1887

Abstract

A facultatively anaerobic, spore-forming strain, FSL W8-0169, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified as a group species based on a partial sequence of the gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known group species. Pairwise average nucleotide identity values obtained for FSL W8-0169 compared to the type strains of existing group species were <95 % and predicted DNA–DNA hybridization values were <70 %, suggesting that this strain represents a novel group species. We characterized 10 additional strains with the same or closely related allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169 from other group species. FSL W8-0169 is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169 (=DSM 102050=LMG 29269).

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2016-11-01
2024-03-28
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References

  1. Angiuoli S. V., Gussman A., Klimke W., Cochrane G., Field D., Garrity G., Kodira C. D., Kyrpides N., Madupu R. et al. 2008; Toward an online repository of standard operating procedures (SOPs) for (meta)genomic annotation. OMICS 12:137–141 [View Article][PubMed]
    [Google Scholar]
  2. Bankevich A., Nurk S., Antipov D., Gurevich A. A., Dvorkin M., Kulikov A. S., Lesin V. M., Nikolenko S. I., Pham S. et al. 2012; SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477 [View Article][PubMed]
    [Google Scholar]
  3. Bolger A. M., Lohse M., Usadel B. 2014; Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  4. Ceuppens S., Boon N., Uyttendaele M. 2013; Diversity of Bacillus cereus group strains is reflected in their broad range of pathogenicity and diverse ecological lifestyles. FEMS Microbiol Ecol 84:433–450 [View Article][PubMed]
    [Google Scholar]
  5. Chan J. Z., Halachev M. R., Loman N. J., Constantinidou C., Pallen M. J. 2012; Defining bacterial species in the genomic era: insights from the genus Acinetobacter. BMC Microbiol 12:302 [View Article][PubMed]
    [Google Scholar]
  6. Gardner S. N., Hall B. G. 2013; When whole-genome alignments just won't work: kSNP v2 software for alignment-free SNP discovery and phylogenetics of hundreds of microbial genomes. PLoS One 8:e81760 [View Article][PubMed]
    [Google Scholar]
  7. Guinebretière M. H., Thompson F. L., Sorokin A., Normand P., Dawyndt P., Ehling-Schulz M., Svensson B., Sanchis V., Nguyen-The C. et al. 2008; Ecological diversification in the Bacillus cereus group. Environ Microbiol 10:851–865 [View Article][PubMed]
    [Google Scholar]
  8. Guinebretière M. H., Velge P., Couvert O., Carlin F., Debuyser M. L., Nguyen-The C. 2010; Ability of Bacillus cereus group strains to cause food poisoning varies according to phylogenetic affiliation (groups I to VII) rather than species affiliation. J Clin Microbiol 48:3388–3391 [View Article][PubMed]
    [Google Scholar]
  9. Guinebretière M. H., Auger S., Galleron N., Contzen M., De Sarrau B., De Buyser M. L., Lamberet G., Fagerlund A., Granum P. E. et al. 2013; Bacillus cytotoxicus sp. nov. is a novel thermotolerant species of the Bacillus cereus Group occasionally associated with food poisoning. Int J Syst Evol Microbiol 63:31–40 [View Article][PubMed]
    [Google Scholar]
  10. Gurevich A., Saveliev V., Vyahhi N., Tesler G. 2013; QUAST: quality assessment tool for genome assemblies. Bioinformatics 29:1072–1075 [View Article][PubMed]
    [Google Scholar]
  11. Huck J. R., Hammond B. H., Murphy S. C., Woodcock N. H., Boor K. J. 2007; Tracking spore-forming bacterial contaminants in fluid milk-processing systems. J Dairy Sci 90:4872–4883 [View Article][PubMed]
    [Google Scholar]
  12. Ivy R. A., Ranieri M. L., Martin N. H., den Bakker H. C., Xavier B. M., Wiedmann M., Boor K. J. 2012; Identification and characterization of psychrotolerant sporeformers associated with fluid milk production and processing. Appl Environ Microbiol 78:1853–1864 [View Article][PubMed]
    [Google Scholar]
  13. Jiménez G., Urdiain M., Cifuentes A., López-López A., Blanch A. R., Tamames J., Kämpfer P., Kolstø A. B., Ramón D. et al. 2013; Description of Bacillus toyonensis sp. nov., a novel species of the Bacillus cereus group, and pairwise genome comparisons of the species of the group by means of ANI calculations. Syst Appl Microbiol 36:383–391 [View Article][PubMed]
    [Google Scholar]
  14. Jung M. Y., Paek W. K., Park I. S., Han J. R., Sin Y., Paek J., Rhee M. S., Kim H., Song H. S. et al. 2010; Bacillus gaemokensis sp. nov., isolated from foreshore tidal flat sediment from the Yellow Sea. J Microbiol 48:867–871 [View Article][PubMed]
    [Google Scholar]
  15. Jung M. Y., Kim J. S., Paek W. K., Lim J., Lee H., Kim P. I., Ma J. Y., Kim W., Chang Y. H. 2011; Bacillus manliponensis sp. nov., a new member of the Bacillus cereus group isolated from foreshore tidal flat sediment. J Microbiol 49:1027–1032 [View Article][PubMed]
    [Google Scholar]
  16. Kim M. J., Han J. K., Park J. S., Lee J. S., Lee S. H., Cho J. I., Kim K. S. 2015; Various enterotoxin and other virulence factor genes widespread among Bacillus cereus and Bacillus thuringiensis strains. J Microbiol Biotechnol 25:872–879 [View Article][PubMed]
    [Google Scholar]
  17. Lechner S., Mayr R., Francis K. P., Prüss B. M., Kaplan T., Wiessner-Gunkel E., Stewart G. S., Scherer S. 1998; Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. Int J Syst Bacteriol 48:1373–1382 [View Article][PubMed]
    [Google Scholar]
  18. Li H., Handsaker B., Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R.1000 Genome Project Data Processing Subgroup 2009; The sequence alignment/Map format and SAMtools. Bioinformatics 25:2078–2079 [View Article][PubMed]
    [Google Scholar]
  19. Liu B., Liu G. H., Hu G. P., Sengonca C., Cetin S., Lin N. Q., Tang J. Y., Tang W. Q., Lin Y. Z. 2014; Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin's Terra-cotta warriors in China. Antonie Van Leeuwenhoek 105:501–510 [View Article][PubMed]
    [Google Scholar]
  20. Liu Y., Lai Q., Göker M., Meier-Kolthoff J. P., Wang M., Sun Y., Wang L., Shao Z. 2015; Genomic insights into the taxonomic status of the Bacillus cereus group. Sci Rep 5:14082 [View Article][PubMed]
    [Google Scholar]
  21. Logan N. A., Carman J. A., Melling J., Berkeley R. C. 1985; Identification of Bacillus anthracis by API tests. J Med Microbiol 20:75–85 [View Article][PubMed]
    [Google Scholar]
  22. Logan N. A., De Vos P. 2009; Genus I. Bacillus Cohn 1872, 174AL. In Bergey’s Manual of Systematic Bacteriology, 2nd edn. vol. 3 (The Firmicutes) pp. 21–128 Edited by Vos P., Garrity G., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schleifer K.-H., Whitman W. New York: Springer;
    [Google Scholar]
  23. Lücking G., Stoeckel M., Atamer Z., Hinrichs J., Ehling-Schulz M. 2013; Characterization of aerobic spore-forming bacteria associated with industrial dairy processing environments and product spoilage. Int J Food Microbiol 166:270–279 [View Article][PubMed]
    [Google Scholar]
  24. Meier-Kolthoff J. P., Auch A. F., Klenk H. P., Göker M. 2013; Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14:60 [View Article][PubMed]
    [Google Scholar]
  25. Miller R. A., Kent D. J., Watterson M. J., Boor K. J., Martin N. H., Wiedmann M. 2015a; Spore populations among bulk tank raw milk and dairy powders are significantly different. J Dairy Sci 98:8492–8504 [View Article]
    [Google Scholar]
  26. Miller R. A., Kent D. J., Boor K. J., Martin N. H., Wiedmann M. 2015b; Different management practices are associated with mesophilic and thermophilic spore levels in bulk tank raw milk. J Dairy Sci 98:4338–4351 [View Article]
    [Google Scholar]
  27. Moayeri M., Leppla S. H., Vrentas C., Pomerantsev A. P., Liu S. 2015; Anthrax pathogenesis. Annu Rev Microbiol 69:185–208 [View Article][PubMed]
    [Google Scholar]
  28. Nakamura L. K. 1994; DNA relatedness among Bacillus thuringiensis serovars. Int J Syst Bacteriol 44:125–129 [View Article][PubMed]
    [Google Scholar]
  29. Nakamura L. K. 1998; Bacillus pseudomycoides sp. nov. Int J Syst Bacteriol 48:1031–1035 [View Article][PubMed]
    [Google Scholar]
  30. R Core Team 2014; R: A language and environment for statistical computing. Vienna: R Foundation for Statistical Computing;
  31. Richter M., Rosselló-Móra R. 2009; Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  32. Schindelin J., Arganda-Carreras I., Frise E., Kaynig V., Longair M., Pietzsch T., Preibisch S., Rueden C., Saalfeld S. et al. 2012; Fiji: an open-source platform for biological-image analysis. Nat Method 9:676–682 [View Article]
    [Google Scholar]
  33. Schumann P. 2011; Peptidoglycan structure. Method Microbiol 38:101–129 [CrossRef]
    [Google Scholar]
  34. Smith N. R., Gordon R. E., Clarck F. E. 1952 Aerobic Spore-Forming Bacteria Monograph No 16 Washington, DC: US Department of Agriculture;
    [Google Scholar]
  35. Stamatakis A. 2014; RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 30:1312–1313 [View Article][PubMed]
    [Google Scholar]
  36. Tamura K., Stecher G., Peterson D., Filipski A., Kumar S. 2013; mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729 [View Article][PubMed]
    [Google Scholar]
  37. U.S. Food and Drug Administration 2015; Bacteriological analytical manual (BAM). http://www.fda.gov/Food/FoodScienceResearch/LaboratoryMethods/ucm2006949.htm
  38. Watterson M. J., Kent D. J., Boor K. J., Wiedmann M., Martin N. H. 2014; Evaluation of dairy powder products implicates thermophilic sporeformers as the primary organisms of interest. J Dairy Sci 97:2487–2497 [View Article][PubMed]
    [Google Scholar]
  39. Wright E. S., Yilmaz L. S., Noguera D. R. 2012; DECIPHER, a search-based approach to chimera identification for 16S rRNA sequences. Appl Environ Microbiol 78:717–725 [View Article][PubMed]
    [Google Scholar]
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