1887

Abstract

By investigating wet and dry age-related ripening of beef, strains V3/3/4/13 and V3/K/3/5 were isolated. Strain V3/3/4/13 exhibited more than 99 % 16S rRNA gene-based similarity to and other members of this group, while isolate V3/K/3/5 was very close to and a number of relatives within the group. Additional comparisons of complete sequences and draft genomes allowed us to place isolate V3/3/4/13 close to DSM 26521. In the case of V3/K/3/5 the closest relative was DSM 11331. Average nucleotide identity (ANIb) and digital DNA–DNA hybridization (dDDH) values calculated from the draft genomes of V3/3/4/13 and DSM 26521 were 88.5 and 39.8 %, respectively. For V3/K/3/5 and its closest relative DSM 11331, the ANIb value was 95.1 % and the dDDH value was 60.7 %. The DNA G+C contents of V3/3/4/13 and V3/K/3/5 were 57.4 and 60.8 mol%, respectively. Predominant fatty acids were C, C ω7, C cyclo and summed feature C ω7/C iso 2OH. The main respiratory quinones were Q9, with minor proportions of Q8 and, in the case of V3/K/3/5, additional Q10. The main polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and, in the case of V3/K/3/5, additional phosphatidylcholine. Based on the combined data, isolates V3/3/4/13 and V3/K/3/5 should be considered as representatives of two novel species. The type strain of the newly proposed sp. nov. is V3/3/4/13 (=DSM 113654=LMG 32520), a second strain belonging to the same species is FLM 004-28 (=DSM 113604=LMG 32521); the type strain for the newly proposed sp. nov. is V3/K/3/5 (=DSM 113573=LMG 32518) with a second isolate FLM 11 (=DSM 113572=LMG 32519).

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2024-04-08
2024-05-04
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References

  1. 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]
  2. Palleroni NJ. Genus Pseudomonas. In Brenner DJ, Krieg NR, Staley JT. eds Bergey's Manual of Systematic Microbiology New York: Springer; 2005 pp 323–379
    [Google Scholar]
  3. Scales BS, Dickson RP, LiPuma JJ, Huffnagle GB. Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans. Clin Microbiol Rev 2014; 27:927–948 [View Article] [PubMed]
    [Google Scholar]
  4. Silby MW, Cerdeño-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW et al. Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 2009; 10:R51 [View Article] [PubMed]
    [Google Scholar]
  5. Jackson TC, Acuff GR, Dickson JS. Meat, poultry and seafood. In Doyle MP, Beuchat LR, Montville TJ. eds Food Microbiology - Fundamentals and Frontiers Washington D.C: ASM Press; 1997 pp 83–100
    [Google Scholar]
  6. Nychas GJE, Marshall DL, Sofos JN. Meat, poultry and seafood - microbial spoilage and public health concerns. In Doyle MP, Beuchat LR. eds Food Microbiology - Fundamentals and Frontiers Washington, D.C: ASM Press; 2007 pp 105–140 [View Article]
    [Google Scholar]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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]
    [Google Scholar]
  12. Lick S, Wibberg D, Winkler A, Blom J, Grimmler C et al. Pseudomonas paraversuta sp. nov. isolated from refrigerated dry-aged beef. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  13. Eichholz W. Erdbeerbacillus (Bacterium fragi). Zentralblatt, Bakteriologie, Parasitenkunde, Infektionskrankheiten, Hygiene 1902425–428
    [Google Scholar]
  14. Winslow B, Buchanan K. Pseudomonadaceae. In Robert S, Smith N. eds Bergey´s Manual of Determinative Microbiology Baltimore: The Williams and Wilkins Company; 1957 pp 88–217
    [Google Scholar]
  15. 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]
  16. 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]
  17. 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]
  18. Elomari M, Coroler L, Hoste B, Gillis M, Izard D et al. DNA relatedness among Pseudomonas strains isolated from natural mineral waters and proposal of Pseudomonas veronii sp. nov. Int J Syst Bacteriol 1996; 46:1138–1144 [View Article] [PubMed]
    [Google Scholar]
  19. Pavlov MS, Lira F, Martinez JL, Olivares-Pacheco J, Marshall SH. Pseudomonas fildesensis sp. nov., a psychrotolerant bacterium isolated from Antarctic soil of King George Island, South Shetland Islands. Int J Syst Evol Microbiol 2020; 70:3255–3263 [View Article] [PubMed]
    [Google Scholar]
  20. López NI, Pettinari MJ, Stackebrandt E, Tribelli PM, Põtter M et al. Pseudomonas extremaustralis sp. nov., a poly(3-hydroxybutyrate) producer isolated from an antarctic environment. Curr Microbiol 2009; 59:514–519 [View Article] [PubMed]
    [Google Scholar]
  21. Tchagang CF, Xu R, Overy D, Blackwell B, Chabot D et al. Diversity of bacteria associated with corn roots inoculated with Canadian woodland soils, and description of Pseudomonas aylmerense sp. nov. Heliyon 2018; 4:e00761 [View Article] [PubMed]
    [Google Scholar]
  22. Behrendt U, Ulrich A, Schumann P. Fluorescent pseudomonads associated with the phyllosphere of grasses; Pseudomonas trivialis sp. nov., Pseudomonas poae sp. nov. and Pseudomonas congelans sp. nov. Int J Syst Evol Microbiol 2003; 53:1461–1469 [View Article] [PubMed]
    [Google Scholar]
  23. Behrendt U, Ulrich A, Schumann P, Meyer JM, 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]
  24. Gardan L, Bella P, Meyer J-M, Christen R, Rott P et al. Pseudomonas salomonii sp. nov., pathogenic on garlic, and Pseudomonas palleroniana sp. nov., isolated from rice. Int J Syst Evol Microbiol 2002; 52:2065–2074 [View Article] [PubMed]
    [Google Scholar]
  25. Park Y-D, Lee HB, Yi H, Kim Y, Bae KS et al. Pseudomonas panacis sp. nov., isolated from the surface of rusty roots of Korean ginseng. Int J Syst Evol Microbiol 2005; 55:1721–1724 [View Article] [PubMed]
    [Google Scholar]
  26. Sawada H, Fujikawa T, Tsuji M, Satou M. Pseudomonas allii sp. nov., a pathogen causing soft rot of onion in Japan. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  27. Sawada H, Fujikawa T, Satou M. Pseudomonas lactucae sp. nov., a pathogen causing bacterial rot of lettuce in Japan. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  28. Sawada H, Fujikawa T, Satou M. Pseudomonas aegrilactucae sp. nov. and Pseudomonas morbosilactucae sp. nov., pathogens causing bacterial rot of lettuce in Japan. Int J Syst Evol Microbiol 2022; 72:11 [View Article] [PubMed]
    [Google Scholar]
  29. Sawada H, Takeuchi K, Someya N, Morohoshi T, Satou M. Pseudomonas solani sp. nov. isolated from the rhizosphere of eggplant in Japan. Int J Syst Evol Microbiol 2023; 73: [View Article] [PubMed]
    [Google Scholar]
  30. Sawada H, Fujikawa T, Osada S, Satou M. Pseudomonas petroselini sp. nov., a pathogen causing bacterial rot of parsley in Japan. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  31. Sawada H, Fujikawa T, Horita H. Pseudomonas brassicae sp. nov., a pathogen causing head rot of broccoli in Japan. Int J Syst Evol Microbiol 2020; 70:5319–5329 [View Article] [PubMed]
    [Google Scholar]
  32. 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]
  33. 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]
  34. 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]
  35. Lick S, Wibberg D, Winkler A, Blom J, Grimmler C et al. Pseudomonas paracarnis sp. nov., isolated from refrigerated beef. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  36. 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]
  37. Gieschler S, Fiedler G, Böhnlein C, Grimmler C, Franz C et al. Pseudomonas kielensis sp. nov. and Pseudomonas baltica sp. nov., isolated from raw milk in Germany. Int J Syst Evol Microbiol 2021; 71: [View Article] [PubMed]
    [Google Scholar]
  38. Versalovic J, Schneider M, De Brujin FJ, Lupski JR. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods Mol Cell Biol 1994; 5:25–40
    [Google Scholar]
  39. Hall TA. Bioedit, a user-friendly biological sequence alignment editor and analysis program for 570 windows 95/98/NT; version 7.2.5. Nucl Acids Symp 199995–98
    [Google Scholar]
  40. 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]
  41. Tamura K, Nei M. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Mol Biol Evol 1993; 10:512–526 [View Article] [PubMed]
    [Google Scholar]
  42. Lane DJ. 16S/23S rRNA sequencing. In Goodfellow M, Stackebrandt E. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: John Wiley and Sons; 1991 pp 115–175
    [Google Scholar]
  43. 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]
  44. López G, Diaz-Cárdenas C, Shapiro N, Woyke T, Kyrpides NC et al. Draft genome sequence of Pseudomonas extremaustralis strain USBA-GBX 515 isolated from Superparamo soil samples in Colombian Andes. Stand Genomic Sci 2017; 12:78 [View Article] [PubMed]
    [Google Scholar]
  45. 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]
  46. Wibberg D, Genzel F, Verwaaijen B, Blom J, Rupp O et al. Draft genome sequence of the potato pathogen Rhizoctonia solani AG3-PT isolate Ben3. Arch Microbiol 2017; 199:1065–1068 [View Article] [PubMed]
    [Google Scholar]
  47. 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]
  48. 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]
  49. Li HW. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv: Genomics 2013
    [Google Scholar]
  50. Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods 2012; 9:357–359 [View Article] [PubMed]
    [Google Scholar]
  51. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article] [PubMed]
    [Google Scholar]
  52. Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T et al. GenDB--an open source genome annotation system for prokaryote genomes. Nucleic Acids Res 2003; 31:2187–2195 [View Article] [PubMed]
    [Google Scholar]
  53. 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]
  54. 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 [View Article] [PubMed]
    [Google Scholar]
  55. 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]
  56. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  57. 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]
  58. 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]
  59. Drula E, Garron M-L, Dogan S, Lombard V, Henrissat B et al. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res 2022; 50:D571–D577 [View Article] [PubMed]
    [Google Scholar]
  60. Zheng J, Ge Q, Yan Y, Zhang X, Huang L et al. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res 2023; 51:W115–W121 [View Article] [PubMed]
    [Google Scholar]
  61. Blin K, Shaw S, Augustijn HE, Reitz ZL, Biermann F et al. antiSMASH 7.0: new and improved predictions for detection, regulation, chemical structures and visualisation. Nucleic Acids Res 2023; 51:W46–W50 [View Article] [PubMed]
    [Google Scholar]
  62. Arndt D, Grant JR, Marcu A, Sajed T, Pon A et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res 2016; 44:W16–W21 [View Article] [PubMed]
    [Google Scholar]
  63. Bertelli C, Laird MR, Williams KP, Lau BY, Hoad G et al. IslandViewer 4: expanded prediction of genomic islands for larger-scale datasets. Nucleic Acids Res 2017; 45:W30–W35 [View Article] [PubMed]
    [Google Scholar]
  64. Alcock BP, Huynh W, Chalil R, Smith KW, Raphenya AR et al. CARD 2023: expanded curation, support for machine learning, and resistome prediction at the comprehensive antibiotic resistance database. Nucleic Acids Res 2023; 51:D690–D699 [View Article] [PubMed]
    [Google Scholar]
  65. 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]
  66. 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]
  67. 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:W22–8 [View Article] [PubMed]
    [Google Scholar]
  68. 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]
  69. Hugh R, Guarraia L, Hatt H. The proposed neotype strains of Pseudomonas fluorescens (Trevisan) Migula 1895. Int Bull Bacteriol Nomencl Taxon 1964; 14:145–156 [View Article]
    [Google Scholar]
  70. Campos VL, Valenzuela C, Yarza P, Kämpfer P, Vidal R et al. Pseudomonas arsenicoxydans sp. nov., an arsenite-oxidizing strain isolated from the Atacama desert. Syst Appl Microbiol 2010; 33:193–197 [View Article] [PubMed]
    [Google Scholar]
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