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Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis

Abstract

A novel Gram-negative, strictly aerobic, short rod-shaped, non-motile bacterium, designated YIM 101302T, was isolated from the faeces of Rhinoceros unicornis dwelling in the Yunnan Wild Animal Park, Yunnan province, South-West China. The 16S rRNA gene sequence analysis revealed a clear affiliation of strain YIM 101302T to the genus Sphingobacterium. The newly isolated bacterium was found to be closely related to Sphingobacterium composti T5-12T (97.1 % 16S rRNA sequence identity) and Sphingobacterium alimentarium WCC 4521T (95.6 % 16S rRNA sequence identity) forming a distinct clade with these two species. Polar lipids of strain YIM 101302T were identified as phosphatidylethanolamine, phosphatidylmethylethanolamine, phosphatidylglycerol, phosphatidylinositol, an unidentified aminophospholipid, and three unidentified polar lipids; the predominant menaquinone as MK-7 and the major fatty as iso-C15:0. The genomic DNA G+C content was determined to be 38.9 mol%. The DNA–DNA hybridization values between strain YIM 101302T and S. composti T5-12T, was 53.6 ± 5.8 %. These results indicates that strain YIM 101302T represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium rhinocerotis sp. nov. is proposed. The type strain is YIM 101302T (=CCTCC AB 2013218T = KCTC 42533T).

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References

  1. Cerny G (1978) Studies on aminopeptidase for the distinction of Gram-negative from Gram-positive bacteria. Appl Microbiol Biotechnol 5:113–122

    CAS  Article  Google Scholar 

  2. Choi HA, Lee SS (2012) Sphingobacterium kyonggiense sp. nov., isolated from chloroethene-contaminated soil, and emended descriptions of sphingobacterium daejeonense and Sphingobacterium mizutaii. Int J Syst Evol Microbiol 62:2559–2564

    CAS  Article  PubMed  Google Scholar 

  3. Christensen H, Angen O, Mutters R, Olsen JE, Bisgaard M (2000) DNA–DNA hybridization determined in microwells using covalent attachment of DNA. Int J Syst Evol Microbiol 50:1095–1102

    CAS  Article  PubMed  Google Scholar 

  4. Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2,4-diaminobutyric acid. J Appl Bacteriol 48:459–470

    CAS  Article  Google Scholar 

  5. Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230

    CAS  Article  PubMed  Google Scholar 

  6. Duan SW, Liu ZC, Feng XY, Zheng K, Cheng LF (2009) Sphingobacterium bambusae sp. nov., isolated from soil of bamboo plantation. J Microbiol 47:693–698

    Article  PubMed  Google Scholar 

  7. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Bacteriol 39:224–229

    Article  Google Scholar 

  8. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376

    CAS  Article  PubMed  Google Scholar 

  9. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791

    Article  Google Scholar 

  10. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416

    Article  Google Scholar 

  11. He L, Li W, Huang Y, Wang LM, Liu ZH, Lanoot BJ, Vancanneyt M, Swings J (2005) Streptomyces jietaisiensis sp. nov., isolated from soil in northern China. Int J Syst Evol Microbiol 55:1939–1944

    CAS  Article  PubMed  Google Scholar 

  12. He X, Xiao T, Kuang H, Lan X, Tudahong M, Osman G, Fang C, Rahman E (2010) Sphingobacterium shayense sp. nov., isolated from forest soil. Int J Syst Evol Microbiol 60:2377–2381

    CAS  Article  PubMed  Google Scholar 

  13. Holmes B, Owen RJ, Hollis DG (1982) Flavobacterium spiritivorum, a new species isolated from human clinical specimens. Int J Syst Bacteriol 32:157–165

    CAS  Article  Google Scholar 

  14. Hsu SC, Lockwood JL (1975) Powdered chitin agar as selective medium for enumeration of actinomycetes in water and soil. Appl Microbiol 29:422–426

    PubMed Central  CAS  PubMed  Google Scholar 

  15. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716–721

    CAS  Article  PubMed  Google Scholar 

  16. Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120

    CAS  Article  PubMed  Google Scholar 

  17. Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5:2359–2387

    CAS  Article  Google Scholar 

  18. Lee DH, Hur JS, Kahng HY (2013) Sphingobacterium cladoniae sp. nov., isolated from lichen, Cladonia sp., and emended description of Sphingobacterium siyangense. Int J Syst Evol Microbiol 63:755–760

    CAS  Article  PubMed  Google Scholar 

  19. Leifson E (1960) Atlas of bacterial flagellation. Academic Press, London

    Book  Google Scholar 

  20. Li WJ, Xu P, Schumann P, Zhang YQ, Pukall R, Xu LH, Stackebrandt E, Jiang CL (2007) Georgenia ruanii sp. nov., a novel actinobacterium isolated from forest soil in Yunnan (China) and emended description of the genus Georgenia. Int J Syst Evol Microbiol 57:1424–1428

    Article  PubMed  Google Scholar 

  21. Liu J, Yang LL, Xu CK, Xi JQ, Yang FX, Zhou F, Zhou Y, Mo MH, Li WJ (2012) Sphingobacterium nematocida sp. nov., a nematicidal endophytic bacterium isolated from tobacco. Int J Syst Evol Microbiol 62:1809–1813

    CAS  Article  PubMed  Google Scholar 

  22. Matsuyama H, Katoh H, Ohkushi T, Satoh A, Kawahara K, Yumoto I (2008) Sphingobacterium kitahiroshimense sp. nov., isolated from soil. Int J Syst Evol Microbiol 58:1576–1579

    CAS  Article  PubMed  Google Scholar 

  23. Mehnaz S, Weselowski B, Lazarovits G (2007) Sphingobacterium canadense sp. nov., an isolate from corn roots. Syst Appl Microbiol 30:519–524

    CAS  Article  PubMed  Google Scholar 

  24. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167

    CAS  Article  Google Scholar 

  25. Minnikin DE, Collins MD, Goodfellow M (1979) Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Bacteriol 47:87–95

    CAS  Article  Google Scholar 

  26. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425

    CAS  PubMed  Google Scholar 

  27. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI technical note 101. MIDI Inc, Newark, DE

  28. Schmidt VS, Wenning M, Scherer S (2012) Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. Int J Syst Evol Microbiol 62:1506–1511

    CAS  Article  PubMed  Google Scholar 

  29. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–654

    Google Scholar 

  30. Son HM, Yang JE, Kook MC, Shin HS, Park SY, Lee DG, Yi TH (2013) Sphingobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from the soil of a ginseng field. J Gen Appl Microbiol 59:345–352

    CAS  Article  PubMed  Google Scholar 

  31. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849

    CAS  Article  Google Scholar 

  32. Steyn PL, Segers P, Vancanneyt M, Sandra P, Kersters K, Joubert JJ (1998) Classification of heparinolytic bacteria into a new genus, Pedobacter, comprising four species: Pedobacter heparinus comb. nov., Pedobacter piscium comb. nov., Pedobacter africanus sp. nov. and Pedobacter saltans sp. nov. Proposal of the family Sphingobacteriaceae fam. nov. Int J Syst Bacteriol 48:165–177

    CAS  Article  PubMed  Google Scholar 

  33. Sun LN, Zhang J, Chen Q, He J, Li SP (2013) Sphingobacterium caeni sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 63:2260–2264

    CAS  Article  PubMed  Google Scholar 

  34. Takeuchi M, Yokota A (1992) Proposals of Sphingobacterium faecium sp. nov., Sphingobacterium piscium sp. nov., Sphingobacterium heparinum comb. nov., Sphingobacterium thalpophilum comb. nov. and two genospecies of the genus Sphingobacterium, and synonymy of Flavobacterium yabuuchiae and Sphingobacterium spiritivorum. J Gen Appl Microbiol 38:465–482

    Article  Google Scholar 

  35. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  36. Ten LN, Liu QM, Im WT, Aslam Z, Lee ST (2006) Sphingobacterium composti sp. nov., a Novel DNase-producing bacterium isolated from compost. J Microbiol Biotechnol 16:1728–1733

    CAS  Google Scholar 

  37. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882

    PubMed Central  CAS  Article  PubMed  Google Scholar 

  38. Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular microbiology. American Society for Microbiology, Washington, DC, pp 330–393

    Google Scholar 

  39. Verena SJS, Mareike W, Siegfried S (2012) Sphingobacterium lactis sp. nov. and Sphingobacterium alimentarium sp. nov., isolated from raw milk and a dairy environment. Int J Syst Evol Microbiol 62:1506–1511

    Article  Google Scholar 

  40. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464

    Article  Google Scholar 

  41. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu H, Jiang CL (2005) Naxibacter alkalitolerans gen. nov., sp. nov., a novel member of the family Oxalobacteraceae isolated from China. Int J Syst Evol Microbiol 55:1149–1153

    CAS  Article  PubMed  Google Scholar 

  42. Yabe S, Aiba Y, Sakai Y, Hazaka M, Kawahara K, Yokota A (2013) Sphingobacterium thermophilum sp. nov., of the phylum Bacteroidetes, isolated from compost. Int J Syst Evol Microbiol 63:1584–1588

    CAS  Article  PubMed  Google Scholar 

  43. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N (1983) Sphingobacterium gen. nov., Sphingobacterium spiritivorum comb. nov., Sphingobacterium multivorum comb. nov., Sphingobacterium mizutae sp. nov., and Flavobacterium indologenes sp. nov. glucose-nonfermenting gram-negative rods in CDC Groups IIK-2 and IIb. Int J Syst Bacteriol 33:580–598

    Article  Google Scholar 

  44. Yoo SH, Weon HY, Jang HB, Kim BY, Kwon SW, Go SJ, Stackebrandt E (2007) Sphingobacterium composti sp. nov., isolated from cotton-waste composts. Int J Syst Evol Microbiol 57:1590–1593

    Article  PubMed  Google Scholar 

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Acknowledgments

This research was supported by the National Natural Science Foundation of China (No. 31270001 and No. 31460005) and Yunnan Provincial Society Development Project (2014BC006). Thank for the help of teachers Ling-ling Yang and Chun-hua Yang.

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Correspondence to Yi Jiang.

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Gui-Ding Li and Xiu Chen contributed equally to this work.

The GenBank accession number for the 16S rRNA gene sequence of strain YIM 101302T is KJ190943.

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Li, GD., Chen, X., Li, QY. et al. Sphingobacterium rhinocerotis sp. nov., isolated from the faeces of Rhinoceros unicornis . Antonie van Leeuwenhoek 108, 1099–1105 (2015). https://doi.org/10.1007/s10482-015-0563-7

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Keywords

  • Sphingobacterium rhinocerotis sp. nov.
  • Faeces
  • Rhinoceros unicornis