1887

Abstract

Strains HY041 and HY039 were oxidase- and Gram-stain-negative, catalase-positive, rod-shaped, non-motile, and facultatively anaerobic bacteria. They were isolated from the feces of bats of the and spp. collected from Chongqing City and Guangxi province (PR China), respectively. Phylogenetic analysis based on the 16S rRNA gene and 463 core genes indicated that HY041 and HY039 represent members of the genus , forming a clade with wkB301 (95.2 % 16S rRNA gene sequence similarity) and R-53146 (94.0 %). DNA–DNA hybridization (DDH) and average nucleotide identity (ANI) values of our isolates with the most closely related species were lower than the 70 % and 95–96 % threshold, respectively, in contrast to values above these two thresholds (DDH value: 89.1 %; ANI value: 98.5 %) between strains HY041 and HY039. The novel isolates could grow on nutrient and MacConkey agar. HY041 and HY039 could produce β-galactosidase and -acetyl-β-glucosaminidase, and utilize -adonitol, -mannose, gentiobiose, glucose and salicin. The major fatty acids (>10.0 %) of HY041 were C 3OH, C, C, summed feature 9 (C 10-methyl and/or -Cω9) and C 3OH. Polar lipids included phosphatidylethanolamine, glycolipid, two unidentified aminolipids and four unidentified lipids. Menaquinone 6 (MK-6) was the sole respiratory quinone. On the basis of all analyses so far, strains HY041 and HY039 represent a novel species of the genus , for which the name sp. nov. is proposed. The type strain is HY041 (=CGMCC 1.16567=JCM 33423) with a genomic DNA G+C content of 32.2 mol%.

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2019-10-29
2019-11-17
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References

  1. Kwong WK, Moran NA. Apibacter adventoris gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from honey bees. Int J Syst Evol Microbiol 2016;66: 1323– 1329 [CrossRef]
    [Google Scholar]
  2. Praet J, Aerts M, Brandt ED, Meeus I, Smagghe G et al. Apibacter mensalis sp. nov.: a rare member of the bumblebee gut microbiota. Int J Syst Evol Microbiol 2016;66: 1645– 1651 [CrossRef]
    [Google Scholar]
  3. Yang X-L, Zhang Y-Z, Jiang R-D, Guo H, Zhang W et al. Genetically diverse filoviruses in Rousettus and Eonycteris spp. bats, China, 2009 and 2015. Emerg Infect Dis 2017;23: 482– 486 [CrossRef]
    [Google Scholar]
  4. Ge X-Y, Li J-L, Yang X-L, Chmura AA, Zhu G et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature 2013;503: 535– 538 [CrossRef]
    [Google Scholar]
  5. Wang X, Yang J, Lu S, Lai X-H, Jin D et al. Nocardioides houyundeii sp. nov., isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2018;68: 3874– 3880 [CrossRef]
    [Google Scholar]
  6. Wang X, Yang J, Lu S, Lai X-H, Jin D et al. Paraliobacillus zengyii sp. nov., a slightly halophilic and extremely halotolerant bacterium isolated from Tibetan antelope faeces. Int J Syst Evol Microbiol 2019;69: 1426– 1432 [CrossRef]
    [Google Scholar]
  7. Bai X, Xiong Y, Lu S, Jin D, Lai X et al. Streptococcus pantholopis sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii). Int J Syst Evol Microbiol 2016;66: 3281– 3286 [CrossRef]
    [Google Scholar]
  8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990;215: 403– 410 [CrossRef]
    [Google Scholar]
  9. 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 [CrossRef]
    [Google Scholar]
  10. Yarza P, Richter M, Peplies J, Euzeby J, Amann R et al. The All-Species Living Tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2008;31: 241– 250 [CrossRef]
    [Google Scholar]
  11. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016;33: 1870– 1874 [CrossRef]
    [Google Scholar]
  12. Zhu W, Yang J, Lu S, X-h L, Jin D et al. Fudania jinshanensis gen. nov., sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii) in China. Int J Syst Evol Microbiol 2019;ijsem003586: 001466– 005026
    [Google Scholar]
  13. Huang Y, Wang X, Yang J, Lu S, Lai X-H et al. Nocardioides yefusunii sp. nov., isolated from Equus kiang (Tibetan wild ass) faeces. Int J Syst Evol Microbiol 2019;ijsem003674: 001466– 005026
    [Google Scholar]
  14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987;4: 406– 425 [CrossRef]
    [Google Scholar]
  15. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981;17: 368– 376 [CrossRef]
    [Google Scholar]
  16. Kolaczkowski B, Thornton JW. Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogeneous. Nature 2004;431: 980– 984 [CrossRef]
    [Google Scholar]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985;39: 783– 791 [CrossRef]
    [Google Scholar]
  18. 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 [CrossRef]
    [Google Scholar]
  19. Zwickl DJ, Holder MT. Model parameterization, prior distributions, and the general time-reversible model in Bayesian phylogenetics. Syst Biol 2004;53: 877– 888 [CrossRef]
    [Google Scholar]
  20. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003;52: 696– 704 [CrossRef]
    [Google Scholar]
  21. Nei M, Kumar S. Molecular Evolution and Phylogenetics Oxford University Press; 2000
    [Google Scholar]
  22. 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 [CrossRef]
    [Google Scholar]
  23. Luo R, Liu B, Xie Y, Li Z, Huang W et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience 2012;1: 18 [CrossRef]
    [Google Scholar]
  24. Kwong WK, Steele MI, Moran NA. Genome sequences of Apibacter spp., gut symbionts of Asian honey bees. Genome Biol Evol 2018;10: 1174– 1179 [CrossRef]
    [Google Scholar]
  25. 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 [CrossRef]
    [Google Scholar]
  26. Huson DH, Scornavacca C. Dendroscope 3: an interactive tool for rooted phylogenetic trees and networks. Syst Biol 2012;61: 1061– 1067 [CrossRef]
    [Google Scholar]
  27. Mehlen A, Goeldner M, Ried S, Stindl S, Ludwig W et al. Development of a fast DNA-DNA hybridization method based on melting profiles in microplates. Syst Appl Microbiol 2004;27: 689– 695 [CrossRef]
    [Google Scholar]
  28. 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 [CrossRef]
    [Google Scholar]
  29. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids 1990
    [Google Scholar]
  30. Collins MD, JONES D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 1980;48: 459– 470 [CrossRef]
    [Google Scholar]
  31. Komagata K, Suzuki K-I. 4 lipid and cell-wall analysis in bacterial systematics. Method Microbiol 1988; 161– 207
    [Google Scholar]
  32. 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 [CrossRef]
    [Google Scholar]
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