1887

Abstract

Four aerobic, Gram-stain-positive, rod-shaped bacteria (HY60, HY54, HY82 and HY89) were isolated from bat faeces of and species collected in PR China. Phylogenetic analyses based on 16S rRNA gene sequences indicated that the four novel strains formed two separate but adjacent subclades close to CGMCC 1.12260 (97.6–97.7 % similarity), JCM 18706 (97.3–97.5 %) and JCM 30493 (97.3–97.4 %). The 16S rRNA gene sequence similarity was 98.3 % between strains HY60 and HY82, and identical within strain pairs HY60/HY54 and HY82/HY89. The DNA G+C contents of strains HY60 and HY82 were 61.9 and 63.3 mol%, respectively. The digital DNA–DNA hybridization and average nucleotide identity values between each novel strain and their closest relatives were all below the 70 % and 95–96 % thresholds for species delimitation, respectively. All four novel strains contained -C, -C, -C and -C as the main fatty acids, MK-11 and MK-12 as the major respiratory quinones, and diphosphatidylglycerol, phosphatidylglycerol and one unidentified glycolipid as the predominant polar lipids. The cell-wall peptidoglycan was of B type and contained alanine, glutamate, glycine and ornithine. The acyl type of the muramic acid was glycolyl. The whole-cell sugars were rhamnose and ribose. Based on the foregoing polyphasic analyses, it was concluded that the four uncharacterized strains represented two novel species of the genus , for which the names sp. nov. [type strain HY60 (=CGMCC 1.17468=GDMCC 1.1951=KACC 22102)] and sp. nov. [type strain HY82 (=CGMCC 1.17469=GDMCC 1.1949=KACC 22101)] are proposed, respectively.

Funding
This study was supported by the:
  • Research Units of Discovery of Unknown Bacteria and Function (Award 2018RU010)
    • Principle Award Recipient: JianguoXu
  • National Key R&D Program of China (Award 2019YFC1200505)
    • Principle Award Recipient: JingYang
  • National Key R&D Program of China (Award 2019YFC1200500)
    • Principle Award Recipient: JingYang
  • National Science and Technology Major Project of China (Award 2017ZX10303405-005-002)
    • Principle Award Recipient: HanZheng
  • National Science and Technology Major Project of China (Award 2017ZX10303405-002)
    • Principle Award Recipient: HanZheng
  • National Science and Technology Major Project of China (Award 2018ZX10712001-018)
    • Principle Award Recipient: ShanLu
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2021-07-07
2021-07-29
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References

  1. Orla-Jensen S. The Lactic Acid Bacteria Copenhagen: Høst & Sons; 1919
    [Google Scholar]
  2. Takeuchi M, Hatano K. Union of the genera Microbacterium Orla-Jensen and Aureobacterium Collins et al. in a redefined genus Microbacterium. Int J Syst Bacteriol 1998; 48:739–747
    [Google Scholar]
  3. Krishnamurthi S, Bhattacharya A, Schumann P, Dastager SG, Tang SK et al. Microbacterium immunditiarum sp. nov., an actinobacterium isolated from landfill surface soil, and emended description of the genus Microbacterium. Int J Syst Evol Microbiol 2012; 62:2187–2193 [View Article] [PubMed]
    [Google Scholar]
  4. Alves A, Correia A, Igual JM, Trujillo ME. Microbacterium endophyticum sp. nov. and Microbacterium halimionae sp. nov., endophytes isolated from the salt-marsh plant Halimione portulacoides and emended description of the genus Microbacterium. Syst Appl Microbiol 2014; 37:474–479 [View Article] [PubMed]
    [Google Scholar]
  5. Fidalgo C, Riesco R, Henriques I, Trujillo ME, Alves A. Microbacterium diaminobutyricum sp. nov., isolated from Halimione portulacoides, which contains diaminobutyric acid in its cell wall, and emended description of the genus Microbacterium. Int J Syst Evol Microbiol 2016; 66:4492–4500 [View Article] [PubMed]
    [Google Scholar]
  6. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  7. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  8. Young CC, Busse HJ, Langer S, Chu JN, Schumann P et al. Microbacterium agarici sp. nov., Microbacterium humi sp. nov. and Microbacterium pseudoresistens sp. nov., isolated from the base of the mushroom Agaricus blazei. Int J Syst Evol Microbiol 2010; 60:854–860 [View Article] [PubMed]
    [Google Scholar]
  9. Lal D, Gupta SK, Schumann P, Lal R. Microbacterium lindanitolerans sp. nov., isolated from hexachlorocyclohexane-contaminated soil. Int J Syst Evol Microbiol 2010; 60:2634–2638 [View Article] [PubMed]
    [Google Scholar]
  10. Huang Y, Wang X, Yang J, Lu S, Lai XH et al. Apibacter raozihei sp. nov. isolated from bat feces of Hipposideros and Taphozous spp. Int J Syst Evol Microbiol 2020; 70:611–617 [View Article] [PubMed]
    [Google Scholar]
  11. Wang X, Yang J, Lu S, Lai XH, Jin D et al. Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2018; 68:3874–3880 [View Article] [PubMed]
    [Google Scholar]
  12. 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]
    [Google Scholar]
  13. 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]
  14. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  15. 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]
  16. 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]
  17. 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]
  18. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H et al. Gene ontology: tool for the unification of biology. Nat Genet 2000; 25:25–29 [View Article] [PubMed]
    [Google Scholar]
  19. Gene Ontology C. The gene ontology resource: enriching a GOld mine. Nucleic Acids Res 2021; 49:D325–D334
    [Google Scholar]
  20. Hyatt D, Chen GL, 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]
  21. 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]
  22. 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]
  23. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012; 61:1061–1067 [View Article] [PubMed]
    [Google Scholar]
  24. Yutin N, Puigbo P, Koonin EV, Wolf YI. Phylogenomics of prokaryotic ribosomal proteins. PLoS One 2012; 7:e36972 [View Article] [PubMed]
    [Google Scholar]
  25. Richert K, Brambilla E, Stackebrandt E. The phylogenetic significance of peptidoglycan types: Molecular analysis of the genera Microbacterium and Aureobacterium based upon sequence comparison of gyrB, rpoB, recA and ppk and 16SrRNA genes. Syst Appl Microbiol 2007; 30:102–108 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
    [Google Scholar]
  27. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe 2014; 9:111–118
    [Google Scholar]
  28. Rodriguezr LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016
    [Google Scholar]
  29. Auch AF, von Jan M, Klenk HP, Goker 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]
  30. Ciufo S, Kannan S, Sharma S, Badretdin A, Clark K et al. Using average nucleotide identity to improve taxonomic assignments in prokaryotic genomes at the NCBI. Int J Syst Evol Microbiol 2018; 68:2386 [View Article] [PubMed]
    [Google Scholar]
  31. Thompson CC, Chimetto L, Edwards RA, Swings J, Stackebrandt E et al. Microbial genomic taxonomy. BMC Genomics 2013; 14:913 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note. 1990
    [Google Scholar]
  34. Peter K, Reiner MK. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005
    [Google Scholar]
  35. Minnikin DE, Alshamaony L, Goodfellow M. Differentiation of Mycobacterium, Nocardia, and related taxa by thin-layer chromatographic analysis of whole-organism methanolysates. J Gen Microbiol 1975; 81:200–204
    [Google Scholar]
  36. Minnikin D, O’donnell A, 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]
  37. 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]
  38. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407 [View Article] [PubMed]
    [Google Scholar]
  39. Schleifer KH. Analysis of the Chemical Composition and Primary Structure of Murein Method Microbiol 1985 pp 123–156
    [Google Scholar]
  40. Uchida K, Kudo T, Suzuki K-I, Nakase T. A new rapid method of glycolate test by diethyl ether extraction, which is applicable to a small amount of bacterial cells of less than one milligram. J Gen Appl Microbiol 1999; 45:49–56 [View Article]
    [Google Scholar]
  41. Suzuki KI, Hamada M. Microbacterium. In Bergey’s Manual of Systematics of Archaea and Bacteria John Wiley & Sons, Ltd; 2015
    [Google Scholar]
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