1887

Abstract

Sampling of agricultural and natural environments in two US states (Colorado and Florida) yielded 18 -like isolates that could not be assigned to previously described species using traditional methods. Using whole-genome sequencing and traditional phenotypic methods, we identified five novel species, each with a genome-wide average nucleotide identity (ANIb) of less than 85 % to currently described species. Phylogenetic analysis based on 16S rRNA gene sequences and amino acid sequences of 31 conserved loci showed the existence of four well-supported clades within the genus ; (i) a clade representing , , , , and , which we refer to as , (ii) a clade consisting of and two newly described species, sp. nov. (type strain FSL S10-1188 = DSM 26686 = LMG 28120 = BEI NR-42633) and sp. nov. (type strain FSL S10-1187 = DSM 26687 = LMG 28121 = BEI NR-42632), (iii) a clade consisting of , and three novel species, sp. nov. (type strain TTU A1-0210 = FSL F6-0969 = DSM 26689 = LMG 28123 = BEI NR-42630), sp. nov. (type strain TTU A1-0212 = FSL F6-0971 = DSM 26688 = LMG 28122 = BEI NR-42631) and sp. nov. (type strain FSL S10-1204 = DSM 26685 = LMG 28119 = BEI NR- 42634) and (iv) a clade containing . Genomic and phenotypic data suggest that the novel species are non-pathogenic.

Funding
This study was supported by the:
  • USDA NIFA (Award Special Research Grant 2010-34459-20756)
  • USDA NIFA National Integrated Food Safety Initiative (Award 2008-51110-04688 and 2008-51110-04333)
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijs.0.052720-0
2014-06-01
2024-03-19
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/64/6/1882.html?itemId=/content/journal/ijsem/10.1099/ijs.0.052720-0&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. ( 1990 ). Basic local alignment search tool. . J Mol Biol 215, 403410.[PubMed] [CrossRef]
    [Google Scholar]
  2. Bertsch D., Rau J., Eugster M. R., Haug M. C., Lawson P. A., Lacroix C., Meile L. ( 2013 ). Listeria fleischmannii sp. nov., isolated from cheese. . Int J Syst Evol Microbiol 63, 526532. [View Article] [PubMed]
    [Google Scholar]
  3. Bille J., Catimel B., Bannerman E., Jacquet C., Yersin M. N., Caniaux I., Monget D., Rocourt J. ( 1992 ). API Listeria, a new and promising one-day system to identify Listeria isolates. . Appl Environ Microbiol 58, 18571860.[PubMed]
    [Google Scholar]
  4. Boerlin P., Rocourt J., Grimont F., Grimont P. A. D., Jacquet C., Piffaretti J.-C. ( 1992 ). Listeria ivanovii subsp. londoniensis subsp. nov.. Int J Syst Bacteriol 42, 6973. [View Article]
    [Google Scholar]
  5. Castresana J. ( 2000 ). Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. . Mol Biol Evol 17, 540552. [View Article] [PubMed]
    [Google Scholar]
  6. Chan J. Z.-M., 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. [CrossRef]
    [Google Scholar]
  7. Chevreux B., Wetter T., Suhai S. ( 1999 ). Genome sequence assembly using trace signals and additional sequence information. . In German Conference on Bioinformatics, October 4–6 1999, Hannover, Germany:, pp. 4556.
    [Google Scholar]
  8. Cohan F. M. ( 2001 ). Bacterial species and speciation. . Syst Biol 50, 513524. [View Article] [PubMed]
    [Google Scholar]
  9. den Bakker H. C., Manuel C. S., Fortes E. D., Wiedmann M., Nightingale K. K. ( 2013 ). Genome sequencing identifies Listeria fleischmannii subsp. coloradonensis subsp. nov., isolated from a ranch. . Int J Syst Evol Microbiol 63, 32573268. [View Article] [PubMed]
    [Google Scholar]
  10. Domínguez-Bernal G., Müller-Altrock S., González-Zorn B., Scortti M., Herrmann P., Monzó H. J., Lacharme L., Kreft J., Vázquez-Boland J. A. ( 2006 ). A spontaneous genomic deletion in Listeria ivanovii identifies LIPI-2, a species-specific pathogenicity island encoding sphingomyelinase and numerous internalins. . Mol Microbiol 59, 415432. [View Article] [PubMed]
    [Google Scholar]
  11. Errebo Larsen H., Seeliger H. P. R. & other authors ( 1966 ). A mannitol fermenting Listeria, Listeria grayi sp. n. . In Proceedings of the Third International Symposium on Listeriosis, 13–16 July 1996, Bilthoven, Netherlands:, p. 35.
    [Google Scholar]
  12. Graves L. M., Helsel L. O., Steigerwalt A. G., Morey R. E., Daneshvar M. I., Roof S. E., Orsi R. H., Fortes E. D., Milillo S. R. & other authors ( 2010 ). Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest. . Int J Syst Evol Microbiol 60, 12801288. [View Article] [PubMed]
    [Google Scholar]
  13. Koboldt D. C., Zhang Q., Larson D. E., Shen D., McLellan M. D., Lin L., Miller C. A., Mardis E. R., Ding L., Wilson R. K. ( 2012 ). VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. . Genome Res 22, 568576. [View Article] [PubMed]
    [Google Scholar]
  14. Konstantinidis K. T., Tiedje J. M. ( 2005 ). Towards a genome-based taxonomy for prokaryotes. . J Bacteriol 187, 62586264. [View Article] [PubMed]
    [Google Scholar]
  15. Konstantinidis K. T., Tiedje J. M. ( 2007 ). Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead. . Curr Opin Microbiol 10, 504509. [View Article] [PubMed]
    [Google Scholar]
  16. Konstantinidis K. T., Ramette A., Tiedje J. M. ( 2006 ). The bacterial species definition in the genomic era. . Philos Trans R Soc Lond B Biol Sci 361, 19291940. [View Article] [PubMed]
    [Google Scholar]
  17. Kuenne C., Billion A., Mraheil M. A., Strittmatter A., Daniel R., Goesmann A., Barbuddhe S., Hain T., Chakraborty T. ( 2013 ). Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome. . BMC Genomics 14, 47. [View Article] [PubMed]
    [Google Scholar]
  18. Lang Halter E., Neuhaus K., Scherer S. ( 2013 ). Listeria weihenstephanensis sp. nov., isolated from the water plant Lemna trisulca taken from a freshwater pond. . Int J Syst Evol Microbiol 63, 641647. [View Article] [PubMed]
    [Google Scholar]
  19. Leclercq A., Clermont D., Bizet C., Grimont P. A. D., Le Flèche-Matéos A., Roche S. M., Buchrieser C., Cadet-Daniel V., Le Monnier A. & other authors ( 2010 ). Listeria rocourtiae sp. nov.. Int J Syst Evol Microbiol 60, 22102214. [View Article] [PubMed]
    [Google Scholar]
  20. Li H., Durbin R. ( 2009 ). Fast and accurate short read alignment with Burrows-Wheeler transform. . Bioinformatics 25, 17541760. [View Article] [PubMed]
    [Google Scholar]
  21. McLauchlin J., Rees C. ( 2009 ). Genus I. Listeria Pirie 1940a 383AL . . In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 3, pp. 244257. Edited by De Vos P., Garrity G., Jones D., Krieg N. R., Ludwig W., Rainey F. A., Schleifer K.-H., Whitman W. B. . New York:: Springer;.
    [Google Scholar]
  22. Pirie J. H. ( 1940 ). The genus Listerella Pirie. . Science 91, 383. [View Article] [PubMed]
    [Google Scholar]
  23. Richter M., Rosselló-Móra R. ( 2009 ). Shifting the genomic gold standard for the prokaryotic species definition. . Proc Natl Acad Sci U S A 106, 1912619131. [View Article] [PubMed]
    [Google Scholar]
  24. Rijpens N., Vlaemynck G., Rossau R., Herman L., Jannes G. ( 1998 ). Unidentified Listeria-like bacteria isolated from cheese. . Lett Appl Microbiol 27, 198202. [View Article] [PubMed]
    [Google Scholar]
  25. Rocourt J., Grimont P. A. D. ( 1983 ). Listeria welshimeri sp. nov. and Listeria seeligeri sp. nov.. Int J Syst Bacteriol 33, 866869. [View Article]
    [Google Scholar]
  26. Sauders B. D., Overdevest J., Fortes E., Windham K., Schukken Y., Lembo A., Wiedmann M. ( 2012 ). Diversity of Listeria species in urban and natural environments. . Appl Environ Microbiol 78, 44204433. [View Article] [PubMed]
    [Google Scholar]
  27. Schmid M. W., Ng E. Y. W., Lampidis R., Emmerth M., Walcher M., Kreft J., Goebel W., Wagner M., Schleifer K.-H. ( 2005 ). Evolutionary history of the genus Listeria and its virulence genes. . Syst Appl Microbiol 28, 118. [View Article] [PubMed]
    [Google Scholar]
  28. Seeliger H. P. R. ( 1981 ). Apathogene Listerien: L. innocua sp.n. (Seeliger et Schoofs, 1977). . Zentralbl Bakteriol Parasitenkd Infektionskr Hyg Abt 1 Orig A 249, 487493 (in German).
    [Google Scholar]
  29. Seeliger H. P. R., Rocourt J., Schrettenbrunner A., Grimont P. A. D., Jones D. ( 1984 ). Listeria ivanovii sp. nov.. Int J Syst Bacteriol 34, 336337. [View Article]
    [Google Scholar]
  30. Stuart S. E., Welshimer H. J. ( 1973 ). Intrageneric relatedness of Listeria Pirie. . Int J Syst Bacteriol 23, 814. [View Article]
    [Google Scholar]
  31. US Food and Drug Administration ( 2013 ). Bacteriological Analytical Manual. http://www.fda.gov/food/foodscienceresearch/laboratorymethods/ucm2006949.htm
    [Google Scholar]
  32. Wilgenbusch J. C., Swofford D. ( 2003 ). Inferring evolutionary trees with paup*. . In Current Protocols in Bioinformatics, unit 6.4. New York:: Wiley;. [View Article]
    [Google Scholar]
  33. Wu M., Eisen J. A. ( 2008 ). A simple, fast, and accurate method of phylogenomic inference. . Genome Biol 9, R151. [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijs.0.052720-0
Loading
/content/journal/ijsem/10.1099/ijs.0.052720-0
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF
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