Hou Y, Du C et al. Rhodococcus oryzae sp. nov., a novel actinobacterium isolated from rhizosphere soil of rice (Oryza sativa L.). Int J Syst Evol Microbiol 2020; 70:3300–3308 [View Article] [PubMed]
    [Google Scholar]
  29. Lee SD, Kim IS. Rhodococcus spelaei sp. nov., isolated from a cave, and proposals that Rhodococcus biphenylivorans is a later synonym of Rhodococcus pyridinivorans, Rhodococcus qingshengii and Rhodococcus baikonurensis are later synonyms of Rhodococcus erythropolis, and Rhodococcus percolates and Rhodococcus imtechensis are later synonyms of Rhodococcus opacus. Int J Syst Evol Microbiol 2021; 71:004890
    [Google Scholar]
  30. Zhang D, Su Z, Li L, Tang W. Rhodococcus spongiicola sp. nov. and Rhodococcus xishaensis sp. nov., from marine sponges. Int J Syst Evol Microbiol 2021; 71:004863 [View Article]
    [Google Scholar]
  31. Langer AJ, Feja K, Lasker BA, Hinrikson HP, Morey RE et al. Investigation of an apparent outbreak of Rhodococcus equi bacteremia. Diagn Microbiol Infect Dis 2010; 67:95–100 [View Article] [PubMed]
    [Google Scholar]
  32. Gulvik CA, Batra D, Howard DT, Sheth M, Humrighouse BW et al. Complete genome sequence of Rhodococcus sp. strain W8901, a human clinical specimen, assembled using miseq and minion sequence data. Microbiol Res Announc 2021; 10:e0061321
    [Google Scholar]
  33. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article] [PubMed]
    [Google Scholar]
  34. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Syst Evol Microbiol 2018; 68:2393–2411 [View Article]
    [Google Scholar]
  35. Nicholson AC, Gulvik CA, Whitney AM, Humrighouse BW, Bell ME et al. Division of the genus Chryseobacterium: observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. Int J Syst Evol Microbiol 2021; 70:4432–4450 [View Article]
    [Google Scholar]
  36. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  37. Aliyu H, Lebre P, Blom J, Cowan D, De Maayer P. Phylogenomic re-assessment of the thermophilic genus Geobacillus. Syst Appl Microbiol 2016; 39:527–533 [View Article] [PubMed]
    [Google Scholar]
  38. Gupta RS. Distinction between Borrelia and Borreliella is more robustly supported by molecular and phenotypic characteristics than all other neighbouring prokaryotic genera: response to Margos’ et al. “The genus Borrelia reloaded” (PLoS ONE 13(12): e0208432). PLoS ONE 2019; 14:e0221397 [View Article]
    [Google Scholar]
  39. de la Haba RR, Minegishi H, Kamekura M, Shimane Y, Ventosa A. Phylogenomics of Haloarchaea: the controversy of the genera Natrinema-Haloterrigena. Front Microbiol 2021; 12:740909 [View Article]
    [Google Scholar]
  40. Xu Z, Masuda Y, Wang X, Ushijima N, Shiratori Y et al. Genome-Based taxonomic rearrangement of the order geobacterales including the description of Geomonas azotofigens sp. nov. and Geomonas diazotrophica sp. nov. Front Microbiol 2021; 12:737531 [View Article]
    [Google Scholar]
  41. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article]
    [Google Scholar]
  42. Segata N, Börnigen D, Morgan XC, Huttenhower C. PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes. Nat Commun 2013; 4:2304 [View Article]
    [Google Scholar]
  43. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  44. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics 2008; 9:75 [View Article] [PubMed]
    [Google Scholar]
  45. Kim SM, Lee SD, Koh YS, Kim IS. Antrihabitans stalagmiti sp. nov., isolated from a larva cave and a proposal to transfer Rhodococcus cavernicola Lee et al. 2020 to a new genus Spelaeibacter as Spelaeibacter cavernicola gen. nov. comb. nov. Antonie Van Leeuwenhoek 2022; 115:521–532 [View Article]
    [Google Scholar]
  46. Lee SD, Kim IS, Kim YJ, Joung Y. Rhodococcus cavernicola sp. nov., isolated from a cave, and Rhodococcus degradans is a later heterosynonym of Rhodococcus qingshengii. Int J Syst Evol Microbiol 2020; 70:4409–4415 [View Article]
    [Google Scholar]
  47. Kang Y, Chen Y, Zhang Z, Shen H, Zhou W et al. A case of peritoneal dialysis-associated peritonitis caused by Rhodococcus kroppenstedtii. BMC Infect Dis 2021; 21:565 [View Article]
    [Google Scholar]
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