1887

Abstract

A novel actinobacterium, designated CFH 10395, was isolated from the foregut of grass carp (), which had been fed with ginseng extract supplement. The taxonomic position was investigated by a polyphasic approach. Cells of CFH 10395 were Gram-staining-positive, aerobic, ovoid-shaped, non-spore-forming and non-motile. On the basis of the results of 16S rRNA gene sequence analysis, CFH 10395 was most closely related to KCTC 49087, JCM 16464 and JCM 17781 (97.85%, 97.51 and 97.29% similarity, respectively). CFH 10395 grew at 4–37 °C, pH 5.0–9.0 and in the presence of up to 10.0 % NaCl (w/v). The dominant menaquinone was MK-7. The whole-cell sugars were rhamnose, glucose, mannose and galactose. -diaminopimelic acid was the diagnostic diamino acid in the cell-wall peptidoglycan. The major fatty acids were anteiso-C, anteiso-C and iso-C. The genome size was 3.99 Mbp with a DNA G+C content of 71.9 mol%. On the basis of the results of phylogenetic analysis, physiological properties, chemotaxonomic characteristics, low average nucleotide identity (ANI) and digital DDH (dDDH) results [ANI calculated using MUMmer (ANIm) <87 %, ANI calculated using (ANIb) <83 % and dDDH <23 %], it is concluded that CFH 10395 represents a novel species of the genus , for which the name sp. nov., is proposed. The type strain is CFH 10395 (=CGMCC 1.13804=KCTC 49235).

Funding
This study was supported by the:
  • Doctor Scientific Research Fund of Xinxiang Medical University (Award XYBSKYZZ201625)
    • Principle Award Recipient: HongMing
  • Key Technologies R&D Program of Henan Province (Award 202102110107)
    • Principle Award Recipient: HongMing
  • Innovation Scientists and Technicians Troop Construction Projects of Henan Province (Award CXTD2016043)
    • Principle Award Recipient: Guo-XingNie
  • National Natural Science Foundation of China (Award 31800001)
    • Principle Award Recipient: Bing-bingLiu
  • Key Scientific Research Project of Colleges and Universities in Henan Province (Award 20B530005)
    • Principle Award Recipient: Cai-xiaCui
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2021-06-25
2021-08-02
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References

  1. Collins MD, Brown J, Jones D. Brachybacterium faecium gen. nov., sp. nov., a coryneform bacterium from poultry deep litter. Int J Syst Bacteriol 1988; 38:45–48 [View Article]
    [Google Scholar]
  2. Takeuchi M, Fang C-X, Yokota A. Taxonomic study of the genus Brachybacterium: proposal of Brachybacterium conglomeratum sp. nov., nom. rev., Brachybacterium paraconglomeratum sp. nov., and Brachybacterium rhamnosum sp. nov. Int J Syst Bacteriol 1995; 45:160–168 [View Article]
    [Google Scholar]
  3. Schubert K, Ludwig W, Springer N, Kroppenstedt RM, Accolas JP. Two coryneform bacteria isolated from the surface of French Gruyère and Beaufort cheeses are new species of the genus Brachybacterium: Brachybacterium alimentarium sp. nov. and Brachybacterium tyrofermentans sp. nov. Int J Syst Bacteriol 1996; 46:81–87 [View Article] [PubMed]
    [Google Scholar]
  4. Buczolits S, Schumann P, Weidler G, Radax C, Busse H-J. Brachybacterium muris sp. nov., isolated from the liver of a laboratory mouse strain. Int J Syst Evol Microbiol 2003; 53:1955–1960 [View Article] [PubMed]
    [Google Scholar]
  5. Chou J-H, Lin K-Y, Lin M-C, Sheu S-Y, Wei Y-H et al. Brachybacterium phenoliresistens sp. nov., isolated from oil-contaminated coastal sand. Int J Syst Evol Microbiol 2007; 57:2674–2679 [View Article] [PubMed]
    [Google Scholar]
  6. Park S-K, Kim M-S, Jung M-J, Nam Y-D, Park E-J et al. Brachybacterium squillarum sp. nov., isolated from salt-fermented seafood. Int J Syst Evol Microbiol 2011; 61:1118–1122 [View Article] [PubMed]
    [Google Scholar]
  7. Gontia I, Kavita K, Schmid M. Brachybacterium saurashtrense sp. nov., a halotolerant root-associated bacterium with plant growth-promoting potential. Int J Syst Evol Microbiol 2011; 61:2799–2804 [View Article] [PubMed]
    [Google Scholar]
  8. Liu Y, Xie Q-Y, Shi W, Li L, An J-Y. Brachybacterium huguangmaarense sp. nov., isolated from lake sediment. Int J Syst Evol Microbiol 2014; 64:1673–1678
    [Google Scholar]
  9. Liu Y, Zhai L, Yao S, Cao Y, Cao Y et al. Brachybacterium hainanense sp. nov., isolated from noni (Morinda citrifolia L.) branch. Int J Syst Evol Microbiol 2015; 65:4196–4201 [View Article] [PubMed]
    [Google Scholar]
  10. Kaur G, Kumar N, Mual P, Kumar A, Kumar RM et al. Brachybacterium aquaticum sp. nov., a novel actinobacterium isolated from seawater. Int J Syst Evol Microbiol 2016; 66:4705–4710 [View Article] [PubMed]
    [Google Scholar]
  11. Singh H, Du J, Yang J-E, Yin CS, Kook MC et al. Brachybacterium horti sp. nov., isolated from garden soil. Int J Syst Evol Microbiol 2016; 66:189–195 [View Article] [PubMed]
    [Google Scholar]
  12. Tuo L, Yan X-R, Li F-N, Bao Y-X, Shi H-C et al. Brachybacterium endophyticum sp. nov., a novel endophytic actinobacterium isolated from bark of Scutellaria baicalensis Georgi. Int J Syst Evol Microbiol 2018; 68:3563–3568 [View Article]
    [Google Scholar]
  13. Kiran GS, Sabarathnam B, Thajuddin N, Selvin J. Production of glycolipid biosurfactant from sponge-associated marine actinobacterium Brachybacterium paraconglomeratum MSA21. J Surfact Deterg 2014; 17:531–542 [View Article]
    [Google Scholar]
  14. Liu T, Wu S, Zhang R, Wang D, Zhao J et al. Diversity and antimicrobial potential of Actinobacteria isolated from diverse marine sponges along the Beibu Gulf of the South China Sea. FEMS Microbiol Ecol 2019; 95: [View Article] [PubMed]
    [Google Scholar]
  15. Shirling EB, Gottlieb D. Methods for characterization of Streptomyces species. Int J Syst Bacteriol 1966; 16:313–340 [View Article]
    [Google Scholar]
  16. Li W-J, Xu P, Schumann P, Zhang Y-Q, Pukall R. 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 2007; 57:1424–1428 [View Article]
    [Google Scholar]
  17. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: A taxonomically united database of 16S rRNA and whole genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617
    [Google Scholar]
  18. Hall TA. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 1999; 41:95–98
    [Google Scholar]
  19. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
    [Google Scholar]
  20. 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]
  21. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1985; 17:368–376
    [Google Scholar]
  22. 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]
  23. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549 [View Article] [PubMed]
    [Google Scholar]
  24. 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]
  25. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  26. 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 [View Article] [PubMed]
    [Google Scholar]
  27. Parks DH, Imelfort M, Skennerton CT, Hugenholtz P. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 2015; 25:1043–1055 [View Article] [PubMed]
    [Google Scholar]
  28. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955–964 [View Article] [PubMed]
    [Google Scholar]
  29. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article] [PubMed]
    [Google Scholar]
  30. Delcher AL. Glimmer Release Notes Version 3.02 2006
    [Google Scholar]
  31. Meier-Kolthoff JP, Göker M, Spröer C, Klenk HP. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article] [PubMed]
    [Google Scholar]
  32. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  33. Kurtz S, Phillippy A, Delcher AL, Smoot M, Shumway M et al. Versatile and open software for comparing large genomes. Genome Biol 2004; 5:R12–2483 [View Article] [PubMed]
    [Google Scholar]
  34. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article] [PubMed]
    [Google Scholar]
  35. Wu M, Scott AJ. Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2. Bioinform 2012; 28:1033 [View Article]
    [Google Scholar]
  36. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article] [PubMed]
    [Google Scholar]
  37. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540–552 [View Article] [PubMed]
    [Google Scholar]
  38. Price MN, Dehal PS, Arkin AP. FastTree 2 - Approximately Maximum-Likelihood Trees for Targe Alignments. PLOS One 2010; 5:e9490 [View Article] [PubMed]
    [Google Scholar]
  39. 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]
    [Google Scholar]
  40. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  41. Ming H, Yin Y-R, Li S, Nie G-X, Yu T-T et al. Thermus caliditerrae sp. nov., a novel thermophilic species isolated from a geothermal area. Int J Syst Evol Microbiol 2014; 64:650–656 [View Article]
    [Google Scholar]
  42. Cerny G. Studies on the aminopeptidase test for the distinction of Gram-negative from Gram-positive bacteria. Appl Microbiol Biotechnol 1978; 5:113–122 [View Article]
    [Google Scholar]
  43. Leifson E. Atlas of Bacterial Flagellation New York: Academic Press; 1960 p 242
    [Google Scholar]
  44. Waksman SA. The Actinomycetes. A summary of current knowledge New York: Ronald Press; 1967
    [Google Scholar]
  45. Atlas RM. Handbook of Microbiological Media Boca Raton, FL: CRC Press; 1993
    [Google Scholar]
  46. Kelly KL. Inter-Society Color Council–National Bureau of Standards Color Name Charts Illustrated with Centroid Colors Washington, DC: US Government Printing Office; 1964
    [Google Scholar]
  47. Nie G-X, Ming H, Li S, Zhou E-M, Cheng J. Amycolatopsis dongchuanensis sp. nov. an actinobacterium isolated from soil. Int J Syst Evol Microbiol 2012; 62:2650–2656 [View Article] [PubMed]
    [Google Scholar]
  48. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. An amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
    [Google Scholar]
  49. Gordon RE, Barnett DA, Handerhan JE. Nocardia coeliaca, Nocardia autotrophica, and the Nocardin strain. Int J Syst Bacteriol 1974; 24:54–63 [View Article]
    [Google Scholar]
  50. Williams ST, Goodfellow M, Alderson G. Genus Streptomyces Waksman and Henrici 1943, 339AL. Williams S, Sharpe M, Holt J. eds In Bergey’s Manual of Systematic Bacteriology Vol 4 Baltimore: Williams & Wilkins, Baltimore; 1989 pp 2452–2492
    [Google Scholar]
  51. Groth I, Rodríguez C, Schütze B, Schmitz P, Leistner E et al. Five novel Kitasatospora species from soil: Kitasatospora arboriphila sp. nov., K. gansuensis sp. nov., K. nipponensis sp. nov., K. paranensis sp. nov. and K. terrestris sp. nov. Int J Syst Evol Microbiol 2004; 54:2121–2129 [View Article] [PubMed]
    [Google Scholar]
  52. 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]
  53. Minnikin D, O’Donnell A, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Appl Bacteriol 1984; 2:233–241
    [Google Scholar]
  54. 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 [View Article]
    [Google Scholar]
  55. Tamaoka J, Katayama-Fujimura Y, Kuraishi H. Analysis of bacterial menaquinone mixtures by high performance liquid chromatography. J Appl Bacteriol 1983; 54:31–36 [View Article]
    [Google Scholar]
  56. Staneck JL, Roberts GD. Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 1974; 28:226–231 [View Article] [PubMed]
    [Google Scholar]
  57. 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; 59:2025–2031 [View Article]
    [Google Scholar]
  58. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark: Microbial ID, Inc; 1990
    [Google Scholar]
  59. Minnikin DE, Collins 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]
  60. 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 [View Article]
    [Google Scholar]
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