1887

Abstract

Two isolates derived independently from raw refrigerated processing meat of bovine origin intended for the manufacture of Bologna-type cooked sausage could be distinguished from other known species in subsequent phylogenetic analyses. Comparison of the complete B gene sequences in combination with nearly complete 16S rRNA gene sequences revealed a separate branch within the group. In further analyses, comprising phenotypic and chemotaxonomic characterization as well as average nucleotide identity (ANI) values obtained from the draft genome assemblies, the two isolates could be distinguished from all so far published closely related species. The closest relative was DSM 3456 with ANI values of about 90.2 %. Other close neighbours were DSM 17535 (86.5 %), DSM 26521 (86.4 %), DSM 101070 (83.8 %), DSM 21104 (83.2 %), DSM 29166 (82.3 %), DSM 29165 (82.7 %) and DSM 6252 (81.9 %). The G+C contents of isolates TH39 and TH26 were both 58.2 mol%. The major cellular lipids of strain TH39 were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol; the major quinone was Q9 with small amounts of Q8. Based on these data, the isolates TH39 and TH26 (=DSM 107389=LMG 30831) represent a novel species within the genus for which the name sp. nov. is proposed. The type strain is TH39 (=DSM 107390=LMG 30830)

Keyword(s): Pseudomonas , meat microbiota and beef
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2019-10-17
2019-11-18
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References

  1. Euzéby JP. List of bacterial names with standing in nomenclature: a folder available on the Internet. Int J Syst Evol Microbiol 1997;47: 590– 592 [CrossRef]
    [Google Scholar]
  2. Parte AC. LPSN-List of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014;42: D613– D616 [CrossRef]
    [Google Scholar]
  3. Jackson TC, Acuff GR, Dickson JS. Meat, Poultry and Seafood In Doyle MP, Beuchat LR, Montville TJ. (editors) Food Microbiology - Fundamentals and Frontiers Washington D.C: ASM Press; 1997; pp 83– 100
    [Google Scholar]
  4. Molin G, Ternström A. Phenotypically based taxonomy of psychrotrophic Pseudomonas isolated from spoiled meat, water, and soil. Int J Syst Bacteriol 1986;36: 257– 274 [CrossRef]
    [Google Scholar]
  5. Nychas GJE, Marshall DL, Meat SJN. Poultry and Seafood - Microbial Spoilage and Public Health Concerns In Boyle MP, Beuchat LR. (editors) Food Microbiology - Fundamentals and Frontiers Washington, D.C: ASM Press; 2007; pp 105– 140
    [Google Scholar]
  6. Shaw BG, Latty JB. A study of the relative incidence of different Pseudomonas groups on meat using a computer-assisted identification technique employing only carbon source tests. J Appl Bacteriol 1984;57: 59– 67 [CrossRef]
    [Google Scholar]
  7. Molin G, Ternström A, Ursing J. Notes: Pseudomonas lundensis, a new bacterial species isolated from meat. Int J Syst Bacteriol 1986;36: 339– 342 [CrossRef]
    [Google Scholar]
  8. Versalovic J, Koeuth T, Lupski JR. Distribution of repetitive DNA sequences in eubacteria and application to fingerprinting of bacterial genomes. Nucleic Acids Res 1991;19: 6823– 6831 [CrossRef]
    [Google Scholar]
  9. Hilario E, Buckley TR, Young JM. Improved resolution on the phylogenetic relationships among Pseudomonas by the combined analysis of atpD, carA, recA and 16S rDNA. Antonie Van Leeuwenhoek 2004;86: 51– 64 [CrossRef]
    [Google Scholar]
  10. Mulet M, Lalucat J, García-Valdés E. DNA sequence-based analysis of the Pseudomonas species. Environ Microbiol 2010;12: 1513– 1530 [CrossRef]
    [Google Scholar]
  11. Yamamoto S, Harayama S. Phylogenetic relationships of Pseudomonas putida strains deduced from the nucleotide sequences of gyrB, rpoD and 16S rRNA genes. Int J Syst Bacteriol 1998;48: 813– 819 [CrossRef]
    [Google Scholar]
  12. Adékambi T, Shinnick TM, Raoult D, Drancourt M. Complete rpoB gene sequencing as a suitable supplement to DNA-DNA hybridization for bacterial species and genus delineation. Int J Syst Evol Microbiol 2008;58: 1807– 1814 [CrossRef]
    [Google Scholar]
  13. Konstantinidis KT, Tiedje JM. Towards a genome-based taxonomy for prokaryotes. J Bacteriol 2005;187: 6258– 6264 [CrossRef]
    [Google Scholar]
  14. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005;102: 2567– 2572 [CrossRef]
    [Google Scholar]
  15. Dahllöf I, Baillie H, Kjelleberg S. rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 2000;66: 3376– 3380 [CrossRef]
    [Google Scholar]
  16. Sharma V, Patil PB. Resolving the phylogenetic and taxonomic relationship of Xanthomonas and Stenotrophomonas strains using complete rpoB gene sequence. PLoS Curr 2011;3: RRN1239 [CrossRef]
    [Google Scholar]
  17. Ait Tayeb L, Ageron E, Grimont F, Grimont PAD. Molecular phylogeny of the genus Pseudomonas based on rpoB sequences and application for the identification of isolates. Res Microbiol 2005;156: 763– 773 [CrossRef]
    [Google Scholar]
  18. Lane DJ. 16S/23S rRNA Sequencing In Goodfellow S. editor Nucleic Acid Techniques in Bacterial Systematics Chichester: John Wiley and Sons; 1991; pp 115– 148
    [Google Scholar]
  19. Olofsson TC, Ahrné S, Molin G. Composition of the bacterial population of refrigerated beef, identified with direct 16S rRNA gene analysis and pure culture technique. Int J Food Microbiol 2007;118: 233– 240 [CrossRef]
    [Google Scholar]
  20. Hall TA. BioEdit, A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT; version 7.2.5. (2013). Nucl Acids Symp 1999; 95– 98
    [Google Scholar]
  21. Tamura K, Peterson D, Peterson N, Stecher G, Nei M et al. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 2011;28: 2731– 2739 [CrossRef]
    [Google Scholar]
  22. Yumoto I, Kusano T, Shingyo T, Nodasaka Y, Matsuyama H et al. Assignment of Pseudomonas sp. strain E-3 to Pseudomonas psychrophila sp. nov., a new facultatively psychrophilic bacterium. Extremophiles 2001;5: 343– 349 [CrossRef]
    [Google Scholar]
  23. Eichholz W. Erdbeerbacillus (Bacterium fragi). Zentralbl Bakteriol Parasitenkd Infektionskr Hyg 1902; 425– 428
    [Google Scholar]
  24. von Neubeck M, Huptas C, Glück C, Krewinkel M, Stoeckel M et al. Pseudomonas helleri sp. nov. and Pseudomonas weihenstephanensis sp. nov., isolated from raw cow's milk. Int J Syst Evol Microbiol 2016;66: 1163– 1173 [CrossRef]
    [Google Scholar]
  25. Ramírez-Bahena M-H, Cuesta MJ, Igual JM, Tejedor C, Fernández-Pascual M et al. Pseudomonas endophytica sp. nov., isolated from stem tissue of Solanum tuberosum L. in Spain. Int J Syst Evol Microbiol 2015;65: 2110– 2117 [CrossRef]
    [Google Scholar]
  26. See-Too WS, Salazar S, Ee R, Convey P, Chan KG et al. Pseudomonas versuta sp. nov., isolated from Antarctic soil. Syst Appl Microbiol 2017;40: 191– 198 [CrossRef]
    [Google Scholar]
  27. Carrión O, Miñana-Galbis D, Montes MJ, Mercadé E, Jesús Montes M. Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic. Int J Syst Evol Microbiol 2011;61: 2401– 2405 [CrossRef]
    [Google Scholar]
  28. Haynes WC, Burkholder WH. Pseudomonas In: Breed, Murray, Smith (editors). Bergey`s Manual of Determinative Bacteriology. Baltimore: The Williams and Wilkins C 1957; 89– 152
    [Google Scholar]
  29. JGI –Joint genome Institute JGI bacterial DNA isolation CTAB-2012. https://jgi.doe.gov/user-program-info/pmo-overview/protocols-sample-preparation-information
  30. Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 2013;20: 714– 737 [CrossRef]
    [Google Scholar]
  31. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014;30: 2068– 2069 [CrossRef]
    [Google Scholar]
  32. Blom J, Kreis J, Spänig S, Juhre T, Bertelli C et al. EDGAR 2.0: an enhanced software platform for comparative gene content analyses. Nucleic Acids Res 2016;44: W22– W28 [CrossRef]
    [Google Scholar]
  33. Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter FJ et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009;10: 14 [CrossRef]
    [Google Scholar]
  34. 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 [CrossRef]
    [Google Scholar]
  35. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106: 19126– 19131 [CrossRef]
    [Google Scholar]
  36. Price MN, Dehal PS, Arkin AP. FastTree 2-Approximately maximum-likelihood trees for large alignments. PLoS One 2010;5: e9490 [CrossRef]
    [Google Scholar]
  37. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013;14: 60 [CrossRef]
    [Google Scholar]
  38. King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954;44: 301– 307
    [Google Scholar]
  39. Powers EM. Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 1995;61: 3756– 3758
    [Google Scholar]
  40. Ryu E. A simple method of differentiation between gram-positive and gram-negative organisms without staining. Kitasato Arch Exp Med 1940;17: 58– 63
    [Google Scholar]
  41. Xu P, Li WJ, Tang SK, Zhang YQ, Chen GZ 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 [CrossRef]
    [Google Scholar]
  42. Miller LT. Single derivatization method for routine analysis of bacterial whole-cell fatty acid methyl esters, including hydroxy acids. J Clin Microbiol 1982;16: 584– 586
    [Google Scholar]
  43. Kuykendall LD, Roy MA, O'Neill JJ, Devine TE. Fatty acids, antibiotic resistance, and deoxyribonucleic acid homology groups of Bradyrhizobium japonicum. Int J Syst Bacteriol 1988;38: 358– 361 [CrossRef]
    [Google Scholar]
  44. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959;37: 911– 917 [CrossRef]
    [Google Scholar]
  45. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990;13: 128– 130 [CrossRef]
    [Google Scholar]
  46. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990;66: 199– 202 [CrossRef]
    [Google Scholar]
  47. Tindall BJ, Sikorski J, Smibert RM, Krieg NR. Phenotypic characterization and the principles of comparative systematics In Reddy C, Beverage T, Breznak JA, Marzluf G, Schmidt TM. (editors) Methods for General and Molecular Microbiology Washington. DC: American Society for Microbiology; 2007; pp 330– 393
    [Google Scholar]
  48. Moore EB, Tindall B, Martins Dos Santos VP, Pieper D, Ramos JL. Nonmedical: Pseudomonas In Dworkin M SF, Rosenberg E, Schleifer K-H, Stackebrandt E. (editors) The Prokaryotes New York: Springer; 2006; p 57
    [Google Scholar]
  49. Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999;16: 1114– 1116 [CrossRef]
    [Google Scholar]
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