1887

Abstract

The intraspecific diversity of 31 strains of , 27 strains of and 29 strains of was determined by partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy. As a prerequisite for the analyses, 27 strains derived from culture collections which had carried invalid or wrong species designations were reclassified in accordance with polyphasic taxonomical data. FT-IR spectroscopy proved to be a rapid and reliable method for screening for similar isolates and for identifying these actinomycetes at the species level. Two main conclusions emerged from the analyses. (1) Comparison of intraspecific 16S rDNA similarities suggested that strains have a very low diversity, displays high diversity and occupies an intermediate position. (2) No correlation of FT-IR spectral similarity and 16S rDNA sequence similarity below the species level (i.e. between strains of one species) was observed. Therefore, diversification of 16S rDNA sequences and microevolutionary change of the cellular components detected by FT-IR spectroscopy appear to be de-coupled.

Loading

Article metrics loading...

/content/journal/micro/10.1099/00221287-148-5-1523
2002-05-01
2024-03-29
Loading full text...

Full text loading...

/deliver/fulltext/micro/148/5/1481523a.html?itemId=/content/journal/micro/10.1099/00221287-148-5-1523&mimeType=html&fmt=ahah

References

  1. Altschul S. F., Madden T. L., Zhang J., Zhang Z., Miller W., Lipman D. J., Schäffer A. A. 1997; Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402 [CrossRef]
    [Google Scholar]
  2. Amann R., Ludwig W., Schleifer K.-H. 1994; Identification of uncultured bacteria: a challenging task for molecular taxonomists. ASM News 60:360–365
    [Google Scholar]
  3. Amann R., Ludwig W., Schleifer K.-H. 1995; Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
    [Google Scholar]
  4. Arias C. R., Verdonck L., Swings J., Aznar R., Garay E. 1997; A polyphasic approach to study the intraspecific diversity amongst Vibrio vulnificus isolates. Syst Appl Microbiol 20:622–633 [CrossRef]
    [Google Scholar]
  5. Brosius J., Palmer M. L., Kennedy P. J., Noller H. F. 1978; Complete nucleotide sequence of a 16S ribosomal RNA gene from Escherichia coli. . Proc Natl Acad Sci U S A 75:4801–4805 [CrossRef]
    [Google Scholar]
  6. Bruker. 1998 Charakterisierung von Mikroorganismen mit der FT-IR Spektroskopie – Arbeitsanleitung zum IFS 28/B, Version 3.0 Germany: Bruker;
    [Google Scholar]
  7. Chatellier S., Harel J., Zhang Y., Gottschalk M., Higgins R., Devriese L. A., Brousseau R. 1998; Phylogenetic diversity of Streptococcus suis strains of various serotypes as revealed by 16S rRNA gene sequence comparison. Int J Syst Bacteriol 48:581–589 [CrossRef]
    [Google Scholar]
  8. Chen J., Jarret R. L., Qin X., Hartung J. S., Banks D., Chang C. J., Hopkins D. L. 2000; 16S rDNA sequence analysis of Xylella fastidiosa strains. Syst Appl Microbiol 23:349–354 [CrossRef]
    [Google Scholar]
  9. Christensen J. J., Whitney A. M., Teixeira L. M., Steigerwalt A. G., Facklam R. R., Korner B., Brenner D. J. 1997; Aerococcus urinae : intraspecies genetic and phenotypic relatedness. Int J Syst Bacteriol 47:28–32 [CrossRef]
    [Google Scholar]
  10. Cibik R., Lepage E., Tailliez P. 2000; Molecular diversity of Leuconostoc mesenteroides and Leuconostoc citreum isolated from traditional French cheeses as revealed by RAPD fingerprinting, 16S rDNA sequencing and 16S rDNA fragment amplification. Syst Appl Microbiol 23:267–278 [CrossRef]
    [Google Scholar]
  11. Curk M. C., Peladan F., Hubert J. C. 1994; Fourier transform infrared (FTIR) spectroscopy for identifying Lactobacillus species. FEMS Microbiol Lett 123:241–248 [CrossRef]
    [Google Scholar]
  12. Dahllöf I., Baillie H., Kjelleberg S. 2000; rpoB -based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66:3376–3380 [CrossRef]
    [Google Scholar]
  13. Davies R. L., Quirie M. 1996; Intra-specific diversity within Pasteurella trehalosi based on variation of capsular polysaccharide, lipopolysaccharide and outer-membrane proteins. Microbiology 142:551–560 [CrossRef]
    [Google Scholar]
  14. Facius D., Fartmann B., Huber J., Nikoleit K., Schondelmaier J., Steinhauser S. 1999 Sequencing Brochure. Instructions for DNA Template Preparation, Primer Design And Sequencing with the LI-COR DNA Sequencer 4000 and 4200 series, Version 4 Ebersberg: MWG-BIOTECH AG;
    [Google Scholar]
  15. Farfán M., Miñana D., Fusté M. C., Lorén J. G. 2000; Genetic relationships between clinical and environmental Vibrio cholerae isolates based on multilocus enzyme electrophoresis. Microbiology 146:2613–2626
    [Google Scholar]
  16. Fox G. E., Wisotzkey J. D., Jurtshuk P. Jr 1992; How close is close: 16S rRNA sequence identity may not be sufficient to guarantee species identity. Int J Syst Bacteriol 42:166–170 [CrossRef]
    [Google Scholar]
  17. Giraffa G., Gatti M., Rossetti L., Senini L., Neviani E. 2000; Molecular diversity within Lactobacillus helveticus as revealed by genotypic characterization. Appl Environ Microbiol 66:1259–1265 [CrossRef]
    [Google Scholar]
  18. Goodacre R., Timmins E. M., Burton R., Kaderbhai N., Woodward A. M., Kell D. B., Rooney P. J. 1998; Rapid identification of urinary tract infection bacteria using hyperspectral whole-organism fingerprinting and artificial neural networks. Microbiology 144:1157–1170 [CrossRef]
    [Google Scholar]
  19. Grecz N., Dack G. M. 1961; Taxonomically significant color reactions of Brevibacterium linens . J Bacteriol 82:241–246
    [Google Scholar]
  20. Harrington C. S., On S. L. W. 1999; Extensive 16S rRNA gene sequence diversity in Campylobacter hyointestinalis strains: taxonomic and applied implications. Int J Syst Bacteriol 49:1171–1175 [CrossRef]
    [Google Scholar]
  21. Helm D., Labischinski H., Naumann D. 1991; Elaboration of a procedure for identification of bacteria using Fourier-Transform IR spectral libraries: a stepwise correlation approach. J Microbiol Methods 14:127–142 [CrossRef]
    [Google Scholar]
  22. Holt C., Hirst D., Sutherland A., MacDonald F. 1995; Discrimination of species in the genus Listeria by Fourier transform infrared spectroscopy and canonical variate analysis. Appl Environ Microbiol 61:377–378
    [Google Scholar]
  23. Irmscher H.-M., Fischer R., Beer W., Seltmann G. 1999; Characterization of nosocomial Serratia marcescens isolates: comparison of Fourier-transform infrared spectroscopy with pulsed-field gel electrophoresis of genomic DNA fragments and multilocus enzyme electrophoresis. Zentbl Bakteriol 289:249–263 [CrossRef]
    [Google Scholar]
  24. Jones D., Watkins J., Erickson S. K. 1973; Taxonomically significant colour changes in Brevibacterium linens probably associated with carotenoid-like pigment. J Gen Microbiol 77:145–150 [CrossRef]
    [Google Scholar]
  25. Kämpfer P., Kroppenstedt R. M. 1996; Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 42:989–1005 [CrossRef]
    [Google Scholar]
  26. Kämpfer P., Seiler H., Dott W. 1993; Numerical classification of coryneform bacteria and related taxa. J Gen Appl Microbiol 39:135–214 [CrossRef]
    [Google Scholar]
  27. Kümmerle M., Scherer S., Seiler H. 1998; Rapid and reliable identification of fermentative yeasts by Fourier-transform infrared spectroscopy. Appl Environ Microbiol 64:2207–2214
    [Google Scholar]
  28. Lechner S., Mayr R., Francis K. P., Kaplan T., Wießner-Gunkel E., Stewart G. S. A. B., Scherer S., Prüß B. M. 1998; Bacillus weihenstephanensis sp. nov. is a new psychrotolerant species of the Bacillus cereus group. Int J Syst Bacteriol 48:1373–1382 [CrossRef]
    [Google Scholar]
  29. Ludwig W., Schleifer K.-H. 1999; Phylogeny of Bacteria beyond the 16S rRNA standard. ASM News 65:752–757
    [Google Scholar]
  30. Ludwig W., Strunk O. 1999; arb, a software environment for sequence data. http://www.biol.chemie.tu-muenchen.de/pub/ARB/documentation/arb.ps
  31. Ludwig W., Strunk O., Klugbauer S., Klugbauer N., Weizenegger M., Neumaier J., Bachleitner M. 1998; Bacterial phylogeny based on comparative sequence analysis. Electrophoresis 19:554–568 [CrossRef]
    [Google Scholar]
  32. Maidak B. L., Cole J. R., Lilburn T. G. 9 other authors 2000; The RDP (Ribosomal Database Project) continues. Nucleic Acids Res 28:173–174 [CrossRef]
    [Google Scholar]
  33. Mallet J. 2001; Concept of species. In Encyclopedia of Biodiversity pp 427–440 Edited by Levin S. A. New York: Academic Press;
    [Google Scholar]
  34. Mehta A., Rosato Y. B. 2001; Phylogenetic relationships of Xylella fastidiosa strains from different hosts, based on 16S rDNA and 16S–23S intergenic spacer sequences. Int J Syst Evol Microbiol 51:311–318
    [Google Scholar]
  35. Morton A. C., Begg A. P., Anderson G. A., Takai S., Browning G. F., Lämmler C. 2001; Epidemiology of Rhodococcus equi strains on thoroughbred horse farms. Appl Environ Microbiol 67:2167–2175 [CrossRef]
    [Google Scholar]
  36. Naumann D., Helm D., Schultz C. others 1994; Characterization and identification of micro-organisms by FT-IR spectroscopy and FT-IR microscopy. In Bacterial Diversity and Systematics pp 67–85 Edited by Priest F. G. New York: Plenum;
    [Google Scholar]
  37. Nübel U., Engelen B., Felske A., Snaidr J., Wieshuber A., Amann R. I., Ludwig W., Backhaus H. 1996; Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178:5636–5643
    [Google Scholar]
  38. Oberreuter H., Seiler H., Scherer S. 2002; Identification of coryneform bacteria and related taxa by Fourier-transform infrared (FT-IR) spectroscopy. Int J Syst Evol Microbiol 52:91–100
    [Google Scholar]
  39. Owen R. J., Ferrus M., Gibson J. 2001; Amplified fragment length polymorphism genotyping of metronidazole-resistant Helicobacter pylori infecting dyspeptics in England. Clin Microbiol Infect 7:244–253 [CrossRef]
    [Google Scholar]
  40. Prieto C. I., Aguilar O. M., Yantorno O. M. 1999; Analyses of lipopolysaccharides, outer membrane proteins and DNA fingerprints reveal intraspecies diversity in Moraxella bovis isolated in Argentina. Vet Microbiol 70:213–223 [CrossRef]
    [Google Scholar]
  41. Ridell J., Siitonen A., Paulin L., Lindroos O., Korkeala H., Albert M. J. 1995; Characteriziation of Hafnia alvei by biochemical tests, random amplified polymorphic DNA PCR, and partial sequencing of 16S rRNA gene. J Clin Microbiol 33:2372–2376
    [Google Scholar]
  42. Rosselló-Mora R., Amann R. 2001; The species concept for prokaryotes. FEMS Microbiol Rev 25:39–67 [CrossRef]
    [Google Scholar]
  43. Sander A., Ruess M., Bereswill S., Schuppler M., Steinbrueckner B. 1998; Comparison of different DNA fingerprinting techniques for molecular typing of Bartonella henselae isolates. J Clin Microbiol 36:2973–2981
    [Google Scholar]
  44. Saunders K. E., McGovern K. J., Fox J. G. 1997; Use of pulsed-field gel electrophoresis to determine genomic diversity in strains of Helicobacter hepaticus from geographically distant locations. J Clin Microbiol 35:2859–2863
    [Google Scholar]
  45. Seiler H. 1983; Identification key for coryneform bacteria derived by numerical taxonomic studies. J Gen Microbiol 129:1433–1471
    [Google Scholar]
  46. Seltmann G., Voigt W., Beer W. 1994; Application of physico-chemical typing methods for the epidemiological analysis of Salmonella enteritidis strains of phage type 25/17. Epidemiol Infect 113:411–424 [CrossRef]
    [Google Scholar]
  47. Seltmann G., Beer W., Claus H., Seifert H. 1995; Comparative classification of Acinetobacter baumannii strains using seven different typing methods. Zentbl Bakteriol 282:372–383 [CrossRef]
    [Google Scholar]
  48. Skerman V. B. D., McGowan V., Sneath P. H. A. 1980; Approved lists of bacterial names. Int J Syst Bacteriol 30:225–420 [CrossRef]
    [Google Scholar]
  49. Stackebrandt E., Goebel B. M. 1994; A place for DNA–DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846–849 [CrossRef]
    [Google Scholar]
  50. Stackebrandt E., Rainey F. A., Ward-Rainey N. L. 1997; Proposal for a new hierarchic classification system, Actinobacteria classis nov. Int J Syst Bacteriol 47:479–491 [CrossRef]
    [Google Scholar]
  51. Stan-Lotter H., McGenity T. J., Legat A., Denner E. B. M., Glaser K., Stetter K. O., Wanner G. 1999; Very similar strains of Halococcus salifodinae are found in geographically separated Permo-Triassic salt deposits. Microbiology 145:3565–3574
    [Google Scholar]
  52. Szállás E., Koch C., Fodor A., Burghardt J., Buss O., Szentirmai A., Nealson K. H., Stackebrandt E. 1997; Phylogenetic evidence for the taxonomic heterogeneity of Photorhabdus luminescens . Int J Syst Bacteriol 47:402–407 [CrossRef]
    [Google Scholar]
  53. Taylor D. E., Eaton M., Chang N., Salama S. M. 1992; Construction of a Helicobacter pylori genome map and demonstration of diversity at the genome level. J Bacteriol 174:6800–6806
    [Google Scholar]
  54. Tindall B. J., Brambilla E., Steffen M., Neumann R., Pukall R., Kroppenstedt R. M., Stackebrandt E. 2000; Cultivatable microbial diversity: gnawing at the Gordian knot. Environ Microbiol 2:310–318 [CrossRef]
    [Google Scholar]
  55. von Stetten F., Francis K. P., Lechner S., Neuhaus K., Scherer S. 1998; Rapid discrimination of psychrotolerant and mesophilic strains of the Bacillus cereus group by PCR targeting of 16S rDNA. J Microbiol Methods 34:99–106 [CrossRef]
    [Google Scholar]
  56. Zavaleta A. I., Martı́nez-Murcia A. J., Rodrı́guez-Valera F. 1997; Intraspecific genetic diversity of Oenococcus oeni as derived from DNA fingerprinting and sequence analyses. Appl Environ Microbiol 63:1261–1267
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/00221287-148-5-1523
Loading
/content/journal/micro/10.1099/00221287-148-5-1523
Loading

Data & Media loading...

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