1887

Abstract

A taxonomic study was carried out on four Gram-stain-negative strains P5773, P6169, P4708 and P6245, isolated from anus or mouth samples of Weddell seals at James Ross Island, Antarctica. The results of initial 16S rRNA gene sequence analysis showed that all four strains formed a group placed in the genus and found and to be their closest neighbours with 99.9 and 99.2 % sequence similarity, respectively. Sequence analysis of , and housekeeping genes confirmed the highest similarity of isolates to () and to ( and ). The average nucleotide identity value below 86 %, as calculated from the whole-genome sequence data, showed the low genomic relatedness of P5773 to its phylogenetic neighbours. The complete genome of strain P5773 was 4.4 Mb long and contained genes encoding proteins with biotechnological potential. The major fatty acids of the seal isolates were summed feature 8 (C 7), summed feature 3 (C /C 6) and C. The major respiratory quinone was Q9. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. Putrescine and spermidine are predominant in the polyamine pattern. Further characterization performed using repetitive sequence-based PCR fingerprinting and MALDI-TOF MS analysis showed that the studied isolates formed a coherent cluster separated from the remaining species and confirmed that they represent a novel species within the genus , for which the name sp. nov. is suggested. The type strain is P5773 (=CCM 8849=LMG 30618).

Funding
This study was supported by the:
  • Masarykova Univerzita (Award MUNI/A/0958/2018)
    • Principle Award Recipient: Roman Pantůček
  • Ministerstvo Zdravotnictví Ceské Republiky (Award 16-29916A)
    • Principle Award Recipient: Roman Pantůček
  • Ministerstvo Školství, Mládeže a Tělovýchovy (Award CZ.02.1.01/0.0/0.0/16_013/0001708)
    • Principle Award Recipient: Ivo Sedláček
  • Ministerstvo Školství, Mládeže a Tělovýchovy (Award LM2015078)
    • Principle Award Recipient: Ivo Sedláček
  • Ministerstvo Školství, Mládeže a Tělovýchovy (Award LM2015043)
    • Principle Award Recipient: Not Applicable
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003753
2020-02-03
2021-07-27
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/1/302.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003753&mimeType=html&fmt=ahah

References

  1. Parte AC. LPSN-list of prokaryotic names with standing in nomenclature. Nucleic Acids Res 2014; 42:D613–D616 [View Article]
    [Google Scholar]
  2. Bozal N, Montes MJ, Mercadé E. Pseudomonas guineae sp. nov., a novel psychrotolerant bacterium from an Antarctic environment. Int J Syst Evol Microbiol 2007; 57:2609–2612 [View Article]
    [Google Scholar]
  3. Kosina M, Barták M, Mašlaňová I, Pascutti AV, Šedo O et al. Pseudomonas prosekii sp. nov., a novel psychrotrophic bacterium from Antarctica. Curr Microbiol 2013; 67:637–646 [View Article]
    [Google Scholar]
  4. Kosina M, Švec P, Černohlávková J, Barták M, Snopková K et al. Description of Pseudomonas gregormendelii sp. nov., a novel psychrotrophic bacterium from James Ross Island, Antarctica. Curr Microbiol 2016; 73:84–90 [View Article]
    [Google Scholar]
  5. 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 [View Article]
    [Google Scholar]
  6. 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]
    [Google Scholar]
  7. 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]
    [Google Scholar]
  8. Lockwood SK, Chovan JL, Gaydos JK. Aerobic bacterial isolations from harbor seals (Phoca vitulina) stranded in Washington: 1992-2003. J Zoo Wildl Med 2006; 37:281–291 [View Article]
    [Google Scholar]
  9. Thornton SM, Nolan S, Gulland FM. Bacterial isolates from California sea lions (Zalophus californianus), harbor seals (Phoca vitulina), and northern elephant seals (Mirounga angustirostris) admitted to a rehabilitation center along the central California coast, 1994-1995. J Zoo Wildl Med 1998; 29:171–176
    [Google Scholar]
  10. Fleming M, Bexton S. Conjunctival flora of healthy and diseased eyes of grey seals (Halichoerus grypus): implications for treatment. Vet Rec 2016; 179:99 [View Article]
    [Google Scholar]
  11. Sedláček I, Králová S, Kýrová K, Mašlaňová I, Busse HJ et al. Red-pink pigmented Hymenobacter coccineus sp. nov., Hymenobacter lapidarius sp. nov. and Hymenobacter glacialis sp. nov., isolated from rocks in Antarctica. Int J Syst Evol Microbiol 2017; 67:1975–1983 [View Article]
    [Google Scholar]
  12. Švec P, Nováková D, Žáčková L, Kukletová M, Sedláček I. Evaluation of (GTG)5-PCR for rapid identification of Streptococcus mutans . Antonie van Leeuwenhoek 2008; 94:573–579 [View Article]
    [Google Scholar]
  13. Edwards U, Rogall T, Blöcker H, Emde M, Böttger EC. Isolation and direct complete nucleotide determination of entire genes. Characterization of a gene coding for 16S ribosomal RNA. Nucleic Acids Res 1989; 17:7843–7853 [View Article]
    [Google Scholar]
  14. Kýrová K, Sedláček I, Pantůček R, Králová S, Holochová P et al. Rufibacter ruber sp. nov., isolated from fragmentary rock. Int J Syst Evol Microbiol 2016; 66:4401–4405 [View Article]
    [Google Scholar]
  15. Yoon S-H, Ha SM, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
    [Google Scholar]
  16. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article]
    [Google Scholar]
  17. Mulet M, Bennasar A, Lalucat J, García-Valdés E. An rpoD-based PCR procedure for the identification of Pseudomonas species and for their detection in environmental samples. Mol Cell Probes 2009; 23:140–147 [View Article]
    [Google Scholar]
  18. 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 [View Article]
    [Google Scholar]
  19. 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]
    [Google Scholar]
  20. Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A. Assembling genomes and mini-metagenomes from highly chimeric reads. In Deng M, Jiang R, Sun F, Zhang X. (editors) Research in Computational Molecular Biology. RECOMB 2013. Lecture Notes in Computer Science 7821 Berlin, Heidelberg: Springer; 2013 pp 7158–7170
    [Google Scholar]
  21. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article]
    [Google Scholar]
  22. Lagesen K, Hallin P, Rødland EA, Staerfeldt HH, Rognes T et al. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 2007; 35:3100–3108 [View Article]
    [Google Scholar]
  23. Koudelakova T, Bidmanova S, Dvorak P, Pavelka A, Chaloupkova R et al. Haloalkane dehalogenases: biotechnological applications. Biotechnol J 2013; 8:32–45 [View Article]
    [Google Scholar]
  24. Yoon SH, Ha SM, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  25. 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]
    [Google Scholar]
  26. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009; 106:19126–19131 [View Article]
    [Google Scholar]
  27. Meier-Kolthoff JP, Klenk HP, Göker M. Taxonomic use of DNA G+C content and DNA-DNA hybridization in the genomic age. Int J Syst Evol Microbiol 2014; 64:352–356 [View Article]
    [Google Scholar]
  28. Na SI, Kim YO, Yoon SH, Ha SM, Baek I et al. UBCG: up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 2018; 56:280–285 [View Article]
    [Google Scholar]
  29. Christensen WB. Urea decomposition as a means of differentiating Proteus and paracolon cultures from each other and from Salmonella and Shigella types. J Bacteriol 1946; 52:461–466
    [Google Scholar]
  30. Hugh R, Leifson E. The taxonomic significance of fermentative versus oxidative metabolism of carbohydrates by various gram negative bacteria. J Bacteriol 1953; 66:24–26
    [Google Scholar]
  31. Brooks K, Sodeman T. A rapid method for determining decarboxylase and dihydrolase activity. J Clin Pathol 1974; 27:148–152 [View Article]
    [Google Scholar]
  32. Weyant RS, Moss CW, Weaver RE, Hollis DG, Jordan JG et al. Identification of Unusual Pathogenic Gram-Negative Aerobic and Facultatively Anaerobic Bacteria, 2nd ed. Baltimore, MD: Williams & Wilkins; 1996 pp 15–16
    [Google Scholar]
  33. Páčová Z, Kocur M. New medium for detection of esterase and gelatinase activity. Zb Bakt Hyg 1984; 258:69–73
    [Google Scholar]
  34. Kurup VP, Babcock JB. Use of casein, tyrosine, and hypoxanthine in the identification of nonfermentative gram-negative bacilli. Med Microbiol Immunol 1979; 167:71–75 [View Article]
    [Google Scholar]
  35. Owens JJ. The egg yolk reaction produced by several species of bacteria. J Appl Bacteriol 1974; 37:137–148 [View Article]
    [Google Scholar]
  36. Lowe GH. The rapid detection of lactose fermentation in paracolon organisms by the demonstration of beta-D-galactosidase. J Med Lab Technol 1962; 19:21–25
    [Google Scholar]
  37. Barrow GI, Feltham RKA. Cowan and Steel’s Manual for the Identification of Medical Bacteria, 3rd ed. Great Britain: Cambridge University Press; 1993
    [Google Scholar]
  38. Oberhofer TR, Rowen JW. Acetamide agar for differentiation of nonfermentative bacteria. Appl Microbiol 1974; 28:720–721
    [Google Scholar]
  39. Ewing WH. Enterobacteriaceae. Biochemical Methods for Group Differentiation Atlanta: Public Health Service Publication no 734 CDC; 1960
    [Google Scholar]
  40. CLSI Performance standards for antimicrobial susceptibility testing. Twenty-Fifth Informational Supplement 2015; 35:No. 3. ISBN 1-56238-989-0
    [Google Scholar]
  41. EUCAST Breakpoint tables for interpretation of MICs and zone diameters, version 7.1. The European Committee on Antimicrobial Susceptibility Testing
    [Google Scholar]
  42. Gevers D, Huys G, Swings J. Applicability of rep-PCR fingerprinting for identification of Lactobacillus species. FEMS Microbiol Lett 2001; 205:31–36 [View Article]
    [Google Scholar]
  43. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. Newark, DE: MIDI Inc; 1990
    [Google Scholar]
  44. Mašlaňová I, Wertheimer Z, Sedláček I, Švec P, Indráková A et al. Description and comparative genomics of Macrococcus caseolyticus subsp. hominis subsp. nov., Macrococcus goetzii sp. nov., Macrococcus epidermidis sp. nov., and Macrococcus bohemicus sp. nov., novel macrococci from human clinical material with virulence potential and suspected uptake of foreign DNA by natural transformation. Front Microbiol 2018; 9:1178 [View Article]
    [Google Scholar]
  45. Altenburger P, Kämpfer P, Makristathis A, Lubitz W, Busse HJ. Classification of bacteria isolated from a medieval wall painting. J Biotechnol 1996; 47:39–52 [View Article]
    [Google Scholar]
  46. Stolz A, Busse HJ, Kämpfer P. Pseudomonas knackmussii sp. nov. Int J Syst Evol Microbiol 2007; 57:572–576 [View Article]
    [Google Scholar]
  47. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990a; 66:199–202 [View Article]
    [Google Scholar]
  48. Tindall BJ. A comparative study of the lipid composition of Halobacterium saccharovorum from various sources. Syst Appl Microbiol 1990b; 13:128–130 [View Article]
    [Google Scholar]
  49. Busse J, Auling G. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria . Syst Appl Microbiol 1988; 11:1–8 [View Article]
    [Google Scholar]
  50. Busse HJ, Bunka S, Hensel A, Lubitz W. Discrimination of members of the family Pasteurellaceae based on polyamine patterns. Int J Syst Bacteriol 1997; 47:698–708 [View Article]
    [Google Scholar]
  51. Hauser E, Kämpfer P, Busse HJ. Pseudomonas psychrotolerans sp. nov. Int J Syst Evol Microbiol 2004; 54:1633–1637 [View Article]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003753
Loading
/content/journal/ijsem/10.1099/ijsem.0.003753
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