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

Volume 76, Issue 4

sp. nov. and sp. nov., isolated from the pharyngeal swabs of coal miners No Access

Abstract

Four Gram-stain-positive, catalase-negative, oxidase-negative, strictly anaerobic, non-spore-forming, non-motile, coccoid bacteria (G1425/G1967 and G1604/G1641) were isolated from the pharyngeal swabs of coal miners in Shanxi Province of China. Phylogenetic analysis of the 16S rRNA gene and 194 core genes revealed that these 4 strains belong to the genus . These strains were most closely related to ATCC 33270 and S3374. Average nucleotide identity (84.0–90.9%) and digital DNA–DNA hybridization values (27.3–42.0%) were below the species-level thresholds. The major fatty acids of all four strains were C, C 9 and C. Major polar lipids were composed of diphosphatidylglycerol and phosphatidylethanolamine. Ubiquinone-8 was the sole ubiquinone detected in strains G1425ᵀ and G1604ᵀ. Based on phenotypic and phylogenetic evidence, we propose that strains G1425 and G1604 represent two novel species of the genus , respectively, with the names sp. nov. and sp. nov. The type strains are G1425 (=GDMCC 1.5468=JCM 37774) and G1604 (=GDMCC1.5469=JCM 37775).

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  • Accepted:
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Keyword(s): coal miners , novel species , Parvimonas and pharyngeal swabs
Funding
This study was supported by the:
  • Health Commission of Shanxi Province (Award 2024149)
    • Principal Award Recipient: KuiDong
  • Education Department of Shanxi Province (Award 2023L117)
    • Principal Award Recipient: ZhimingKang
  • Young Top-notch Talent Project in the Medical and Health Field of the Sanjin Talents Program (Award SJYC2024469)
    • Principal Award Recipient: KuiDong
  • Youth Fund for Enhancing Capability of Infectious Disease Surveillance and Prevention (Award 102393240020020000003)
    • Principal Award Recipient: JiPu
  • Open Project Fund of the Key Laboratory of Coal Environmental Pathogenicity and Prevention (Shanxi Medical University), Ministry of Education, China (Award MEKLCEPP/SXMU-202419)
    • Principal Award Recipient: HanZheng
  • Shanxi Provincial Basic Research Program Youth Project (Award 202503021212162)
    • Principal Award Recipient: CaixinYang
© 2026 The Authors
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2026-04-08
2026-04-14

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References

  1. Jansson MK, Hering S, Buhl MEJ. Parvimonas parva sp. nov., derived from a human genito-urinary lesion. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
     [Google Scholar]
  2. Tindall BJ, Euzéby JP. Proposal of Parvimonas gen. nov. and Quatrionicoccus gen. nov. as replacements for the illegitimate, prokaryotic, generic names micromonas Murdoch and Shah 2000 and Quadricoccus Maszenan et al. 2002, respectively. Int J Syst Evol Microbiol 2006; 56:2711–2713 [View Article]
     [Google Scholar]
  3. Duan Y, Feng W, Shen Y, Li Y, Li N et al. Severe pneumonia with empyema caused by Parvimonas micra and Streptococcus constellatus co-infection: a case report. J Int Med Res 2023; 51:3000605231210657 [View Article] [PubMed]
     [Google Scholar]
  4. Qi H, Gao H, Li M, Sun T, Gu X et al. Parvimonas micra promotes oral squamous cell carcinoma metastasis through TmpC-CKAP4 axis. Nat Commun 2025; 16:2305 [View Article]
     [Google Scholar]
  5. Bergsten E, Mestivier D, Donnadieu F, Pedron T, Barau C et al. Parvimonas micra, an oral pathobiont associated with colorectal cancer, epigenetically reprograms human colonocytes. Gut Microbes 2023; 15:2265138 [View Article] [PubMed]
     [Google Scholar]
  6. Tian C, Liu J, Chen Z, Li L. Case report: Analysis of the efficacy and safety of anti-infectious treatment for brain abscess caused by oral anaerobes. Front Pharmacol 2025; 16:1506879 [View Article] [PubMed]
     [Google Scholar]
  7. Phagoora J, Agrest B, Kabariti M, Saini S, Hedjar Y. A rare bacteremia in a patient with osteomyelitis and sacral ulcer: a case report of Tissierella praeacuta and Parvimonas micra. Cureus 2024; 16:e74314 [View Article] [PubMed]
     [Google Scholar]
  8. Zhang Y, Luo J, Chen K, Li N, Luo C et al. Cross-cohort analysis identifies shared gut microbial signatures and validates microbial risk scores for colorectal cancer. J Transl Med 2025; 23:676 [View Article]
     [Google Scholar]
  9. Coker OO, Dai Z, Nie Y, Zhao G, Cao L et al. Mucosal microbiome dysbiosis in gastric carcinogenesis. Gut 2018; 67:1024–1032 [View Article] [PubMed]
     [Google Scholar]
  10. Li X, Yang M, Zhang Y, Wan F, Zheng Z et al. The temporal characteristics of pharyngeal microbiota and plasma lipidomics by silica exposure in coal miner. Sci Rep 2025; 16: [View Article]
     [Google Scholar]
  11. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
     [Google Scholar]
  12. Chalita M, Kim YO, Park S, Oh H-S, 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]
  13. Berlin K, Koren S, Chin C-S, Drake JP, Landolin JM et al. Assembling large genomes with single-molecule sequencing and locality-sensitive hashing. Nat Biotechnol 2015; 33:623–630 [View Article] [PubMed]
     [Google Scholar]
  14. Xie Y, Wu G, Tang J, Luo R, Patterson J et al. SOAPdenovo-Trans: de novo transcriptome assembly with short RNA-Seq reads. Bioinformatics 2014; 30:1660–1666 [View Article] [PubMed]
     [Google Scholar]
  15. Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ et al. The SEED and the rapid annotation of microbial genomes using subsystems technology (RAST). Nucleic Acids Res 2014; 42:D206–14 [View Article] [PubMed]
     [Google Scholar]
  16. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 2016; 44:D457–62 [View Article] [PubMed]
     [Google Scholar]
  17. Chklovski A, Parks DH, Woodcroft BJ, Tyson GW. CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning. Nat Methods 2023; 20:1203–1212 [View Article] [PubMed]
     [Google Scholar]
  18. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  19. 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]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  21. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004; 431:980–984 [View Article] [PubMed]
     [Google Scholar]
  22. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article] [PubMed]
     [Google Scholar]
  23. Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006; 22:1658–1659 [View Article]
     [Google Scholar]
  24. Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 2009; 26:1641–1650 [View Article] [PubMed]
     [Google Scholar]
  25. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
     [Google Scholar]
  26. Yoon SH, Ha SM, 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]
  27. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  28. Minnikin DE, Patel PV, Alshamaony L, Goodfellow M. Polar lipid composition in the classification of nocardia and related bacteria. Int J Syst Bacteriol 1977; 27:104–117 [View Article]
     [Google Scholar]
  29. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  30. Kroppenstedt RM. Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 1982; 5:2359–2367 [View Article]
     [Google Scholar]
  31. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  33. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
     [Google Scholar]
  34. Knook DL, Planta RJ. Function of ubiquinone in electron transport from reduced nicotinamide adenine dinucleotide to nitrate and oxygen in Aerobacter aerogenes. J Bacteriol 1971; 105:483–488 [View Article] [PubMed]
     [Google Scholar]
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Parvimonas oralis sp. nov. and Parvimonas pharyngis sp. nov., isolated from the pharyngeal swabs of coal miners
Int J Syst Evol Microbiol 76, 007123 (2026); https://doi.org/10.1099/ijsem.0.007123
/content/journal/ijsem/10.1099/ijsem.0.007123
/content/journal/ijsem/10.1099/ijsem.0.007123
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