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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 75, Issue 3

sp. nov., a new species isolated from equine farm soil closely related to the pathogen Open Access

Abstract

We present the description of the new species, , found during phylogenomic investigations of a global collection of strains identified as () . Strain PAM 2766 was isolated from horse-breeding farm soil in Normandy, France, and was indistinguishable from based on the usual identification tests. Whole-genome phylogenetic analyses located PAM 2766 in the same sublineage as , together with , , , , and . PAM 2766 is most closely related to, but sufficiently distinct from, DSM 20307 to be considered a separate species. The average identity (ANI) and average identity (AAI) values are 88.60% and 92.35, respectively, well below the species cutoff. The PAM 2766 draft genome is ~5.3 Mb in size with 68.98% G+C mol content. PAM 2766 is strictly aerobic and non-motile and produces smooth, creamy to buff-coloured colonies very similar to those of . It phenotypically differs from the latter by the ability to grow at 5 °C, a strongly positive urease test at 24 h and specificities in the carbon and nitrogen source utilization profile as determined by phenotype microarray screens. Our data indicate that PAM 2766 belongs to a novel species, for which the name sp. nov. is proposed. was avirulent in macrophage infection assays and is assumed to be non-pathogenic. The type strain is PAM 2766 (=CETC 30995=NCTC 14987).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): genus Rhodococcus , Rhodococcus equi , Rhodococcus parequi , Rhodococcus phylogenomics , Rhodococcus systematics and Rhodococcus taxonomy
Funding
This study was supported by the:
  • Horserace Betting Levy Board (Award vet/prj/796 and vet/prj/814)
    • Principal Award Recipient: JoséA. Vazquez-Boland
© 2025 The Authors
  • 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.

Erratum

A correction has been published for this content:
Corrigendum: sp. nov., a new species isolated from equine farm soil closely related to the pathogen
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2026-03-13

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References

  1. Arahal DR, Bull CT, Christensen H, Chuvochina M, Dunlap C et al. Judicial opinion 130. Int J Syst Evol Microbiol 2024; 74:006414 [View Article] [PubMed]
     [Google Scholar]
  2. Zopf W. Ueber ausscheidung von fettfarbstoffen (Lipochromen) seitens gewisser spaltpilze. Berichte der Deutschen Botanischen Gesellschaft 1891; 9:22–28 [View Article]
     [Google Scholar]
  3. 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] [PubMed]
     [Google Scholar]
  4. 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]
  5. Alvarez HM. Biology of Rhodococcus, 2nd ed Springer Nature; 2019 [View Article]
     [Google Scholar]
  6. Lee SD, Kim Y-J, 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]
  7. Prescott JF. Rhodococcus equi: an animal and human pathogen. Clin Microbiol Rev 1991; 4:20–34 [View Article]
     [Google Scholar]
  8. 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]
  9. Sangal V, Goodfellow M, Jones AL, Sutcliffe IC. A stable home for an equine pathogen: valid publication of the binomial prescottella equi gen. Int J Syst Evol Microbiol 2022; 72:005551 [View Article]
     [Google Scholar]
  10. Oren A, Göker M. Notification of changes in taxonomic opinion previously published outside the IJSEM. List of changes in taxonomic opinion no. 40. Int J Syst Evol Microbiol 2024; 74:006482 [View Article]
     [Google Scholar]
  11. Val-Calvo J, Vázquez-Boland JA. Mycobacteriales taxonomy using network analysis-aided, context-uniform phylogenomic approach for non-subjective genus demarcation. mBio 2023; 14:e0220723 [View Article] [PubMed]
     [Google Scholar]
  12. Navas J, González-Zorn B, Ladrón N, Garrido P, Vázquez-Boland JA. Identification and mutagenesis by allelic exchange of choE, encoding a cholesterol oxidase from the intracellular pathogen Rhodococcus equi. J Bacteriol 2001; 183:4796–4805 [View Article] [PubMed]
     [Google Scholar]
  13. González-Zorn B, Domínguez-Bernal G, Suárez M, Ripio MT, Vega Y et al. The smcL gene of Listeria ivanovii encodes a sphingomyelinase C that mediates bacterial escape from the phagocytic vacuole. Mol Microbiol 1999; 33:510–523 [View Article] [PubMed]
     [Google Scholar]
  14. Ladrón N, Fernández M, Agüero J, González Zörn B, Vázquez-Boland JA et al. Rapid identification of Rhodococcus equi by a PCR assay targeting the choE gene. J Clin Microbiol 2003; 41:3241–3245 [View Article] [PubMed]
     [Google Scholar]
  15. Rodríguez-Lázaro D, Lewis DA, Ocampo-Sosa AA, Fogarty U, Makrai L et al. Internally controlled real-time PCR method for quantitative species-specific detection and vapA genotyping of Rhodococcus equi. . Appl Environ Microbiol 2006; 72:4256–4263 [View Article] [PubMed]
     [Google Scholar]
  16. Ocampo-Sosa AA, Lewis DA, Navas J, Quigley F, Callejo R et al. Molecular epidemiology of Rhodococcus equi based on traA, vapA, and vapB virulence plasmid markers. J Infect Dis 2007; 196:763–769 [View Article]
     [Google Scholar]
  17. Halbert ND, Reitzel RA, Martens RJ, Cohen ND. Evaluation of a multiplex polymerase chain reaction assay for simultaneous detection of Rhodococcus equi and the vapA gene. Am J Vet Res 2005; 66:1380–1385 [View Article] [PubMed]
     [Google Scholar]
  18. Valero-Rello A, Hapeshi A, Anastasi E, Alvarez S, Scortti M et al. An invertron-like linear plasmid mediates intracellular survival and virulence in bovine isolates of Rhodococcus equi. Infect Immun 2015; 83:2725–2737 [View Article] [PubMed]
     [Google Scholar]
  19. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article] [PubMed]
     [Google Scholar]
  20. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
     [Google Scholar]
  21. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article] [PubMed]
     [Google Scholar]
  22. Riesco R, Trujillo ME. Update on the proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2024; 74:006300 [View Article] [PubMed]
     [Google Scholar]
  23. Letek M, González P, Macarthur I, Rodríguez H, Freeman TC et al. The genome of a pathogenic Rhodococcus: cooptive virulence underpinned by key gene acquisitions. PLoS Genet 2010; 6:e1001145 [View Article] [PubMed]
     [Google Scholar]
  24. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article]
     [Google Scholar]
  25. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article] [PubMed]
     [Google Scholar]
  26. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
     [Google Scholar]
  27. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
     [Google Scholar]
  28. Lane DJ. 16S/23S rRNA Sequencing. In Stackebrandt E, Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991
     [Google Scholar]
  29. 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] [PubMed]
     [Google Scholar]
  30. Rainey FA, Burghardt J, Kroppenstedt RM, Klatte S, Stackebrandt E. Phylogenetic analysis of the genera Rhodococcus and Nocardia and evidence for the evolutionary origin of the genus Nocardia from within the radiation of Rhodococcus species. Microbiol 1995; 141:523–528 [View Article]
     [Google Scholar]
  31. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article]
     [Google Scholar]
  32. Zhang D, Su Z, Li L, Tang WZ. Rhodococcus spongiicola sp. nov. and Rhodococcus xishaensis sp. nov., from marine sponges. Int J Syst Evol Microbiol 2021; 71:004863 [View Article]
     [Google Scholar]
  33. Kämpfer P, Glaeser SP, Blom J, Wolf J, Benning S et al. Rhodococcus pseudokoreensis sp. nov. isolated from the rhizosphere of young M26 apple rootstocks. Arch Microbiol 2022; 204:505 [View Article] [PubMed]
     [Google Scholar]
  34. Beak JH, Baek W, Jeong SE, Lee SC, Jin HM et al. Rhodococcus oxybenzonivorans sp. nov., a benzophenone-3-degrading bacterium, isolated from stream sediment. Int J Syst Evol Microbiol 2022; 72:005433
     [Google Scholar]
  35. Kusuma AB, Fenylestari G, Ammar F, Nououi I, Goodfellow M. Rhodococcus indonesiensis sp. nov. a new member of the Rhodococcus ruber lineage isolated from sediment of a neutral hot spring and reclassification of Rhodococcus electrodiphilus (ramaprasad et al. 2018) as a later heterotypic synonym of Rhodococcus ruber (Kruse 1896) goodfellow and alderson 1977 (approved lists 1980). Int J Syst Evol Microbiol 2018; 74:006236
     [Google Scholar]
  36. Hassler HB, Probert B, Moore C, Lawson E, Jackson RW et al. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. Microbiome 2022; 10:104 [View Article] [PubMed]
     [Google Scholar]
  37. Bartoš O, Chmel M, Swierczková I. The overlooked evolutionary dynamics of 16S rRNA revises its role as the “gold standard” for bacterial species identification. Sci Rep 2024; 14:9067 [View Article] [PubMed]
     [Google Scholar]
  38. Chalita M, Kim YO, Park S, Oh HS, Cho JH et al. EzBioCloud: a genome-driven database and platform for microbiome identification and discovery. Int J Syst Evol Microbiol 2024; 74:006421 [View Article] [PubMed]
     [Google Scholar]
  39. Oren A, Göker M. Validation List no. 216. Valid publication of new names and new combinations effectively published outside the IJSEM. Int J Syst Evol Microbiol 2024; 74:006229 [View Article] [PubMed]
     [Google Scholar]
  40. Contreras-Moreira B, Vinuesa P. GET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis. Appl Environ Microbiol 2013; 79:7696–7701 [View Article] [PubMed]
     [Google Scholar]
  41. Vinuesa P, Ochoa-Sánchez LE, Contreras-Moreira B. Get_phyloMarkers, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genus Stenotrophomonas. Front Microbiol 2018; 9:771 [View Article] [PubMed]
     [Google Scholar]
  42. Nguyen LT, 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]
  43. Orro A, Cappelletti M, D’Ursi P, Milanesi L, Di Canito A et al. Genome and phenotype microarray analyses of Rhodococcus sp. BCP1 and Rhodococcus opacus R7: Genetic determinants and metabolic abilities with environmental relevance. PLoS One 2015; 10:e0139467 [View Article] [PubMed]
     [Google Scholar]
  44. Round J, Roccor R, Li SN, Eltis LD. A fatty acyl coenzyme A reductase promotes wax ester accumulation in Rhodococcus jostii RHA1. Appl Environ Microbiol 2017; 83:e00902-17 [View Article] [PubMed]
     [Google Scholar]
  45. MacArthur I, Anastasi E, Alvarez S, Scortti M, Vázquez-Boland JA. Comparative genomics of Rhodococcus equi virulence plasmids indicates host-driven evolution of the vap pathogenicity island. Genome Biol Evol 2017; 9:1241–1247 [View Article] [PubMed]
     [Google Scholar]
  46. von Bargen K, Haas A. Molecular and infection biology of the horse pathogen Rhodococcus equi. FEMS Microbiol Rev 2009; 33:870–891 [View Article] [PubMed]
     [Google Scholar]
  47. Hondalus MK, Mosser DM. Survival and replication of Rhodococcus equi in macrophages. Infect Immun 1994; 62:4167–4175 [View Article] [PubMed]
     [Google Scholar]
  48. González-Iglesias P, Scortti M, MacArthur I, Hapeshi A, Rodriguez H et al. Mouse lung infection model to assess Rhodococcus equi virulence and vaccine protection. Vet Microbiol 2014; 172:256–264 [View Article] [PubMed]
     [Google Scholar]
  49. Giguère S, Hondalus MK, Yager JA, Darrah P, Mosser DM et al. Role of the 85-kilobase plasmid and plasmid-encoded virulence-associated protein a in Iitracellular survival and virulence of Rhodococcus equi. Infect Immun 1999; 67:3548–3557 [View Article] [PubMed]
     [Google Scholar]
  50. Coulson GB, Agarwal S, Hondalus MK. Characterization of the role of the pathogenicity island and vapG in the virulence of the intracellular actinomycete pathogen Rhodococcus equi. . Infect Immun 2010; 78:3323–3334 [View Article] [PubMed]
     [Google Scholar]
  51. Oren A, Arahal DR, Göker M, Moore ERB, Rossello-Mora R et al. International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision). Int J Syst Evol Microbiol 2023; 73:005585 [View Article]
     [Google Scholar]
  52. Ripio MT, Geoffroy C, Domínguez G, Alouf JE, Vázquez-Boland JA. The sulphydryl-activated cytolysin and a sphingomyelinase C are the major membrane-damaging factors involved in cooperative (CAMP-like) haemolysis of Listeria spp. Res Microbiol 1995; 146:303–313 [View Article] [PubMed]
     [Google Scholar]
  53. Sun M, Zhu B, Liu J, Qin K, Peng F. Rhodococcus antarcticus sp. nov., isolated from a till sample of Collins glacier front, Antarctica. Int J Syst Evol Microbiol 2023; 73:005940 [View Article]
     [Google Scholar]
  54. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article] [PubMed]
     [Google Scholar]
  55. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4e1900v1901 [View Article]
     [Google Scholar]
  56. Goodfellow M, Beckham AR, Barton MD. Numerical classification of Rhodococcus equi and related actinomycetes. J App Bacteriol 1982; 53:199–207 [View Article]
     [Google Scholar]
  57. Kelly BG, Wall DM, Boland CA, Meijer WG. Isocitrate lyase of the facultative intracellular pathogen Rhodococcus equi. Microbiol 2002; 148:793–798 [View Article]
     [Google Scholar]
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Rhodococcus parequi sp. nov., a new species isolated from equine farm soil closely related to the pathogen Rhodococcus equi
Int J Syst Evol Microbiol 75, 006679 (2025); https://doi.org/10.1099/ijsem.0.006679
/content/journal/ijsem/10.1099/ijsem.0.006679
/content/journal/ijsem/10.1099/ijsem.0.006679
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