1887

Abstract

During a project focusing on the diversity of meat microbiota associated with beef ripening, a strain was isolated exhibiting high 16S rRNA gene sequence similarities (>99 %) to DSM 107652, DSM 29167, DSM 29164 and DSM 18862. Phylogenetic analysis of the complete gene sequences of the isolate V5/DAB/2/5 indicated a separate branch with about 99.0 % nucleotide identities to the closest relatives DSM 107652, DSM 29167 and DSM 29164, while average nucleotide identities (ANIb) calculated from the draft genomes were 94.8, 94.2 and 90.2 %, respectively. Pairwise genome-to-genome distance calculations (GGDC) resulted in values of 67.7, 63.5 and 45.7 %, respectively, lying below the actual species demarcation line as well. A second isolate, UBT403, was detected some years later by using matrix-assisted laser desorption ionization-time of flight MS of the microbiota of minced beef. The fatty acid profile of V5/DAB/2/5 consisted of C, summed feature C 7/iso-C 2-OH, C c, C cyclo, C, C 3-OH, C 3-OH and C 2-OH. The major cellular lipids were aminopholipids, phospholipids, phosphatidylethanolamine and phosphatidylglycerol; the major quinone was Q9 with a minor proportion of Q8. Based on phenotypic and chemotaxonomic characterizations, the isolates can be considered as representing a novel species, for which the name sp. nov. is proposed. The type strain is V5/DAB/2/5 (=DSM 111363=LMG 31846); a second strain is UBT403 (=DSM 111362=LMG 31847).

Keyword(s): beef , dry ageing , meat , meat ripening and Pseudomonas
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004652
2021-01-22
2021-10-19
Loading full text...

Full text loading...

References

  1. Tran PN, Savka MA, Gan HM. In-silico taxonomic classification of 373 genomes reveals species misidentification and new genospecies within the genus Pseudomonas. Front Microbiol 2017; 8:1296 [View Article][PubMed]
    [Google Scholar]
  2. 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]
  3. 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]
  4. Parte AC. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article][PubMed]
    [Google Scholar]
  5. Madigan MT, Martinko JM, Parker J. Procaryotic Diversity: Bacteria. Brock Biology of Microorganisms Upper Saddle River, New Jersey: Prentice Hall International, Inc; 1997
    [Google Scholar]
  6. Pieterse CMJ, Zamioudis C, Berendsen RL, Weller DM, Van Wees SCM et al.. Induced Systemic resistance by beneficial microbes. In Van Alfen NK. editor Annu Rev Phytopathol 52 2014 pp 347–375 [View Article]
    [Google Scholar]
  7. Hol WHG, Bezemer TM, Biere A. Getting the ecology into interactions between plants and the plant growth-promoting bacterium Pseudomonas fluorescens. Front Plant Sci 2013; 4:81 [View Article][PubMed]
    [Google Scholar]
  8. Andreani NA, Martino ME, Fasolato L, Carraro L, Montemurro F et al. Reprint of 'Tracking the blue: a MLST approach to characterise the Pseudomonas fluorescens group'. Food Microbiol 2015; 45:148–158 [View Article][PubMed]
    [Google Scholar]
  9. von Neubeck M, Huptas C, Glück C, Krewinkel M, Stoeckel M et al.. Pseudomonas lactis sp. nov. and Pseudomonas paralactis sp. nov., isolated from bovine raw milk. Int J Syst Evol Microbiol 2017; 67:1656–1664 [View Article][PubMed]
    [Google Scholar]
  10. Nychas GJE, Marshall DL, Sofos JN. Meat, 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. Kröckel L. Beef maturation using starter cultures. Mitteilungsblatt der Fleischforschung Kulmbach 2012; 51:87–95
    [Google Scholar]
  12. 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]
  13. 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]
  14. 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]
  15. 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]
  16. Lick S, Kröckel L, Wibberg D, Winkler A, Blom J et al.. Pseudomonas carnis sp. nov., isolated from meat. Int J Syst Evol Microbiol 2020; 70:1528–1540 [View Article][PubMed]
    [Google Scholar]
  17. 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 199995–98
    [Google Scholar]
  18. 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]
  19. Iizuka H, Komagata K. An attempt at grouping of the genus Pseudomonas. J Gen Appl Microbiol 1963; 9:73–82 [View Article]
    [Google Scholar]
  20. Tambong JT, Xu R, Bromfield ESP. Pseudomonas canadensis sp. nov., a biological control agent isolated from a field plot under long-term mineral fertilization. Int J Syst Evol Microbiol 2017; 67:889–895 [View Article][PubMed]
    [Google Scholar]
  21. Vela AI, Gutiérrez MC, Falsen E, Rollán E, Simarro I et al.. Pseudomonas simiae sp. nov., isolated from clinical specimens from monkeys (Callithrix geoffroyi). Int J Syst Evol Microbiol 2006; 56:2671–2676 [View Article][PubMed]
    [Google Scholar]
  22. Verhille S, Baïda N, Dabboussi F, Hamze M, Izard D et al. Pseudomonas gessardii sp. nov. and Pseudomonas migulae sp. nov., two new species isolated from natural mineral waters. Int J Syst Bacteriol 1999; 49:1559–1572 [View Article][PubMed]
    [Google Scholar]
  23. Paine S. Studies on bacteriosis II, a brown blotch disease of cultivated mushrooms. Ann Appl Biol 1919; 5:206–219
    [Google Scholar]
  24. Behrendt U, Ulrich A, Schumann P, Meyer J-M, Spröer C. Pseudomonas lurida sp. nov., a fluorescent species associated with the phyllosphere of grasses. Int J Syst Evol Microbiol 2007; 57:979–985 [View Article][PubMed]
    [Google Scholar]
  25. Ivanova EP, Gorshkova NM, Sawabe T, Hayashi K, Kalinovskaya NI et al. Pseudomonas extremorientalis sp. nov., isolated from a drinking water reservoir. Int J Syst Evol Microbiol 2002; 52:2113–2120 [View Article][PubMed]
    [Google Scholar]
  26. Hofmann K, Huptas C, Doll EV, Scherer S, Wenning M. Pseudomonas haemolytica sp. nov., isolated from raw milk and skimmed milk concentrate. Int J Syst Evol Microbiol 2020; 70:2339–2347 [View Article][PubMed]
    [Google Scholar]
  27. Ehrenberg CG. Charakteristik von 274 neuen Berlin: Arten von Infusorien; 1840
    [Google Scholar]
  28. Dabboussi F, Hamze M, Elomari M, Verhille S, Baida N, Baїda N et al.. Taxonomic study of bacteria isolated from Lebanese spring waters: proposal for Pseudomonas cedrella sp. nov. and P. orientalis sp. nov. Res Microbiol 1999; 150:303–316 [View Article][PubMed]
    [Google Scholar]
  29. Dabboussi F, Hamze M, Elomari M, Verhille S, Baida N et al. Pseudomonas libanensis sp. nov., a new species isolated from Lebanese spring waters. Int J Syst Bacteriol 1999; 49 Pt 3:1091–1101 [View Article][PubMed]
    [Google Scholar]
  30. JGI –Joint genome Institute https://jgi.doe.gov/user-program-info/pmo-overview/protocols-sample-preparation-information, JGI Bacterial DNA isolation CTAB-2012.
  31. 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]
  32. 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]
  33. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  34. 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]
  35. Li HW. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: Genomics 20131303.3997v2
    [Google Scholar]
  36. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [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. 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; 14:14 [View Article]
    [Google Scholar]
  40. 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]
  41. 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]
  42. 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]
  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. Atlas RM. Handbook of Microbiological Media, 2 ed. Boca Raton, Fl: CRC Press Inc; 1997
    [Google Scholar]
  45. Reddy GSN, Matsumoto GI, Schumann P, Stackebrandt E, Shivaji S. Psychrophilic pseudomonads from Antarctica: Pseudomonas antarctica sp. nov., Pseudomonas meridiana sp. nov. and Pseudomonas proteolytica sp. nov. Int J Syst Evol Microbiol 2004; 54:713–719 [View Article][PubMed]
    [Google Scholar]
  46. Stead DE. Grouping of plant-pathogenic and some other Pseudomonas spp. by using cellular fatty acid profiles. Int J Syst Bacteriol 1992; 42:281–295 [View Article]
    [Google Scholar]
  47. Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol 1999; 16:1114–1116 [View Article]
    [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]
  49. Hugh R, Guarraia L, Hatt H. The proposed neotype strains of Pseudomonas fluorescens (Trevisan) Migula 1895. Int Bull Bact Nomencl Tax 1964; 14:145–156 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004652
Loading
/content/journal/ijsem/10.1099/ijsem.0.004652
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month 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