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Abstract

Six aerobic, Gram-stain-positive, non-motile, rod-shaped bacterial strains (P13, P18, P16, P17, P20 and P15) were isolated from the intestinal contents of the plateau vole () collected from the Qinghai–Tibet Plateau, PR China. Phylogenetic analyses showed that these isolates formed three well-separated lineages in all phylogenetic and phylogenomic trees comprising members of the genus . The average nucleotide identity and digital DNA–DNA hybridization values between the three novel type strains (P13/P16/P20) and other known species in this genus were all below the thresholds of 95–96% and 70%. Analysis of fatty acid profiles showed -C and -C as the major fatty acids for all six strains. All novel type strains had diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipids 2 as the major polar lipids. The peptidoglycan amino acids of these three type strains consisted of alanine, glutamic acid, glycine and 2,4-diaminobutyric acid. All novel type strains had MK-11 and MK-10 as the predominant respiratory quinone. The DNA G+C contents of strains P13, P16 and P20 were 70.0, 69.0 and 70.0 mol%, respectively. Based on genotypic, phenotypic, phylogenetic and biochemical properties, the six novel strains represent three novel species in the genus , for which the names sp. nov. (type strain P13=GDMCC 1.4677=JCM 37540), sp. nov. (type strain P16=GDMCC 1.4678=JCM 37541) and sp. nov. (type strain P20=GDMCC 1.4681=JCM 37542) are proposed, respectively.

Funding
This study was supported by the:
  • Tengfei initiative by the National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases. (Award 2024NITFID503)
    • Principal Award Recipient: JianguoXu
  • Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
    • Principal Award Recipient: JianguoXu
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/content/journal/ijsem/10.1099/ijsem.0.006845
2025-07-15
2026-04-20

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References

  1. Behrendt U, Schumann P, Hamada M, Suzuki K-I, Spröer C et al. Reclassification of Leifsonia ginsengi (Qiu et al. 2007) as Herbiconiux ginsengi gen. nov., comb. nov. and description of Herbiconiux solani sp. nov., an actinobacterium associated with the phyllosphere of Solanum tuberosum L. Int J Syst Evol Microbiol 2011; 61:1039–1047 [View Article] [PubMed]
    [Google Scholar]
  2. Hamada M, Komukai C, Tamura T, Evtushenko LI, Vinokurova NG et al. Description of Herbiconiux flava sp. nov. and emended description of the genus Herbiconiux. Int J Syst Evol Microbiol 2012; 62:795–799 [View Article] [PubMed]
    [Google Scholar]
  3. Suzuki K, Suzuki M, Sasaki J, Park Y-H, Komagata K. Leifsonia gen. nov., a genus for 2,4-diaminobutyric acid-containing actinomycetes to accommodate “Corynebacterium aquaticum” Leifson 1962 and Clavibacter xyli subsp. cynodontis Davis et al. 1984. J Gen Appl Microbiol 1999; 45:253–262 [View Article]
    [Google Scholar]
  4. Qiu F, Huang Y, Sun L, Zhang X, Liu Z et al. Leifsonia ginsengi sp. nov., isolated from ginseng root. Int J Syst Evol Microbiol 2007; 57:405–408 [View Article] [PubMed]
    [Google Scholar]
  5. Deng Y, Jiang Z-M, Han X-F, Su J, Yu L-Y et al. Pangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants. Front Microbiol 2023; 14:1119226 [View Article]
    [Google Scholar]
  6. Kim B-C, Park D-S, Kim H, Oh H-W, Lee KH et al. Herbiconiux moechotypicola sp. nov., a xylanolytic bacterium isolated from the gut of hairy long-horned toad beetles, Moechotypa diphysis (Pascoe). Int J Syst Evol Microbiol 2012; 62:90–95 [View Article] [PubMed]
    [Google Scholar]
  7. Li X, Li M, Huang M, Li J, Huang S et al. Hypoxic response patterns in lung tissue: an integrated analysis of comparative physiological and transcriptomic studies from Neodon fuscus and Lasiopodomys brandtii. Sci Total Environ 2023; 892:164537 [View Article]
    [Google Scholar]
  8. Li JQ, Li L, Fu BQ, Yan HB, Jia WZ. Complete mitochondrial genomes confirm the generic placement of the plateau vole, Neodon fuscus. Biosci Rep 2019; 39:BSR20182349 [View Article] [PubMed]
    [Google Scholar]
  9. Zhang X, Jian Y, Li X, Ma L, Karanis G et al. The first report of Cryptosporidium spp. in Microtus fuscus (Qinghai vole) and Ochotona curzoniae (wild plateau pika) in the Qinghai-Tibetan Plateau area, China. Parasitol Res 2018; 117:1401–1407 [View Article]
    [Google Scholar]
  10. Li M, Tian X, Li X, Huang M, Huang S et al. Diverse energy metabolism patterns in females in Neodon fuscus, Lasiopodomys brandtii, and Mus musculus revealed by comparative transcriptomics under hypoxic conditions. Sci Total Environ 2021; 783:147130 [View Article]
    [Google Scholar]
  11. Zhang X-X, Lou Z-Z, Huang S-Y, Zhou D-H, Jia W-Z et al. Genetic characterization of Toxoplasma gondii from Qinghai vole, Plateau pika and Tibetan ground-tit on the Qinghai-Tibet Plateau, China. Parasit Vectors 2013; 6:291 [View Article] [PubMed]
    [Google Scholar]
  12. Lopez Marin MA, Strejcek M, Junkova P, Suman J, Santrucek J et al. Exploring the potential of Micrococcus luteus culture supernatant with resuscitation-promoting factor for enhancing the culturability of soil bacteria. Front Microbiol 2021; 12:685263 [View Article] [PubMed]
    [Google Scholar]
  13. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article] [PubMed]
    [Google Scholar]
  14. Zhao L, Yang C, Chen M, Zhang J, Kong M et al. Marnyiella aurantia, gen. nov., sp. nov., a novel bacterial species of the family Weeksellaceae that could produce flexirubin type pigments. Int J Syst Evol Microbiol 2023; 73: [View Article]
    [Google Scholar]
  15. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Ostell J et al. GenBank. Nucleic Acids Res 2018; 46:D41–D47 [View Article] [PubMed]
    [Google Scholar]
  16. 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]
  17. 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]
  18. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  19. Rzhetsky A, Nei M. Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 1993; 10:1073–1095 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. 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]
  22. Rhoads A, Au KF. PacBio sequencing and its applications. Genom Proteom Bioinform 2015; 13:278–289 [View Article] [PubMed]
    [Google Scholar]
  23. Korostin D, Kulemin N, Naumov V, Belova V, Kwon D et al. Comparative analysis of novel MGISEQ-2000 sequencing platform vs Illumina HiSeq 2500 for whole-genome sequencing. PLoS One 2020; 15:e0230301 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. 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]
  26. 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]
  27. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
    [Google Scholar]
  28. 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] [PubMed]
    [Google Scholar]
  29. 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]
  30. Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O. PathogenFinder--distinguishing friend from foe using bacterial whole genome sequence data. PLoS One 2013; 8:e77302 [View Article] [PubMed]
    [Google Scholar]
  31. Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Res 2023; 51:D690–D699 [View Article] [PubMed]
    [Google Scholar]
  32. Medema MH, Blin K, Cimermancic P, de Jager V, Zakrzewski P et al. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences. Nucleic Acids Res 2011; 39:W339–46 [View Article] [PubMed]
    [Google Scholar]
  33. Athalye M, Noble WC, Minnikin DE. Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 1985; 58:507–512 [View Article] [PubMed]
    [Google Scholar]
  34. Baldoni E, Bolognani L, Vitaioli L. A rapid procedure for elimination of non-polar lipids hampering the usual polar lipid extraction and TLC separation. Eur J Histochem 1995; 39:253–257 [PubMed]
    [Google Scholar]
  35. 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]
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