A novel actinobacterium, designated strain CFH 30183T, was isolated from a soil sample collected from a karst cave in Luoyang, Henan Province. The taxonomic position of the strain was investigated using a polyphasic approach. Cells of strain CFH 30183T were observed to be Gram-stain positive, motile, asporogenous and coccoid to rod shaped. The strain was found to be aerobic and oxidase positive. On the basis of 16S rRNA gene sequence analysis, strain CFH 30183T was found to be closely related to Ornithinimicrobium murale 01-Gi-040T (97.8% sequence identity). The ANIb/ANIm values between strain CFH 30183T and O. murale DSM 22056T were found to be 80.3%/85.9%. Strain CFH 30183T was found to grow optimally at 28–32 °C, at pH 8.0–9.0 and in the presence of up to 7% NaCl (w/v). Whole cell hydrolysates of strain CFH 30183T contained l-ornithine as the diagnostic diamino acid, and arabinose, glucose, mannose and rhamnose as whole cell sugars. The respiratory quinone was determined to be MK-8(H4), while the major fatty acids were found to consist of iso-C15:0 and iso-C16:0. The polar lipids profile was found to include diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified phospholipid, an unidentified phosphoglycolipid and four unidentified lipids. The DNA G + C content of strain CFH 30183T was calculated to be 70.9%. Based on the phenotypic, genotypic and phylogenetic data obtained, strain CFH 30183T is considered to represent a novel species of the genus Ornithinimicrobium, for which the name Ornithinimicrobium cavernae sp. nov. is proposed. The type strain is CFH 30183T (= KCTC 49018T = CGMCC 1.16393T).
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Atlas RM (1993) Handbook of microbiological media. CRC Press, Boca Raton
Buck JD (1982) Nonstaining (KOH) method for determination of gram reactions of marine bacteria. Appl Environ Microbiol 44:992–993
Burleigh JG, Bansal MS, Eulenstein O, Hartmann S, Wehe A, Vision TJ (2011) Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees. Syst Biol 60(2):117
Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycan based on 2,4-diaminobutyric acid. J Appl Bacteriol 48:459–470
Collins MD, Pirouz T, Goodfellow M, Minnikin DE (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 100:221–230
Edgar RC (2004) MUSCLE multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Fang XM, Yan D, Bai JL, Su J, Liu HY, Ma BP, Zhang YQ, Yu LY (2017) Ornithinimicrobium flavum sp. nov., isolated from the leaf of Paris polyphylla. Int J Syst Evol Microbiol 67:4541–4545
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Finn RD, Coggil P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Potter SC, Punta M, Qureshi M, Sangrador-Vegas A, Salazar GA, Tate J, Bateman A (2016) The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 44:D279–D285
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416
Gordon RE, Barnett DA, Handerhan JE, Pang CHN (1974) Nocardia coeliaca, Nocardia autotrophica, and the nocardin strain. Int J Syst Bacteriol 24:54–63
Groth I, Schumann P, Weiss N, Schuetze B, Augsten K, Stackebrandt E (2001) Ornithinimicrobium humiphilum gen. nov., sp. nov., a novel soil actinomycete with l-ornithine in the peptidoglycan. Int J Syst Evol Microbiol 51:81–87
Harrison P, Strulo B (2000) SPADES—a process algebra for discrete event simulation. J Log Comput 10:3–42
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinform 11:119
Kampfer P, Glaeser SP, Schafer J, Lodders N, Martin K, Schumann P (2013) Ornithinimicrobium murale sp. nov., isolated from an indoor wall colonized by moulds. Int J Syst Evol Microbiol 63:119–123
Kanehisa FM, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45:D353–D361
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
Kimura M (1985) The neutral theory of molecular evolution. Evol Genes Prot 241:98–100
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 5:2359–2367
Kumar S, Stecher G, Tamura K (2016) MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
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
Liu XY, Wang BJ, Jiang CY, Liu SJ (2008) Ornithinimicrobium pekingense sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 58:116–119
Liu LZ, Liu Y, Chen Z, Liu HC, Zhou YG, Liu ZP (2013) Ornithinimicrobium tianjinense sp. nov., isolated from a recirculating aquaculture system. Int J Syst Evol Microbiol 63:4489–4494
Locci R (1989) Streptomyces and related genera. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2451–2508
Mayilraj S, Saha P, Suresh K, Saini HS (2006) Ornithinimicrobium kibberense sp. nov., isolated from the Indian Himalayas. Int J Syst Evol Microbiol 56:1657–1661
Ming H, Nie GX, Jiang HC, Yu TT, Zhou EM, Feng HG, Tang SK, Li WJ (2012) Paenibacillus frigoriresistens sp. nov., a novel psychrotroph isolated from a peat bog in Heilongjiang, Northern China. Antonie van Leeuwenhoek 102:297–305
Ming H, Yin YR, Li S, Nie GX, Yu TT, Zhou EM, Liu L, Dong L, Li WJ (2014) Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area. Int J Syst Evol Microbiol 64:650–656
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
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Appl Bacteriol 2:233–241
Ramaprasad EVV, Sasikala C, Ramana CV (2015) Ornithinimicrobium algicola sp. nov., a marine actinobacterium isolated from the green alga of the genus Ulva. Int J Syst Evol Microbiol 65:4627–4631
Rosselló-Móra R, Trujillo ME, Sutcliffe IC (2017) Introducing a digital protologue: a timely move towards a database-driven systematics of archaea and bacteria. Antonie Van Leeuwenhoek 110:455–456
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. Microbial ID, Inc., Newark
Shirling EB, Gottlieb D (1966) Methods for characterization of Streptomyces species. Int J Syst Bacteriol 16:313–340
Stackebrandt E, Rainey FA, Wardrainey NL (1997) Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491
Stamatakis A (2006) Raxml-vi-hpc: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22(21):2688
Tamaoka J, Katayama-Fujimura Y, Kuraishi H (1983) Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 54:31–36
Tang SK, Wang Y, Chen Y, Lou K, Cao LL, Xu LH, Li WJ (2009) Zhihengliuella alba sp. nov., and emended description of the genus Zhihengliuella. Int J Syst Evol Microbiol 59:2025–2031
Tatusov RL, Galperin MY, Natale DA, Koonin EV (2000) The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res 28:33–36
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
Waksman SA (1967) The actinomycetes. A summary of current knowledge. Ronald Press, New York
Williams ST, Goodfellow M, Alderson G (1989) Genus Streptomyces Waksman and Henrici 1943, 339AL. In: Williams ST, Sharpe ME, Holt JG (eds) Bergey’s manual of systematic bacteriology, vol 4. Williams & Wilkins, Baltimore, pp 2452–2492
Wu M, Scott AJ (2012) Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinformatics 28:1033
Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ, Chen HH, Xu LH, 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
Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 67:1613–1617
This work was supported by National Key Research and Development Program of China (2017YFD0200503), National Natural Science Foundation of China (Nos. 31600015, 31500004), Innovation Scientists and Technicians Troop Construction Projects of Henan Province (CXTD2016043), National Fundamental Fund Project Subsidy Funds of Personnel Training of China (No. J1310025) and Henan Province University youth researcher support project (2017GGJS106). W.-J. Li was also supported by Guangdong Province Higher Vocational Colleges and Schools Pearl River Scholar Funded Scheme (2014). The authors are grateful to Rüdiger Pukall (DSMZ, Germany) for kindly providing the reference type strain.
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Zhang, LY., Ming, H., Meng, XL. et al. Ornithinimicrobium cavernae sp. nov., an actinobacterium isolated from a karst cave. Antonie van Leeuwenhoek 112, 179–186 (2019). https://doi.org/10.1007/s10482-018-1141-6
- Ornithinimicrobium cavernae sp. nov.
- Karst cave
- Polyphasic taxonomy