1887

Abstract

A novel, Gram-positive, facultative anaerobe, coccoid and non-motile bacterium, designated as CoE-012-22 was isolated from dried beef sausage (the original name in Montenegro is Govedji Kulen) manufactured in the municipality of Rozaje (Montenegro) in 2021. Cells of this strain were oxidase- and catalase-negative. Growth occurred at 4–50 °C, at pH 5.0–8.0 and with 0–6.5 % (w/v) NaCl in diverse growth media. MALDI-TOF analysis identified the strain as (log score 2). Phylogenetic analysis of the 16S rRNA gene and whole genome sequences assigned the strain to the genus . The closest relatives were DSM 21207 and ATCC 51266 with 16S rRNA gene sequence pairwise similarities of 99.34 and 98.59 %, respectively. The average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values between isolate CoE-012-22 and other enterococci species were below the thresholds for species delineation thresholds (95.0 % ANI; 70.0 % dDDH) with maximum identities of 84.13 % (ANIb), 86.43 % (ANIm) and 28.4 % (dDDH) to JCM 31193 and 70.97 % (ANIb), 88.99 % (ANIm) and 32.4 % (dDDH) to ATCC 43197. Two unknown isolates, sp. MJM12 and SMC-9, showed identities of 99.87 and 99.94 % (16S rRNA), 98.57 and 98.65 % (ANIb), 98.93 and 99.02 % (ANIm), and 89.8 and 90.0 % (dDDH) to strain CoE-012-22 and can therefore be regarded as the same species. Based on the characterization results, strain CoE-012-22 was considered to represent a novel species, for which the name sp. nov. is proposed. The type strain is CoE-012-22 (=DSM 115843=NCIMB 15468).

Funding
This study was supported by the:
  • European Public Health Microbiology Training Programme (EUPHEM) (Award No1/ECD.13493)
    • Principle Award Recipient: MariaJoao Cardoso
  • Ministry of Science and Technological Development of Montenegro (Award 013660/2)
    • Principle Award Recipient: AleksandraMartinovic
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
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2024-01-19
2024-05-17
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References

  1. Nami Y, Vaseghi Bakhshayesh R, Mohammadzadeh Jalaly H, Lotfi H, Eslami S et al. Probiotic properties of Enterococcus isolated from artisanal dairy products. Front Microbiol 2019; 10:300 [View Article] [PubMed]
    [Google Scholar]
  2. Foulquié Moreno MR, Sarantinopoulos P, Tsakalidou E, De Vuyst L. The role and application of enterococci in food and health. Int J Food Microbiol 2006; 106:1–24 [View Article] [PubMed]
    [Google Scholar]
  3. Jahansepas A, Sharifi Y, Aghazadeh M, Ahangarzadeh Rezaee M. Comparative analysis of Enterococcus faecalis and Enterococcus faecium strains isolated from clinical samples and traditional cheese types in the Northwest of Iran: antimicrobial susceptibility and virulence traits. Arch Microbiol 2020; 202:765–772 [View Article] [PubMed]
    [Google Scholar]
  4. Sanders ME, Benson A, Lebeer S, Merenstein DJ, Klaenhammer TR. Shared mechanisms among probiotic taxa: implications for general probiotic claims. Curr Opin Biotechnol 2018; 49:207–216 [View Article] [PubMed]
    [Google Scholar]
  5. Delpech G, Pourcel G, Schell C, De Luca M, Basualdo J et al. Antimicrobial resistance profiles of Enterococcus faecalis and Enterococcus faecium isolated from artisanal food of animal origin in Argentina. Foodborne Pathog Dis 2012; 9:939–944 [View Article] [PubMed]
    [Google Scholar]
  6. Yerlikaya O, Akbulut N. Potential use of probiotic Enterococcus faecium and Enterococcus durans strains in Izmir Tulum cheese as adjunct culture. J Food Sci Technol 2019; 56:2175–2185 [View Article] [PubMed]
    [Google Scholar]
  7. Giraffa G. Functionality of enterococci in dairy products. Int J Food Microbiol 2003; 88:215–222 [View Article] [PubMed]
    [Google Scholar]
  8. Tsanasidou C, Asimakoula S, Sameli N, Fanitsios C, Vandera E et al. Safety evaluation, biogenic amine formation, and enzymatic activity profiles of autochthonous enterocin-producing Greek cheese isolates of the Enterococcus faecium/durans group. Microorganisms 2021; 9:777 [View Article] [PubMed]
    [Google Scholar]
  9. Abeijón MC, Medina RB, Katz MB, González SN. Technological properties of Enterococcus faecium isolated from ewe’s milk and cheese with importance for flavour development. Can J Microbiol 2006; 52:237–245 [View Article] [PubMed]
    [Google Scholar]
  10. Woods DF, Kozak IM, Flynn S, O’Gara F. The microbiome of an active meat curing brine. Front Microbiol 2018; 9:3346 [View Article] [PubMed]
    [Google Scholar]
  11. Ruppitsch W, Nisic A, Hyden P, Cabal A, Sucher J et al. Genetic diversity of Leuconostoc mesenteroides isolates from traditional montenegrin brine cheese. Microorganisms 2021; 9:1612 [View Article] [PubMed]
    [Google Scholar]
  12. Daza Prieto B, Raicevic N, Ladstätter J, Hyden P, Jovanovic A et al. Draft genome sequence of Enterococcus dispar CoE-457-22, isolated from traditionally produced montenegrin dry sausage. Microbiol Resour Announc 2023; 12:e0103822 [View Article] [PubMed]
    [Google Scholar]
  13. Saboori B, Shahidi F, Hedayati S, Javadmanesh A. Investigating the probiotic properties and antimicrobial activity of lactic acid bacteria isolated from an Iranian fermented dairy product, Kashk. Foods 2022; 11:3904 [View Article] [PubMed]
    [Google Scholar]
  14. Dos Santos KMO, Vieira ADS, Salles HO, Oliveira J da S, Rocha CRC et al. Safety, beneficial and technological properties of Enterococcus faecium isolated from Brazilian cheeses. Braz J Microbiol 2015; 46:237–249 [View Article] [PubMed]
    [Google Scholar]
  15. Lee T, Pang S, Abraham S, Coombs GW. Molecular characterization and evolution of the first outbreak of vancomycin-resistant Enterococcus faecium in Western Australia. Int J Antimicrob Agents 2019; 53:814–819 [View Article] [PubMed]
    [Google Scholar]
  16. De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA et al. Antimicrobial resistance in ESKAPE pathogens. Clin Microbiol Rev 2020; 33:e00181-19 [View Article] [PubMed]
    [Google Scholar]
  17. Huys G, Botteldoorn N, Delvigne F, De Vuyst L, Heyndrickx M et al. Microbial characterization of probiotics–advisory report of the working group “8651 Probiotics” of the Belgian Superior Health Council (SHC). Mol Nutr Food Res 2013; 57:1479–1504 [View Article] [PubMed]
    [Google Scholar]
  18. Koutsoumanis K, Allende A, Alvarez-Ordóñez A, Bolton D, Bover-Cid S et al. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 13: suitability of taxonomic units notified to EFSA until September 2020. EFSA J 2021; 19:e06377 [View Article] [PubMed]
    [Google Scholar]
  19. Ogier J-C, Serror P. Safety assessment of dairy microorganisms: the Enterococcus genus. Int J Food Microbiol 2008; 126:291–301 [View Article] [PubMed]
    [Google Scholar]
  20. Zommiti M, Cambronel M, Maillot O, Barreau M, Sebei K et al. Evaluation of probiotic properties and safety of Enterococcus faecium isolated from artisanal Tunisian meat “dried ossban”. Front Microbiol 2018; 9:1685 [View Article] [PubMed]
    [Google Scholar]
  21. International Organization for Standardization ISO 15214:1998 Microbiology of food and animal feeding stuffs — Horizontal method for the enumeration of mesophilic lactic acid bacteria — Colony -count technique at 30 degrees C 1998. n.d https://doi.org/https://www.iso.org/standard/26853.html
  22. Tanizawa Y, Fujisawa T, Nakamura Y. DFAST: a flexible prokaryotic genome annotation pipeline for faster genome publication. Bioinformatics 2018; 34:1037–1039 [View Article] [PubMed]
    [Google Scholar]
  23. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
    [Google Scholar]
  24. Schwartzman JA, Lebreton F, Salamzade R, Martin MJ, Schaufler K et al. Global diversity of enterococci and description of 18 novel species. bioRxiv 2023 [View Article] [PubMed]
    [Google Scholar]
  25. Ene A, Banerjee S, Wolfe AJ, Putonti C. Exploring the genotypic and phenotypic differences distinguishing Lactobacillus jensenii and Lactobacillus mulieris. mSphere 2023; 8:e0056222 [View Article] [PubMed]
    [Google Scholar]
  26. Tamura K, Stecher G, Kumar S. MEGA11: Molecular Evolutionary Genetics Analysis version 11. Mol Biol Evol 2021; 38:3022–3027 [View Article] [PubMed]
    [Google Scholar]
  27. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  28. Jukes TH, Cantor CR. Chapter 24 - Evolution of Protein Molecules. In Munro HN. eds Mammalian Protein Metabolism Academic Press; 1969 pp 21–132 [View Article]
    [Google Scholar]
  29. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
    [Google Scholar]
  30. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012; 19:455–477 [View Article] [PubMed]
    [Google Scholar]
  31. Jünemann S, Sedlazeck FJ, Prior K, Albersmeier A, John U et al. Updating benchtop sequencing performance comparison. Nat Biotechnol 2013; 31:294–296 [View Article] [PubMed]
    [Google Scholar]
  32. Wick RR, Judd LM, Holt KE. Performance of neural network basecalling tools for Oxford Nanopore sequencing. Genome Biol 2019; 20:129 [View Article] [PubMed]
    [Google Scholar]
  33. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
    [Google Scholar]
  34. Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 2016; 32:2103–2110 [View Article] [PubMed]
    [Google Scholar]
  35. Vaser R, Šikić M. Time- and memory-efficient genome assembly with Raven. Nat Comput Sci 2021; 1:332–336 [View Article]
    [Google Scholar]
  36. Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G et al. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol 2021; 22:266 [View Article] [PubMed]
    [Google Scholar]
  37. Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 2009; 25:1754–1760 [View Article] [PubMed]
    [Google Scholar]
  38. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V et al. RefSeq: expanding the prokaryotic genome annotation pipeline reach with protein family model curation. Nucleic Acids Res 2021; 49:D1020–D1028 [View Article] [PubMed]
    [Google Scholar]
  39. Jolley KA, Bliss CM, Bennett JS, Bratcher HB, Brehony C et al. Ribosomal multilocus sequence typing: universal characterization of bacteria from domain to strain. Microbiology 2012; 158:1005–1015 [View Article] [PubMed]
    [Google Scholar]
  40. Meier-Kolthoff JP, Carbasse JS, Peinado-Olarte RL, Göker M. TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Res 2022; 50:D801–D807 [View Article] [PubMed]
    [Google Scholar]
  41. 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] [PubMed]
    [Google Scholar]
  42. Buton A, Bobay L-M, Zetka M. Evolution of Chi motifs in proteobacteria. G3 2021; 11:jkaa054 [View Article] [PubMed]
    [Google Scholar]
  43. Hyatt D, Chen G-L, Locascio PF, Land ML, Larimer FW et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010; 11:119 [View Article] [PubMed]
    [Google Scholar]
  44. Emms DM, Kelly S. OrthoFinder: phylogenetic orthology inference for comparative genomics. Genome Biol 2019; 20:238 [View Article] [PubMed]
    [Google Scholar]
  45. Emms DM, Kelly S. STAG: species tree inference from all genes. BioRxiv267914 2018 [View Article]
    [Google Scholar]
  46. Emms DM, Kelly S. STRIDE: species tree root inference from gene duplication events. Mol Biol Evol 2017; 34:3267–3278 [View Article] [PubMed]
    [Google Scholar]
  47. Medina RB, Katz MB, González S, Oliver G. Determination of esterolytic and lipolytic activities of lactic acid bacteria. In Spencer JFT, Spencer AL. eds Public Health Microbiology: Methods and Protocols Totowa, NJ: Humana Press; 2004 pp 465–470 [View Article]
    [Google Scholar]
  48. Bortolaia V, Kaas RS, Ruppe E, Roberts MC, Schwarz S et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2020; 75:3491–3500 [View Article] [PubMed]
    [Google Scholar]
  49. Hasman H, Clausen P, Kaya H, Hansen F, Knudsen JD et al. LRE-Finder, a web tool for detection of the 23S rRNA mutations and the optrA, cfr, cfr(B) and poxtA genes encoding linezolid resistance in enterococci from whole-genome sequences. J Antimicrob Chemother 2019; 74:1473–1476 [View Article] [PubMed]
    [Google Scholar]
  50. Joensen KG, Scheutz F, Lund O, Hasman H, Kaas RS et al. Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli. J Clin Microbiol 2014; 52:1501–1510 [View Article] [PubMed]
    [Google Scholar]
  51. Carattoli A, Hasman H. PlasmidFinder and in silico pMLST: identification and typing of plasmid replicons in whole-genome sequencing (WGS). In De la Cruz F. eds Horizontal Gene Transfer: Methods and Protocols New York, NY: Springer US; 2020 pp 285–294 [View Article]
    [Google Scholar]
  52. Cosentino S, Voldby Larsen M, Møller Aarestrup F, Lund O. PathogenFinder–distinguishing friend from foe using bacterial whole genome sequence data. PLoS One 2013; 8:e77302 [View Article] [PubMed]
    [Google Scholar]
  53. 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]
  54. Moyes RB, Reynolds J, Breakwell DP. Differential staining of bacteria: Gram stain. Curr Protoc Microbiol 2009 [View Article] [PubMed]
    [Google Scholar]
  55. van Heel AJ, de Jong A, Song C, Viel JH, Kok J et al. BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins. Nucleic Acids Res 2018; 46:W278–W281 [View Article] [PubMed]
    [Google Scholar]
  56. Blin K, Shaw S, Kloosterman AM, Charlop-Powers Z, van Wezel GP et al. antiSMASH 6.0: improving cluster detection and comparison capabilities. Nucleic Acids Res 2021; 49:W29–W35 [View Article] [PubMed]
    [Google Scholar]
  57. Kamal M, Höög JO, Kaiser R, Shafqat J, Razzaki T et al. Isolation, characterization and structure of subtilisin from a thermostable Bacillus subtilis isolate. FEBS Lett 1995; 374:363–366 [View Article] [PubMed]
    [Google Scholar]
  58. Alvarez-Sieiro P, Montalbán-López M, Mu D, Kuipers OP. Bacteriocins of lactic acid bacteria: extending the family. Appl Microbiol Biotechnol 2016; 100:2939–2951 [View Article] [PubMed]
    [Google Scholar]
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