1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 9

sp. nov., isolated from raw cow's milk Free

Abstract

Strain CA7, a Gram-stain-negative, non-motile, non-spore-forming, aerobic and rod-shaped bacterial strain, was isolated from raw cow’s milk collected from a farm affiliated with Chung-Ang University, Anseong, Korea, and characterized by a polyphasic approach. Optimal growth of strain CA7 was observed on tryptic soy agar at 30 °C and pH 7.0 with 0 % NaCl. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that strain CA7 belonged to the genus . The most closely related strains (16S rRNA gene sequence similarity indicated in parentheses), based on the phylogenetic analysis, were KCTC 22548 (98.08 %), CCUG 60563 (98.61 %), KACC 12501 (97.85 %) and KCTC 62135 (97.78 %). Whole genome sequencing indicated that the genome size was 5 125 723 bp and had a DNA G+C content of 37.4 mol%. Average nucleotide identity values for strain CA7 with , , , , and the type species of the genus were 80.2, 79.8, 79.8, 79.6 and 80.4 %, respectively. The digital DNA–DNA hybridization values of CA7 compared to , , , and were 24.1, 23.9, 23.9, 23.7 and 24.3 %, respectively. The major fatty acids were iso-C, summed feature 9 (iso-C 9 and/or C 10-methyl), iso-C 3-OH and summed feature 3 (iso-C 2-OH and/or C 7). Menaquinone-6 was the only respiratory quinone. The major polar lipid was phosphatidylethanolamine. Based on this polyphasic taxonomic study, strain CA7 represents a novel species of the genus for which the name sp. nov. is proposed. The type strain is CA7 (=KACC 21402=JCM 33749).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): bovine raw milk , Chryseobacterium strain CA7T and Chryseobacterium vaccae
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004250
2020-06-09
2024-05-06
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/9/4859.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.004250&mimeType=html&fmt=ahah

References

  1. Vandamme P, Bernardet J-F, Segers P, Kersters K, Holmes B. Notes: new perspectives in the classification of the flavobacteria: description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. Int J Syst Bacteriol 1994; 44:827–831 [View Article]
     [Google Scholar]
  2. Cho S-H, Lee KS, Shin D-S, Han J-H, Park KS et al. Four new species of Chryseobacterium from the rhizosphere of coastal sand dune plants, Chryseobacterium elymi sp. nov., Chryseobacterium hagamense sp. nov., Chryseobacterium lathyri sp. nov. and Chryseobacterium rhizosphaerae sp. nov. Syst Appl Microbiol 2010; 33:122–127 [View Article][PubMed]
     [Google Scholar]
  3. Holmes B, Steigerwalt AG, Nicholson AC. DNA–DNA hybridization study of strains of Chryseobacterium, Elizabethkingia and Empedobacter and of other usually indole-producing non-fermenters of CDC groups IIc, IIE, IIH and III, mostly from human clinical sources, and proposals of Chryseobacterium bernardetii sp. nov., Chryseobacterium carnis sp. nov., Chryseobacterium lactis sp. nov., Chryseobacterium nakagawai sp. nov. and Chryseobacterium taklimakanense comb. nov; 2013; 634639–4662
  4. Weon H-Y, Kim B-Y, Yoo S-H, Kwon S-W, Stackebrandt E et al. Chryseobacterium soli sp. nov. and Chryseobacterium jejuense sp. nov., isolated from soil samples from Jeju, Korea. Int J Syst Evol Microbiol 2008; 58:470–473 [View Article][PubMed]
     [Google Scholar]
  5. Luo T, Liu Y, Chen C, Luo Q, Rao Q et al. Chryseobacterium aurantiacum sp. nov., isolated from a freshwater pond used for Murray cod (Maccullochella peelii peelii) culture. Int J Syst Evol Microbiol 2018; 68:3397–3403 [View Article][PubMed]
     [Google Scholar]
  6. Lee J-E, Hwang E-M, Cha C-J, Kim G-B. Chryseobacterium aureum sp. nov., isolated from the Han river, Republic of Korea. Int J Syst Evol Microbiol 2019; 69:1628–1633 [View Article][PubMed]
     [Google Scholar]
  7. Kim KK, Lee KC, Oh H-M, Lee J-S. Chryseobacterium aquaticum sp. nov., isolated from a water reservoir. Int J Syst Evol Microbiol 2008; 58:533–537 [View Article][PubMed]
     [Google Scholar]
  8. Hantsis-Zacharov E, Shakéd T, Senderovich Y, Halpern M. Chryseobacterium oranimense sp. nov., a psychrotolerant, proteolytic and lipolytic bacterium isolated from raw cow's milk. Int J Syst Evol Microbiol 2008; 58:2635–2639 [View Article][PubMed]
     [Google Scholar]
  9. Hantsis-Zacharov E, Senderovich Y, Halpern M. Chryseobacterium bovis sp. nov., isolated from raw cow's milk. Int J Syst Evol Microbiol 2008; 58:1024–1028 [View Article][PubMed]
     [Google Scholar]
  10. Kämpfer P, Poppel MT, Wilharm G, Busse H-J, McInroy JA et al. Chryseobacterium gallinarum sp. nov., isolated from a chicken, and Chryseobacterium contaminans sp. nov., isolated as a contaminant from a rhizosphere sample. Int J Syst Evol Microbiol 2014; 64:1419–1427 [View Article][PubMed]
     [Google Scholar]
  11. Jeong J-J, Lee DW, Park B, Sang MK, Choi I-G et al. Chryseobacterium cucumeris sp. nov., an endophyte isolated from cucumber (Cucumis sativus L.) root, and emended description of Chryseobacterium arthrosphaerae . Int J Syst Evol Microbiol 2017; 67:610–616 [View Article][PubMed]
     [Google Scholar]
  12. Oosthuizen L, Charimba G, Hitzeroth A, Nde AL, Steyn L et al. Chryseobacterium pennipullorum sp. nov., isolated from poultry feather waste. Int J Syst Evol Microbiol 2019; 69:2380–2387 [View Article][PubMed]
     [Google Scholar]
  13. Zamora L, Vela AI, Palacios MA, Sánchez-Porro C, Svensson-Stadler LA et al. Chryseobacterium viscerum sp. nov., isolated from diseased fish. Int J Syst Evol Microbiol 2012; 62:2934–2940 [View Article][PubMed]
     [Google Scholar]
  14. Park S-J, Choi J-H, Cha C-J. Chryseobacterium rigui sp. nov., isolated from an estuarine wetland. Int J Syst Evol Microbiol 2013; 63:1062–1067 [View Article][PubMed]
     [Google Scholar]
  15. 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]
  16. Frank JA, Reich CI, Sharma S, Weisbaum JS, Wilson BA et al. Critical evaluation of two primers commonly used for amplification of bacterial 16S rRNA genes. Appl Environ Microbiol 2008; 74:2461–2470 [View Article][PubMed]
     [Google Scholar]
  17. Kim O-S, Cho Y-J, Lee K, Yoon S-H, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  18. 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]
  19. 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]
  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 1981; 17:368–376 [View Article][PubMed]
     [Google Scholar]
  22. Jukes TH, Cantor CR. Evolution of protein molecules. In Munro HN. editor Mammalian Protein Metabolism 3 New York: Academic Press; 1969 pp 21–132
     [Google Scholar]
  23. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article][PubMed]
     [Google Scholar]
  24. Rosselló-Móra R, Amann R. Past and future species definitions for bacteria and archaea. Syst Appl Microbiol 2015; 38:209–216 [View Article][PubMed]
     [Google Scholar]
  25. Stackebrandt E, Ebers J. Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 2006; 33:152–155
     [Google Scholar]
  26. Kim M, Oh H-S, Park S-C, Chun J. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 2014; 64:346–351 [View Article][PubMed]
     [Google Scholar]
  27. Charif D, Lobry JR. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. Structural Approaches to Sequence Evolution: Molecules, Networks, Populations Berlin Heidelberg: Springer; 2007 pp 207–232
     [Google Scholar]
  28. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article][PubMed]
     [Google Scholar]
  29. Lee I, Ouk Kim Y, Park S-C, 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]
  30. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article][PubMed]
     [Google Scholar]
  31. 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]
  32. Stackebrandt E, Goebel BM. Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 1994; 44:846–849 [View Article]
     [Google Scholar]
  33. 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]
  34. Elnar AG, Kim M-G, Lee J-E, Han R-H, Yoon S-H et al. Acinetobacter pullorum sp. nov., Isolated from Chicken Meat. J Microbiol Biotechnol 2020; 30:526–532 [View Article][PubMed]
     [Google Scholar]
  35. Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:1–11 [View Article]
     [Google Scholar]
  36. Steinegger M, Söding J. Clustering huge protein sequence sets in linear time. Nat Commun 2018; 9:1–8 [View Article][PubMed]
     [Google Scholar]
  37. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [View Article][PubMed]
     [Google Scholar]
  38. Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 2015; 32:268–274 [View Article][PubMed]
     [Google Scholar]
  39. Gerhardt P. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994
     [Google Scholar]
  40. Siddiqi MZ, Choi G-M, Kim M-S, Im W-T. Daejeonia ginsenosidivorans gen. nov., sp. nov., a ginsenoside-transforming bacterium isolated from lake water. Int J Syst Evol Microbiol 2017; 67:2665–2671 [View Article][PubMed]
     [Google Scholar]
  41. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
     [Google Scholar]
  42. Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  43. Collins M. Analysis of isoprenoid quinones. Methods Microbiol 1985; 18:329–363
     [Google Scholar]
  44. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990; 13:128–130 [View Article]
     [Google Scholar]
  45. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbial Lett 1990; 60:199–202
     [Google Scholar]
  46. Hudzicki J. Kirby-Bauer disk diffusion susceptibility test protocol. Available at https://www.asm.org/Protocols/Kirby-Bauer-Disk-Diffusion-Susceptibility-Test-Pro/. Accessed Nov. 11, 2019; 2009
  47. CLSI Performance Standards for Antimicrobial Susceptibility Testing. 29th ed. Available from http://em100.edaptivedocs.net/dashboard.aspx. Accessed Dec 12, 2019; 2019
  48. Yabuuchi E, Kaneko T, Yano I, Moss CW, Miyoshi N. 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 1983; 33:580–598 [View Article]
     [Google Scholar]
  49. Montero-Calasanz MdelC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium hispalense sp. nov., a plant-growth-promoting bacterium isolated from a rainwater pond in an olive plant nursery, and emended descriptions of Chryseobacterium defluvii, Chryseobacterium indologenes, Chryseobacterium wanjuense and Chryseobacterium gregarium . Int J Syst Evol Microbiol 2013; 63:4386–4395 [View Article][PubMed]
     [Google Scholar]
  50. Montero-Calasanz MdelC, Göker M, Rohde M, Spröer C, Schumann P et al. Chryseobacterium oleae sp. nov., an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum and C. vrystaatense . Syst Appl Microbiol 2014; 37:342–350 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004250
Loading
Chryseobacterium vaccae sp. nov., isolated from raw cow's milk
Int J Syst Evol Microbiol 70, 4859 (2020); https://doi.org/10.1099/ijsem.0.004250
/content/journal/ijsem/10.1099/ijsem.0.004250
/content/journal/ijsem/10.1099/ijsem.0.004250
Loading

Data & Media loading...

Supplements

Supplementary material 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