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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 9

sp. nov., a novel actinobacterium isolated from faeces Free

Abstract

A novel Gram-stain-positive, aerobic, non-spore-forming, irregular short rod-shaped actinobacterial strain, designated YIM 102482-1, was isolated from the faeces of . Strain YIM 102482-1 grew optimally at 30–37 °C, at pH 8.0 and in the presence of 1.0–3.0% (w/v) NaCl. Similarly, analysis based on 16S rRNA gene sequences showed that strain YIM 102482-1 was a member of the genus and most closely related to NBRC 15706 (97.6 %), NBRC 103089 (97.6 %), KCTC 13959 (96.4 %) and DSM 13485 (96.0 %), respectively. Furthermore, phylogenetic trees based on 16S rRNA gene sequences and genomic sequences demonstrated that strain YIM 102482-1 formed a distinct branch with all type strains of the genus . The major whole-cell sugars and cellular fatty acids (>10.0 %) were ribose and rhamnose, and anteiso-C, iso-C and C, respectively. The predominant menaquinone was MK-9, and 2,4-diaminobutyric acid and ornithine were the diagnostic diamino acids in the cell-wall peptidoglycan. The dominant polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol and unidentified glycolipid. The DNA G+C content of YIM 102482-1 was 63.0 mol%. Based on analysis results of physiological, biochemical and chemotaxonomic data, strain YIM 102482-1 represents a novel species of the genus , for which the name sp. nov. is proposed. The type strain is YIM 102482-1(=DSM 102156=CCTCC AB 2016023).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): faeces , Gulosibacter macacae sp. nov. and Macaca mulatta
Funding
This study was supported by the:
  • National Natural Science Foundation of China, http://dx.doi.org/10.13039/501100001809 (Award 81573327)
  • National Natural Science Foundation of China, http://dx.doi.org/10.13039/501100001809 (Award 31460005)
  • National Natural Science Foundation of China (Award 31270001)
© 2020 The Authors
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2020-08-18
2023-03-21
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References

  1. Manaia CM, Nogales B, Weiss N, Nunes OC. Gulosibacter molinativorax gen. nov., sp. nov., a molinate-degrading bacterium, and classification of 'Brevibacterium helvolum' DSM 20419 as Pseudoclavibacter helvolus gen. nov., sp. nov. Int J Syst Evol Microbiol 2004; 54:783–789 [View Article][PubMed]
     [Google Scholar]
  2. Park M-H, Traiwan J, Jung MY, Kim W. Gulosibacter chungangensis sp. nov., an actinomycete isolated from a marine sediment, and emended description of the genus Gulosibacter . Int J Syst Evol Microbiol 2012; 62:1055–1060 [View Article][PubMed]
     [Google Scholar]
  3. Lin Y-C, Uemori K, de Briel DA, Arunpairojana V, Yokota A et al. Zimmermannella helvola gen. nov., Zimmermannella alba sp. nov., Zimmermannella bifida sp. nov., Zimmermannella faecalis sp. nov. and Leucobacter albus sp. nov., novel members of the family Microbacteriaceae. Int J Syst Evol Microbiol 2004; 54:1669–1676 [View Article]
     [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; 9:1–119 [View Article]
     [Google Scholar]
  5. Kim MK, Jung HY. Pseudoclavibacter soli nov., a β-glucosidase-producing bacterium. Int J Syst Evol Microbiol 2009; 59:835–838
     [Google Scholar]
  6. Li Y-Q, Li L, Fu Y-S, Cui Z-Q, Duan Y-Q et al. Pseudoclavibacter endophyticus sp. nov., isolated from roots of Glycyrrhiza uralensis . Int J Syst Evol Microbiol 2016; 66:1287–1292 [View Article][PubMed]
     [Google Scholar]
  7. Cho S-L, Jung MY, Park M-H, Chang Y-H, Yoon J-H et al. Pseudoclavibacter chungangensis sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2010; 60:1672–1677 [View Article][PubMed]
     [Google Scholar]
  8. Srinivasan S, Kim HS, Kim MK, Lee M. Pseudoclavibacter caeni sp. nov., isolated from sludge of a sewage disposal plant. Int J Syst Evol Microbiol 2012; 62:786–790 [View Article][PubMed]
     [Google Scholar]
  9. Du J, Singh H, Yang J-E, Shik Yin C, Kook M et al. Pseudoclavibacter terrae sp. nov. isolated from rhizosphere soil of Ophiopogon japonicus . Int J Syst Evol Microbiol 2015; 65:4202–4207 [View Article][PubMed]
     [Google Scholar]
  10. Li G-D, Chen X, Li Q-Y, Xu F-J, Qiu S-M et al. Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis . Antonie van Leeuwenhoek 2015; 108:1099–1105 [View Article][PubMed]
     [Google Scholar]
  11. 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][PubMed]
     [Google Scholar]
  12. 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]
  13. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  14. Fitch WM, Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  15. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article][PubMed]
     [Google Scholar]
  16. 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]
  17. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  18. Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 2015; 31:1674–1676 [View Article][PubMed]
     [Google Scholar]
  19. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial bioinformatics database and analysis resource center. Nucleic Acids Res 2017; 45:D535–D542 [View Article][PubMed]
     [Google Scholar]
  20. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015; 5:8365 [View Article][PubMed]
     [Google Scholar]
  21. Schomburg I, Chang A, Ebeling C, Gremse M, Heldt C et al. BRENDA, the enzyme database: updates and major new developments. Nucleic Acids Res 2004; 32:431D–433 [View Article][PubMed]
     [Google Scholar]
  22. 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]
     [Google Scholar]
  23. 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–D462 [View Article][PubMed]
     [Google Scholar]
  24. 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][PubMed]
     [Google Scholar]
  25. Meier-Kolthoff JP, Klenk H-P, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article][PubMed]
     [Google Scholar]
  26. Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe Mag 2014; 9:111–118 [View Article]
     [Google Scholar]
  27. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014; 30:1312–1313 [View Article][PubMed]
     [Google Scholar]
  28. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML web servers. Syst Biol 2008; 57:758–771 [View Article][PubMed]
     [Google Scholar]
  29. Wayne LG et al. International Committee on systematic bacteriology: announcement of the report of the AD hoc Committee on reconciliation of approaches to bacterial Systematics. Syst Appl Microbiol 1988; 10:99–100 [View Article]
     [Google Scholar]
  30. 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]
  31. Cheng J, Zhang Y-G, Chen W, Li L, Zhang D-F et al. Saccharopolyspora cavernae sp. nov., a novel actinomycete isolated from the swallow cave in Yunnan, south-west China. Antonie van Leeuwenhoek 2013; 104:837–843 [View Article][PubMed]
     [Google Scholar]
  32. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article][PubMed]
     [Google Scholar]
  33. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z et al. Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family 'Oxalobacteraceae' isolated from China. Int J Syst Evol Microbiol 2005; 55:1149–1153 [View Article][PubMed]
     [Google Scholar]
  34. Minnikin DE, Cillins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 1979; 47:87–95 [View Article]
     [Google Scholar]
  35. 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]
  36. Groth I, Schumann P, Weiss N, Martin K, Rainey FA. Agrococcus jenensis gen. nov., sp. nov., a new genus of actinomycetes with diaminobutyric acid in the cell wall. Int J Syst Bacteriol 1996; 46:234–239 [View Article][PubMed]
     [Google Scholar]
  37. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1
     [Google Scholar]
  38. Schleifer KH, Kandler O. Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 1972; 36:407–477 [View Article][PubMed]
     [Google Scholar]
  39. Tang S-K, Wang Y, Chen Y, Lou K, Cao L-L et al. Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella . Int J Syst Evol Microbiol 2009; 59:2025–2032 [View Article][PubMed]
     [Google Scholar]
  40. Lechevalier MP, Lechevalier H. Chemical composition as a criterion in the classification of aerobic actinomycetes. Int J Syst Bacteriol 1970; 20:435–443 [View Article]
     [Google Scholar]
  41. Mesbah M, Premachandran U, Whitman WB. Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 1989; 39:159–167 [View Article]
     [Google Scholar]
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Gulosibacter macacae sp. nov., a novel actinobacterium isolated from Macaca mulatta faeces
Int J Syst Evol Microbiol 70, 5115 (2020); https://doi.org/10.1099/ijsem.0.004389
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