1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 9

gen. nov., sp. nov., isolated from faeces of the Tibetan antelope () in China Free

Abstract

Two hitherto unknown bacteria (strains 313 and 352) were recovered from the faeces of Tibetan antelopes on the Tibet–Qinghai Plateau, PR China. Cells were rod-shaped and Gram-stain-positive. The optimal growth conditions were at 37 °C and pH 7. The isolates were closely related to (92.6 % 16S rRNA gene sequence similarity), (92.5 %), (92.4 %), (92.2 %) and (91.6 %). Phylogenetic analyses showed that strains 313 and 352 clustered independently in the vicinity of the genera , and , but could not be classified clearly as a member of any of these genera. Phylogenomic analysis also indicated that strains 313 and 352 formed an independent branch in the family . The major cellular fatty acids of the strains were C and Cω9. The polar lipids comprised diphosphatidylglycerol, phosphatidylinositol mannoside, phosphatidylglycerol, phosphatidylinositol and five unidentified components. The peptidoglycan contained lysine, alanine and glutamic acid. The respiratory quinone was absent. The whole-cell sugars included glucose and rhamnose. The DNA G+C content of strain 313 was 60.6 mol%. Based on the low 16S rRNA gene sequence similarities, its taxonomic position in the phylogenetic and phylogenomic trees and its unique lipid pattern, we propose that strains 313 and 352 represent members of a novel species in a new genus, for which the name gen. nov., sp. nov. is proposed. The type strain is 313 (=CGMCC 4.7453=DSM 106216).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Fudania jinshanensis gen. nov., sp. nov., , Qinghai-Tibet Plateau and Tibetan antelope
© 2019 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003586
2019-09-01
2024-04-16
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/9/2942.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003586&mimeType=html&fmt=ahah

References

  1. Buchanan RE. Studies in the classification and nomenclature of the bacteria VIII. The subgroups and genera of the Actinomycetales . J Bacteriol 1918; 3:403–406
     [Google Scholar]
  2. Skerman VBD, Sneath PHA, McGowan V. Approved lists of bacterial names. Int J Syst Evol Microbiol 1980; 30:225–420 [View Article]
     [Google Scholar]
  3. Schaal KP, Yassin AF. Actinomycetaceae. In Bergey’s Manual of Systematics of Archaea and Bacteria New York: Wiley; 2015
     [Google Scholar]
  4. Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T et al. Genome-based taxonomic classification of the phylum Actinobacteria . Front Microbiol 2018; 9:9 [View Article][PubMed]
     [Google Scholar]
  5. du ZJ, Miao TT, Lin XZ, Liu QQ, Chen GJ. Flaviflexus huanghaiensis gen. nov., sp. nov., an actinobacterium of the family Actinomycetaceae . Int J Syst Evol Microbiol 2013; 63:1863–1867 [View Article][PubMed]
     [Google Scholar]
  6. 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]
  7. An D, Cai S, Dong X. Actinomyces ruminicola sp. nov., isolated from cattle rumen. Int J Syst Evol Microbiol 2006; 56:2043–2048 [View Article][PubMed]
     [Google Scholar]
  8. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York: John Wiley and Sons; 1991 pp. 125–175
     [Google Scholar]
  9. Chun J, Lee JH, Jung Y, Kim M, Kim S et al. EzTaxon: a web-based tool for the identification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259–2261 [View Article][PubMed]
     [Google Scholar]
  10. 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]
  11. 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]
  12. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696–704 [View Article][PubMed]
     [Google Scholar]
  13. 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]
  14. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  15. 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]
  16. Cashion P, Holder-Franklin MA, McCully J, Franklin M. A rapid method for the base ratio determination of bacterial DNA. Anal Biochem 1977; 81:461–466 [View Article][PubMed]
     [Google Scholar]
  17. Chin CS, Alexander DH, Marks P, Klammer AA, Drake J et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013; 10:563–569 [View Article][PubMed]
     [Google Scholar]
  18. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article][PubMed]
     [Google Scholar]
  19. Auch AF, von Jan M, Klenk HP, 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]
  20. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O et al. International Committee on Systematic Bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 1987; 37:463–464
     [Google Scholar]
  21. Fu L, Niu B, Zhu Z, Wu S, Li W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 2012; 28:3150–3152 [View Article][PubMed]
     [Google Scholar]
  22. 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 [View Article][PubMed]
     [Google Scholar]
  23. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note. vol. 101 1990 pp. 1–7
     [Google Scholar]
  24. Schumann P. Peptidoglycan structure. Methods Microbiol 2011; 38:101–129
     [Google Scholar]
  25. Schleifer KH. Analysis of the chemical composition and primary structure of murein. Methods Microbiol 1985; 18:123–156
     [Google Scholar]
  26. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231[PubMed]
     [Google Scholar]
  27. Collins MD, Jones D. Distribution of isoprenoid quinone structural types in bacteria and their taxonomic implication. Microbiol Rev 1981; 45:316[PubMed]
     [Google Scholar]
  28. Ventosa A, Marquez MC, Kocur M, Tindall BJ. Comparative study of "Micrococcus sp." strains CCM 168 and CCM 1405 and members of the genus Salinicoccus . Int J Syst Bacteriol 1993; 43:245–248 [View Article][PubMed]
     [Google Scholar]
  29. Watanabe M, Aoyagi Y, Ohta A, Minnikin DE. Structures of phenolic glycolipids from Mycobacterium kansasii . Eur J Biochem 1997; 248:93–98 [View Article][PubMed]
     [Google Scholar]
  30. Yassin AF, Sproeer C, Pukall R, Sylvester M, Siering C et al. Dissection of the genus Actinobaculum: reclassification of Actinobaculum schaalii Lawson, et al. 1997 and Actinobaculum urinale Hall, et al. 2003 as Actinotignum schaalii gen. nov., comb. nov. and Actinotignum urinale comb. nov., description of Actinotignum sanguinis sp. nov. and emended description of the genus Actinobaculum. Re-examination of Actinobaculum massiliense culture deposited as CCUG 47753T (=DSM 19118T) revealed that it does not represent a strain of this species. Int J Syst Evol Microbiol 2014:615–624
     [Google Scholar]
  31. Lawson PA, Falsen E, Akervall E, Vandamme P, Collins MD. Characterization of some Actinomyces-like isolates from human clinical specimens: reclassification of Actinomyces suis (Soltys and Spratling) as Actinobaculum suis comb. nov. and description of Actinobaculum schaalii sp. nov. Int J Syst Bacteriol 1997; 47:899–903 [View Article][PubMed]
     [Google Scholar]
  32. Jin L, Ko SR, Lee HG, Kim BH, Kim HS, Sr K, Kim HS et al. Flaviflexus salsibiostraticola sp. nov., an actinobacterium isolated from a biofilm reactor. Int J Syst Evol Microbiol 2014; 64:3293–3296 [View Article][PubMed]
     [Google Scholar]
  33. Yassin AF, Hupfer H, Siering C, Schumann P. Comparative chemotaxonomic and phylogenetic studies on the genus Arcanobacterium Collins et al. 1982 emend. Lehnen et al. 2006: proposal for Trueperella gen. nov. and emended description of the genus Arcanobacterium . Int J Syst Evol Microbiol 2011; 61:1265–1274 [View Article][PubMed]
     [Google Scholar]
  34. Azuma R, Murakami S, Ogawa A, Okada Y, Miyazaki S et al. Arcanobacterium abortisuis sp. nov., isolated from a placenta of a sow following an abortion. Int J Syst Evol Microbiol 2009; 59:1469–1473 [View Article][PubMed]
     [Google Scholar]
  35. Lehnen A, Busse HJ, Frölich K, Krasinska M, Kämpfer P et al. Arcanobacterium bialowiezense sp. nov. and Arcanobacterium bonasi sp. nov., isolated from the prepuce of European bison bulls (Bison bonasus) suffering from balanoposthitis, and emended description of the genus Arcanobacterium Collins et al. 1983. Int J Syst Evol Microbiol 2006; 56:861–866 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003586
Loading
Fudania jinshanensis gen. nov., sp. nov., isolated from faeces of the Tibetan antelope (Pantholops hodgsonii) in China
Int J Syst Evol Microbiol 69, 2942 (2019); https://doi.org/10.1099/ijsem.0.003586
/content/journal/ijsem/10.1099/ijsem.0.003586
/content/journal/ijsem/10.1099/ijsem.0.003586
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error