1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 70, Issue 2

sp. nov., a new species isolated from faeces of a red fox in Spain Free

Abstract

A facultative anaerobic, chemoheterotrophic, endospore-forming, Gram-stain-positive rod, designated as strain Z8, was isolated from red fox () faeces sampled at Tablas de Daimiel National Park, Ciudad Real, Spain. Strain Z8 grew at 0–37 °C (optimum, 28 °C), in the presence of 0–5.5 % (w/v) NaCl (2.5 %, w/v) and at pH 6–10 (pH 7). The strain was motile and positive for catalase, oxidase, HS and siderophore production, acid and alkaline phosphatases, and -acetylglucosamine, adipic acid and malate assimilation. It hydrolysed starch, DNA, -tyrosine, Tween 20, Tween 80 and lecithovitellin. Phylogenetic analysis of the 16S rRNA gene sequence indicated that strain Z8 is a member of the genus , showing high sequence similarity to NEAU-3TGS17 (99.2 %) and NHI-2T (99.1 %), and around 98 % to other known species of the genus . Digital DNA–DNA hybridization and average nucleotide identity values were lower than 24 and 79 %, respectively, with the most related species. G+C content was 35.9 mol%. The major cellular fatty acids of strain Z8 were iso-C, iso-C and anteiso-C. The novel strain contained diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylglycerol as predominant polar lipids, and the main respiratory isoprenoid quinone was MK-8. Based on the 16S rRNA phylogenetic analysis, together with MLSA ( and ), phylogenomic, chemotaxonomic and phenotypic results, we demonstrate that strain Z8 represents a novel species of the genus for which the name sp. nov., is proposed. The type strain is Z8 (=CECT 9721=LMG 31001).

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): chemotaxonomy , genome , phylogenetic , polyphasic taxonomy , Psychrobacillus vulpis sp. nov. and red fox
Funding
This study was supported by the:
  • Spanish Ministerio de Educación y Ciencia (Award AGL-2015-68806-R)
    • Principle Award Recipient: Inmaculada Llamas Company
© 2020 The Authors
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003840
2019-12-13
2024-05-04
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/70/2/882.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003840&mimeType=html&fmt=ahah

References

  1. Krishnamurthi S, Ruckmani A, Pukall R, Chakrabarti T. Psychrobacillus gen. nov. and proposal for reclassification of Bacillus insolitus Larkin & Stokes, 1967, B. psychrotolerans Abd-El Rahman et al., 2002 and B. psychrodurans Abd-El Rahman et al., 2002 as Psychrobacillus insolitus comb. nov., Psychrobacillus psychrotolerans comb. nov. and Psychrobacillus psychrodurans comb. nov. Syst Appl Microbiol 2010; 33:367–373 [View Article]
     [Google Scholar]
  2. Larkin JM, Stokes JL. Taxonomy of psychrophilic strains of Bacillus . J Bacteriol 1967; 94:889–895
     [Google Scholar]
  3. Abd El-Rahman HA, Fritze D, Spröer C, Claus D. Two novel psychrotolerant species, Bacillus psychrotolerans sp. nov. and Bacillus psychrodurans sp. nov., which contain ornithine in their cell walls. Int J Syst Evol Microbiol 2002; 52:2127–2133 [View Article]
     [Google Scholar]
  4. Pham VH, Jeong SW, Kim J, sp Psoli. Psychrobacillus soli sp. nov., capable of degrading oil, isolated from oil-contaminated soil. Int J Syst Evol Microbiol 2015; 65:3046–3052 [View Article]
     [Google Scholar]
  5. Shen Y, Fu Y, Yu Y, Zhao J, Li J et al. Psychrobacillus lasiicapitis sp. nov., isolated from the head of an ant (Lasius fuliginosus). Int J Syst Evol Microbiol 2017; 67:4462–4467 [View Article]
     [Google Scholar]
  6. 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]
     [Google Scholar]
  7. Brosius J, Palmer ML, Kennedy PJ, Noller HF. Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli . Proc Natl Acad Sci USA 1978; 75:4801–4805 [View Article]
     [Google Scholar]
  8. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article]
     [Google Scholar]
  9. Yoon SH, 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]
  10. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article]
     [Google Scholar]
  11. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 1971; 20:406–416 [View Article]
     [Google Scholar]
  12. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article]
     [Google Scholar]
  13. 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]
     [Google Scholar]
  14. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega. Mol Syst Biol 2011; 7:539 [View Article]
     [Google Scholar]
  15. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–218 [View Article]
     [Google Scholar]
  16. 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
     [Google Scholar]
  17. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016; 32:929–931 [View Article]
     [Google Scholar]
  18. Yoon SH, Ha S-M, 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]
  19. 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]
  20. 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]
  21. 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]
     [Google Scholar]
  22. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75 [View Article]
     [Google Scholar]
  23. Chaudhari NM, Gupta VK, Dutta C. BPGA- an ultra-fast pan-genome analysis pipeline. Sci Rep 2016; 6:24373 [View Article]
     [Google Scholar]
  24. Alikhan NF, Petty NK, Ben Zakour NLB, Beatson SA. Blast ring image generator (BRIG): simple prokaryote genome comparisons. BMC Genomics 2011; 12:402 [View Article]
     [Google Scholar]
  25. Logan NA, Berge O, Bishop AH, Busse HJ, De Vos P et al. Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 2009; 59:2114–2121 [View Article]
     [Google Scholar]
  26. Schaeffer P, Millet J, Aubert JP. Catabolic repression of bacterial sporulation. Proc Natl Acad Sci U S A 1965; 54:704–711 [View Article]
     [Google Scholar]
  27. Murray RGE, Doetsch RM, Robinow CF et al. Determinative and cytological light microscopy. In Gerhardt PMR, Wood WA. (editors) Methods for General and Molecular Bacteriology Washington: American Society for Microbiology; 1994 pp 21–41
     [Google Scholar]
  28. Stokes EJ. A guide to the identification of the genera of Bacteria . J Clin Pathol 1968; 21:229–230 [View Article]
     [Google Scholar]
  29. Xie QY, Lin H-peng, Li L, Brown R, Goodfellow M et al. Verrucosispora wenchangensis sp. nov., isolated from mangrove soil. Antonie van Leeuwenhoek 2012; 102:1–7 [View Article]
     [Google Scholar]
  30. Kovacs N. Eine vereinfachte methode zum nachweis Der indolbildung durch bakterien. Immunforsch 1928; 55:311–315
     [Google Scholar]
  31. Barritt MM. The intensification of the Voges-Proskauer reaction by the addition of α-naphthol. J Pathol Bacteriol 1936; 42:441–454 [View Article]
     [Google Scholar]
  32. Clarke PH. Hydrogen sulphide production by bacteria. J Gen Microbiol 1953; 8:397–407 [View Article]
     [Google Scholar]
  33. Villalba LS, Mikán JF, Sánchez J. Actividades hidrolíticas Y caracterización isoenzimática de poblaciones microbianas aisladas del patrimonio documental del archivo general de Colombia. Nova 2004; 2:50–58 [View Article]
     [Google Scholar]
  34. Uttley AHC, Collins CH. Cowan and steel's manual for the identification of medical bacteria. 3rd ED. Barrow Gi and Feltham RKA, editors. Cambridge: Cambridge university press. J Hosp Infect 1993; 24:332
     [Google Scholar]
  35. Sierra G. A simple method for the detection of lipolytic activity of micro-organisms and some observations on the influence of the contact between cells and fatty substrates. Antonie van Leeuwenhoek 1957; 23:15–22 [View Article]
     [Google Scholar]
  36. Swan A. The use of a bile-aesculin medium and of Maxted's technique of Lancefield grouping in the identification of enterococci (group D streptococci). J Clin Pathol 1954; 7:160–163 [View Article]
     [Google Scholar]
  37. Esselmann MT, Liu PV. Lecithinase production by gram negative bacteria. J Bacteriol 1961; 81:939–945
     [Google Scholar]
  38. Jeffries CD, Holtman DF, Guse DG. Rapid method for determining the activity of microorganisms on nucleic acids. J Bacteriol 1957; 73:590–591
     [Google Scholar]
  39. Clarke SKR. A simplified plate method for detecting gelatine-liquefying bacteria. J Clin Pathol 1953; 6:246–248 [View Article]
     [Google Scholar]
  40. Baird-Parker AC. A classification of micrococci and staphylococci based on physiological and biochemical tests. J Gen Microbiol 1963; 30:409–427 [View Article]
     [Google Scholar]
  41. Pikovskaya RI. Mobilization of phosphorus in soil connection with the vital activity of some microbial species. Microbiology 1948; 17:362–370
     [Google Scholar]
  42. Alexander DB, Zuberer DA. Use of chrome azurol S reagents to evaluate siderophore production by rhizosphere bacteria. Biol Fert Soils 1991; 12:39–45 [View Article]
     [Google Scholar]
  43. Bauer AW, Kirby WMM, Sherris JC, Turck M. Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 1966; 45:493–496 [View Article]
     [Google Scholar]
  44. Bligh EG, Dyer WJ. A rapid method of total lipid extraction and purification. Can J Biochem Physiol 1959; 37:911–917 [View Article]
     [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
     [Google Scholar]
  46. Tindall BJ. Lipid composition of Halobacterium lacusprofundi . FEMS Microbiol Lett 1990; 66:199–202
     [Google Scholar]
  47. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC News Lett 1990; 20:1–6
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003840
Loading
Psychrobacillus vulpis sp. nov., a new species isolated from faeces of a red fox in Spain
Int J Syst Evol Microbiol 70, 882 (2020); https://doi.org/10.1099/ijsem.0.003840
/content/journal/ijsem/10.1099/ijsem.0.003840
/content/journal/ijsem/10.1099/ijsem.0.003840
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited 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