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

Volume 75, Issue 1

sp. nov., isolated from human epidermis Open Access

Abstract

Five pink-pigmented bacterial strains, isolated from human skin and classified within the genus , were examined. Among them, four were identified as , while strain OT10 was deemed to be a potential novel species. Strain OT10 exhibited characteristics, such as Gram-stain-negative, oxidase positive, motile, strictly aerobic and rod shaped. The cells had multiple flagella at one end, arranged in a lophotrichous pattern. The predominant cellular fatty acids in OT10 were C ω7c/C ω6c and C 2OH; ubiquinone (Q)-10 was identified as the sole quinone. Major polar lipids included phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylcholine and two aminolipids. The G+C content of the genome was determined to be 72.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence similarities revealed that strain OT10 is closely related to subsp. ATCC 49956 (97.7%), subsp. ATCC BAA-691 (97.7%) and ATCC BAA-692 (97.5%). For the comparative genomic analyses, whole-genome sequencing was also conducted for strain OT10. Considering the chemotaxonomic, genotypic and phenotypic features, as well as the low average nucleotide identity and digital DNA–DNA hybridization values compared to its closest phylogenomic neighbours, OT10 is proposed to be a novel species named sp. nov., with OT10 designated as the type strain (=KCTC 92087 =JCM 34968).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): human skin flora , Roseomonas cutis and species novum
Funding
This study was supported by the:
  • National Institute of Health (Award 2023ER210800)
    • Principle Award Recipient: RobertJ. Mitchell
  • Korea Basic Science Institute (Award No. 2023R1A6C101B022)
    • Principle Award Recipient: KyoungLee
  • Changwon National University (Award 2023)
    • Principle Award Recipient: KyoungLee
  • National Research Foundation of Korea (Award No. 2016R1D1A1B01007775)
    • Principle Award Recipient: KyoungLee
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2025-01-14
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References

  1. Rihs JD, Brenner DJ, Weaver RE, Steigerwalt AG, Hollis DG et al. Roseomonas, a new genus associated with bacteremia and other human infections. J Clin Microbiol 1993; 31:3275–3283 [View Article] [PubMed]
     [Google Scholar]
  2. Zhang Y-Q, Yu L-Y, Wang D, Liu H-Y, Sun C-H et al. Roseomonas vinacea sp. nov., a Gram-negative coccobacillus isolated from a soil sample. Int J Syst Evol Microbiol 2008; 58:2070–2074 [View Article] [PubMed]
     [Google Scholar]
  3. Jiang C-Y, Dai X, Wang B-J, Zhou Y-G, Liu S-J. Roseomonas lacus sp. nov., isolated from freshwater lake sediment. Int J Syst Evol Microbiol 2006; 56:25–28 [View Article] [PubMed]
     [Google Scholar]
  4. Kim HM, Khan SA, Han DM, Chun BH, Jeon CO. Roseomonas algicola sp. nov., isolated from a green alga, Pediastrum duplex. Int J Syst Evol Microbiol 2020; 70:5634–5639 [View Article]
     [Google Scholar]
  5. Dé I, Rolston KVI, Han XY. Clinical significance of Roseomonas species isolated from catheter and blood samples: analysis of 36 cases in patients with cancer. Clin Infect Dis 2004; 38:1579–1584 [View Article] [PubMed]
     [Google Scholar]
  6. Damtab J, Nutaratat P, Boontham W, Srisuk N, Duangmal K et al. Roseomonas elaeocarpi sp. nov., isolated from olive (Elaeocarpus hygrophilus Kurz.) phyllosphere. Int J Syst Evol Microbiol 2016; 66:474–480 [View Article] [PubMed]
     [Google Scholar]
  7. Han XY, Pham AS, Tarrand JJ, Rolston KV, Helsel LO et al. Bacteriologic characterization of 36 strains of Roseomonas species and proposal of Roseomonas mucosa sp nov and Roseomonas gilardii subsp rosea subsp nov. Am J Clin Pathol 2003; 120:256–264 [View Article] [PubMed]
     [Google Scholar]
  8. Cosseau C, Romano-Bertrand S, Duplan H, Lucas O, Ingrassia I et al. Proteobacteria from the human skin microbiota: species-level diversity and hypotheses. One Health 2016; 2:33–41 [View Article] [PubMed]
     [Google Scholar]
  9. Struthers M, Wong J, Janda JM. An initial appraisal of the clinical significance of Roseomonas species associated with human infections. Clin Infect Dis 1996; 23:729–733 [View Article] [PubMed]
     [Google Scholar]
  10. Rai A, Jagadeeshwari U, Deepshikha G, Smita N, Sasikala C et al. Phylotaxogenomics for the reappraisal of the genus Roseomonas with the creation of six new genera. Front Microbiol 2021; 12:677842 [View Article] [PubMed]
     [Google Scholar]
  11. Oren A, Garrity GM. Valid publication of new names and new combinations effectively published outside the IJSEM.Validation list no203. Int J Syst Evol Microbiol 2022; 72:005167
     [Google Scholar]
  12. 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]
  13. Romano-Bertrand S, Bourdier A, Aujoulat F, Michon A-L, Masnou A et al. Skin microbiota is the main reservoir of Roseomonas mucosa, an emerging opportunistic pathogen so far assumed to be environmental. Clin Microbiol Infect 2016; 22:737 [View Article] [PubMed]
     [Google Scholar]
  14. Myles IA, Earland NJ, Anderson ED, Moore IN, Kieh MD et al. First-in-human topical microbiome transplantation with Roseomonas mucosa for atopic dermatitis. JCI Insight 2018; 3:e120608 [View Article] [PubMed]
     [Google Scholar]
  15. Barbian K, Bruno D, Sykora L, Ricklefs S, Chaudhary PP et al. De novo assembly of Roseomonas mucosa isolates from healthy human volunteers used to treat atopic dermatitis. Microbiol Resour Announc 2023; 12:e0052023 [View Article] [PubMed]
     [Google Scholar]
  16. Huang SL, Tuan NN, Lee K. Occurrence, human intake and biodegradation of estrogen-like nonylphenols and octylphenols. Curr Drug Metab 2016; 17:293–302 [View Article] [PubMed]
     [Google Scholar]
  17. Stanier RY, Palleroni NJ, Doudoroff M. The aerobic Pseudomonads: a taxonomic study. J Gen Microbiol 1966; 43:159–271 [View Article] [PubMed]
     [Google Scholar]
  18. Son H, Han S-U, Lee K. 2,5-Diketo-D-gluconate hyperproducing Gluconobacter sphaericus SJF2-1 with reporting multiple genes encoding the membrane-associated Flavoprotein-cytochrome c complexed dehydrogenases. Microorganisms 2022; 10:2130 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucl Acids Symp Ser 1999
     [Google Scholar]
  21. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
     [Google Scholar]
  22. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  23. Rzhetsky A, Nei M. A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 1992; 9:945–968
     [Google Scholar]
  24. Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis Version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
     [Google Scholar]
  25. Kimura M. A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 1980; 16:111–120 [View Article] [PubMed]
     [Google Scholar]
  26. Sambrook J, Russell DW. Molecular Cloning A Laboratory Manual, 3rd ed New York: Cold Spring Harbor Laboratory Press; 2001
     [Google Scholar]
  27. Andrews S. Fastqc: A Quality Control Tool for High Throughput Sequence Data. Cambridge, United Kingdom: Babraham Bioinformatics, Babraham Institute; 2010
  28. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [View Article] [PubMed]
     [Google Scholar]
  29. 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]
  30. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
     [Google Scholar]
  31. Harwood CS, Parales RE. The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 1996; 50:553–590 [View Article] [PubMed]
     [Google Scholar]
  32. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  33. 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] [PubMed]
     [Google Scholar]
  34. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinform 2016; 32:929–931 [View Article]
     [Google Scholar]
  35. Yoon S-H, Ha S-M, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 2017; 110:1281–1286 [View Article] [PubMed]
     [Google Scholar]
  36. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 2013; 14:1–14 [View Article]
     [Google Scholar]
  37. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P et al. Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 2002; 52:1043–1047 [View Article] [PubMed]
     [Google Scholar]
  38. Dickerman A, Bandara AB, Inzana TJ. Phylogenomic analysis of Haemophilus parasuis and proposed reclassification to Glaesserella parasuis, gen. nov., comb. nov. Int J Syst Evol Microbiol 2020; 70:180–186 [View Article]
     [Google Scholar]
  39. Chen L, Yang J, Yu J, Yao Z, Sun L et al. VFDB: a reference database for bacterial virulence factors. Nucleic Acids Res 2005; 33:D325–8 [View Article] [PubMed]
     [Google Scholar]
  40. Gerhardt P. Methods for General and Molecular Bacteriology Washington. DC: American Society for Microbiology; 1994
     [Google Scholar]
  41. Choi SY, Mun W, Choi S, Lee K, Mitchell RJ. Bdellovibrio svalbardensis sp. nov., a newly described predator isolated from svalbard, norway. Int J Syst Bacteriol 2024; 74:006248
     [Google Scholar]
  42. Kim M, Mun W, Jung WH, Lee J, Cho G et al. Antimicrobial pegtides: a modular poly(ethylene glycol)-based peptidomimetic approach to combat bacteria. ACS Nano 2021; 15:9143–9153 [View Article] [PubMed]
     [Google Scholar]
  43. CLSI Performance standards for antimicrobial susceptibility testing. Clin Lab Stand Inst 2016; 35:16–38
     [Google Scholar]
  44. Lanyi B. Classical and rapid identification methods for medically important bacteria. Methods in microbiol: Elsevier 19881–67 [View Article]
     [Google Scholar]
  45. Sasser M. Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). In MIDI Technical Note 101 MIDI Inc, Newark, Delaware, USA 1990
     [Google Scholar]
  46. Hiraishi A, Ueda Y, Ishihara J, Mori T. Comparative lipoquinone analysis of influent sewage and activated sludge by high-performance liquid chromatography and photodiode array detection. J Gen Appl Microbiol 1996; 42:457–469 [View Article]
     [Google Scholar]
  47. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  48. Da Costa MS, Albuquerque L, Nobre MF, Wait R. The identification of polar lipids in prokaryotes. Methods Microbiol: Elsevier 2011165–181 [View Article]
     [Google Scholar]
  49. Sanchez-Porro C, Gallego V, Busse H-J, Kampfer P, Ventosa A. Transfer of Teichococcus ludipueritiae and Muricoccus roseus to the genus Roseomonas, as Roseomonas ludipueritiae comb. nov. and Roseomonas rosea comb. nov., respectively, and emended description of the genus Roseomonas. Int J Syst Evol Microbiol 2009; 59:1193–1198 [View Article]
     [Google Scholar]
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Roseomonas cutis sp. nov., isolated from human epidermis
Int J Syst Evol Microbiol 75, 006617 (2025); https://doi.org/10.1099/ijsem.0.006617
/content/journal/ijsem/10.1099/ijsem.0.006617
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