1887

Abstract

A polyphasic approach was applied to investigate the diversity of microbiota that evolved during cold storage beef ripening. Isolate V4/DAB/S4/2a with a unique BOX-rep-PCR fingerprint profile revealed more than 99 % nucleotide identities upon pairwise comparisons of 16S rDNA sequences from the type strains DSM 101070, DSM 108989, DSM 26521 and DSM 29166, placing it within the / branch of the genus . Additional based comparison revealed DSM 101070 as the nearest relative, with 98.5 % nucleotide identity. Calculation of ANIb values of the V4/DAB/S4/2a draft genome identified DSM 101070 with 90.1 %, DSM 26521 with 85.1 %, DSM 3456 with 84.4 %, DSM 17535 and DSM 107389 with 84.2 % similarities each. Pairwise genome-to-genome distance calculations [digital DNA–DNA hybridization (dDDH)] resulted in values of 47.1, 35.1, 34.8, 34.2 and 34.1 %, respectively. A second isolate was detected years later in ground beef and showed ANIb values of 99.3 % and dDDH of 96.1 % relatedness to V4/DAB/S4/2a. The DNA G+C content was 58.6 mol% for both isolates. The predominant cellular fatty acids of V4/DAB/S4/2a were C, Cω7, C cyclo and a summed feature containing Cω7 and/or C iso 2-OH. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol, the major respiratory quinone was Q9, with a small portion of Q8. The combined data on genotypic and phenotypic features support the proposal of a novel species, for which the name sp. nov. is proposed. The type strain is V4/DAB/S4/2a (=DSM 111361=LMG 31844) and a second isolate is UBT376 (=DSM 111360=LMG 31845).

Keyword(s): beef , dry ageing , meat , meat ripening and Pseudomonas
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2021-06-07
2024-10-03
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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 Bacteriol 1997; 47:590–592 [View Article][PubMed]
    [Google Scholar]
  2. Parte AC. LPSN - List of Prokaryotic names with Standing in Nomenclature (bacterio.net), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article][PubMed]
    [Google Scholar]
  3. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article][PubMed]
    [Google Scholar]
  4. Marchand S, Heylen K, Messens W, Coudijzer K, De Vos P et al. Seasonal influence on heat-resistant proteolytic capacity of Pseudomonas lundensis and Pseudomonas fragi, predominant milk spoilers isolated from Belgian raw milk samples. Environ Microbiol 2009; 11:467–482 [View Article][PubMed]
    [Google Scholar]
  5. Marchand S, Vandriesche G, Coorevits A, Coudijzer K, De Jonghe V et al. Heterogeneity of heat-resistant proteases from milk Pseudomonas species. Int J Food Microbiol 2009; 133:68–77 [View Article][PubMed]
    [Google Scholar]
  6. Vithanage NR, Dissanayake M, Bolge G, Palombo EA, Yeager TR et al. Biodiversity of culturable psychrotrophic microbiota in raw milk attributable to refrigeration conditions, seasonality and their spoilage potential. Int Dairy J 2016; 57:80–90 [View Article]
    [Google Scholar]
  7. von Neubeck M, Baur C, Krewinkel M, Stoeckel M, Kranz B et al. Biodiversity of refrigerated raw milk microbiota and their enzymatic spoilage potential. Int J Food Microbiol 2015; 211:57–65 [View Article][PubMed]
    [Google Scholar]
  8. Jackson TC, Acuff GR, Meat DJS. Poultry and seafood. In Doyle MP, Beuchat LR, Montville TJ. (editors) Food Microbiology - Fundamentals and Frontiers Washington, DC: ASM Press; 1997 pp 83–100
    [Google Scholar]
  9. 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
    [Google Scholar]
  10. Nychas GJE, Marshall DL, Meat SJN. Poultry and seafood - microbial spoilage and public health concerns. In Doyle MP, Beuchat LR. (editors) Food Microbiology - Fundamentals and Frontiers Washington, DC: ASM Press; 2007 pp 105–140
    [Google Scholar]
  11. 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 [View Article][PubMed]
    [Google Scholar]
  12. Eichholz W. Erdbeerbacillus (Bacterium fragi) Zentralblatt, Bakteriologie, Parasitenkunde: Infektionskrankheiten, Hygiene; 1902 pp 425–428
    [Google Scholar]
  13. Haynes WC, Burkholder WH. Genus I Pseudomonas . In Breed Murray Smith. editor Bergey's Manual of Determinative Bacteriology Baltimore: The Williams and Wilkins C; 1957 pp 89–152
    [Google Scholar]
  14. Molin G, Ternström A, Ursing J. Notes: Pseudomonas lundensis, a new bacterial species isolated from meat. Int J Syst Bacteriol 1986; 36:339–342 [View Article]
    [Google Scholar]
  15. 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 [View Article][PubMed]
    [Google Scholar]
  16. Saruyama H, Ochiai T, Takada Y, Okuyama H, Sasaki S. Isolation and growth temperature of psychrophiles. Journal of the Faculty of Science 1978; 11:
    [Google Scholar]
  17. Carrión O, Miñana-Galbis D, Montes MJ, Mercadé E. Pseudomonas deceptionensis sp. nov., a psychrotolerant bacterium from the Antarctic. Int J Syst Evol Microbiol 2011; 61:2401-–2405 [View Article][PubMed]
    [Google Scholar]
  18. Ramírez-Bahena M-H, Cuesta MJ, Tejedor C, Igual JM, 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 [View Article][PubMed]
    [Google Scholar]
  19. 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 [View Article][PubMed]
    [Google Scholar]
  20. See-Too WS, Salazar S, Ee R, Convey P, Chan K-G et al. Pseudomonas versuta sp. nov., isolated from Antarctic soil. Syst Appl Microbiol 2017; 40:191–198 [View Article][PubMed]
    [Google Scholar]
  21. Hofmann K, Huptas C, Doll EV, Scherer S, Wenning M. Pseudomonas saxonica sp. nov., isolated from raw milk and skimmed milk concentrate. Int J Syst Evol Microbiol 2020; 70:935–943 [View Article][PubMed]
    [Google Scholar]
  22. Lick S, Kröckel L, Wibberg D, Winkler A, Blom J et al. Pseudomonas bubulae sp. nov., isolated from beef. Int J Syst Evol Microbiol 2020; 70:292–301 [View Article][PubMed]
    [Google Scholar]
  23. Kröckel L. Beef maturation using starter cultures. Mitteilungsblatt der Fleischforschung Kulmbach 2012; 51:87–95
    [Google Scholar]
  24. King EO, Ward MK, Raney DE. Two simple media for the demonstration of pyocyanin and fluorescin. J Lab Clin Med 1954; 44:301–307[PubMed]
    [Google Scholar]
  25. Versalovic J, Schneider M, De Bruijn FJ, Lupski JR. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 1994; 5:25–40
    [Google Scholar]
  26. Lane DJ. 16S/23S rRNA sequencing. In Goodfellow M, Stackebrandt E. (editors) Nucleic Acid Techniques in Bacterial Systematics Chichester: John Wiley and Sons; 1991 pp 115–175
    [Google Scholar]
  27. 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 [View Article][PubMed]
    [Google Scholar]
  28. 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 [View Article][PubMed]
    [Google Scholar]
  29. Tayeb LA, 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 [View Article][PubMed]
    [Google Scholar]
  30. Hall TA. BioEdit, a user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT; version 7.2.5. Nucl Acids Symp 1999; Ser. 41:95–98
    [Google Scholar]
  31. 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]
  32. JGI –Joint genome Institute JGI Bacterial DNA isolation CTAB-2012. https://jgi.doe.gov/user-program-info/pmo-overview/protocols-sample-preparation-information
  33. 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 [View Article][PubMed]
    [Google Scholar]
  34. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [View Article][PubMed]
    [Google Scholar]
  35. Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One 2014; 9:e112963 [View Article][PubMed]
    [Google Scholar]
  36. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  37. 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 [View Article][PubMed]
    [Google Scholar]
  38. Blom J, Albaum SP, Doppmeier D, Pühler A, Vorhölter F-J et al. EDGAR: a software framework for the comparative analysis of prokaryotic genomes. BMC Bioinformatics 2009; 10:154 [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][PubMed]
    [Google Scholar]
  40. Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 201314
    [Google Scholar]
  41. Meier-Kolthoff JP, Göker M, Spröer C, Klenk H-P. When should a DDH experiment be mandatory in microbial taxonomy?. Arch Microbiol 2013; 195:413–418 [View Article][PubMed]
    [Google Scholar]
  42. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article][PubMed]
    [Google Scholar]
  43. 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 [View Article][PubMed]
    [Google Scholar]
  44. 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]
  45. Xu P, Li W-J, Tang S-K, Zhang Y-Q, Chen G-Z 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 [View Article][PubMed]
    [Google Scholar]
  46. See-Too WS, Lim Y-L, Ee R, Convey P, Pearce DA et al. Complete genome of Pseudomonas sp. strain L10.10, a psychrotolerant biofertilizer that could promote plant growth. J Biotechnol 2016; 222:84–85 [View Article][PubMed]
    [Google Scholar]
  47. Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999; 16:1114–1116
    [Google Scholar]
  48. 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]
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