Oligonucleotide microarrays for the detection and identification of viable beer spoilage bacteria

Journal of Applied Microbiology

Volumn 105, Issue 4, 2008, Pages 951-962

  Weber, D G ^a,d   Sahm, K ^b   Polen, T ^c   Wendisch, V F ^c   Antranikian, G ^a  

^a HAMBURG UNIVERSITY OF TECHNOLOGY   (Germany)

^b MUNICH UNIVERSITY OF APPLIED SCIENCES   (Germany)

^c UNIVERSITY OF MÜNSTER   (Germany)

^d INSTITUT DER RUHR UNIVERSITÄT BOCHUM IPA   (Germany)

Author keywords

Biotechnology; Brewery; Food; Microarray; PCR

Indexed keywords

BEER; MICROARRAYS; OLIGONUCLEOTIDES; POLYMERASE CHAIN REACTION; PROBES; RNA; SPOILAGE;

BACTERIAL SPECIES; BEER SPOILAGE; DESIGN AND EVALUATIONS; DETECTION AND IDENTIFICATIONS; INTERGENIC SPACER REGIONS; MEGASPHAERA; OLIGONUCLEOTIDE MICROARRAY; OLIGONUCLEOTIDE PROBES; PCR; PEDIOCOCCUS;

BACTERIA;

RNA 16S; RNA 23S; RNA DIRECTED DNA POLYMERASE; SPACER DNA;

ARRAY; BACTERIUM; BIOTECHNOLOGY; DETECTION METHOD; FEASIBILITY STUDY; FOOD INDUSTRY; FOOD SAFETY; HYBRIDIZATION; IDENTIFICATION METHOD; MICROBIAL COMMUNITY;

ARTICLE; BACTERIUM DETECTION; BACTERIUM IDENTIFICATION; BEER; CONTROLLED STUDY; DNA MICROARRAY; LACTOBACILLUS; MEGASPHAERA; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PECTINATUS; PEDIOCOCCUS; POLYMERASE CHAIN REACTION; RNA STABILITY;

BACTERIA (MICROORGANISMS); LACTOBACILLUS; MEGASPHAERA; PECTINATUS; PEDIOCOCCUS;

EID: 52049103837     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/j.1365-2672.2008.03799.x     Document Type: Article

References (67)

1. Acedo-Felix, E. Perez-Martinez, G. (2003) Significant differences between Lactobacillus casei subsp. casei ATCC 393T and a commonly used plasmid-cured derivative revealed by a polyphasic study. Int J Syst Evol Microbiol 53, 67 75.
2. Al-Khaldi, S.F., Martin, S.A., Rasooly, A. Evans, J.D. (2002) DNA microarray technology used for studying foodborne pathogens and microbial habitats: minireview. J AOAC Int 85, 906 910.
3. Barry, T., Glennon, C.M., Dunican, L.K. Gannon, F. (1991) The 16s/23s ribosomal spacer region as a target for DNA probes to identify eubacteria. PCR Methods Appl 1, 149.
4. Beattie, W.G., Meng, L., Turner, S.L., Varma, R.S., Dao, D.D. Beattie, K.L. (1995) Hybridization of DNA targets to glass-tethered oligonucleotide probes. Mol Biotechnol 4, 213 225.
5. Behr, T., Koob, C., Schedl, M., Mehlen, A., Meier, H., Knopp, D., Frahm, E., Obst, U. et al. (2000) A nested array of rRNA targeted probes for the detection and identification of enterococci by reverse hybridization. Syst Appl Microbiol 23, 563 572.
6. Bej, A.K., Mahbubani, M.H. Atlas, R.M. (1991) Detection of viable Legionella pneumophila in water by polymerase chain reaction and gene probe methods. Appl Environ Microbiol 57, 597 600.
7. Bej, A.K., Ng, W.Y., Morgan, S., Jones, D.D. Mahbubani, M.H. (1996) Detection of viable Vibrio cholerae by reverse-transcriptase polymerase chain reaction (RT-PCR). Mol Biotechnol 5, 1 10.
8. Berthier, F. Ehrlich, S.D. (1998) Rapid species identification within two groups of closely related lactobacilli using PCR primers that target the 16S/23S rRNA spacer region. FEMS Microbiol Lett 161, 97 106.
9. Blaiotta, G., Pepe, O., Mauriello, G., Villani, F., Andolfi, R. Moschetti, G. (2002) 16S-23S rDNA intergenic spacer region polymorphism of Lactococcus garvieae, Lactococcus raffinolactis and Lactococcus lactis as revealed by PCR and nucleotide sequence analysis. Syst Appl Microbiol 25, 520 527.
10. Boyer, S.L., Flechtner, V.R. Johansen, J.R. (2001) Is the 16S-23S rRNA internal transcribed spacer region a good tool for use in molecular systematics and population genetics? A case study in cyanobacteria Mol Biol Evol 18, 1057 1069.
11. Call, D.R., Borucki, M.K. Loge, F.J. (2003) Detection of bacterial pathogens in environmental samples using DNA microarrays. J Microbiol Methods 53, 235 243.
12. Cangelosi, G.A. Brabant, W.H. (1997) Depletion of pre-16S rRNA in starved Escherichia coli cells. J Bacteriol 179, 4457 4463.
13. Cangelosi, G.A., Brabant, W.H., Britschgi, T.B. Wallis, C.K. (1996) Detection of rifampin- and ciprofloxacin-resistant Mycobacterium tuberculosis by using species-specific assays for precursor rRNA. Antimicrob Agents Chemother 40, 1790 1795.
14. Chelack, B.J. Ingledew, W.M. (1987) Anaerobic gram-negative bacteria in brewing - a review. J Am Soc Brew Chem 45, 123 127.
15. Chen, H., Lim, C.K., Lee, Y.K. Chan, Y.N. (2000) Comparative analysis of the genes encoding 23S-5S rRNA intergenic spacer regions of Lactobacillus casei-related strains. Int J Syst Evol Microbiol 50, 471 478.
16. Chiang, Y.C., Yang, C.Y., Li, C., Ho, Y.C., Lin, C.K. Tsen, H.Y. (2006) Identification of Bacillus spp., Escherichia coli, Salmonella spp., Staphylococcus spp. and Vibrio spp. with 16S ribosomal DNA-based oligonucleotide array hybridization. Int J Food Microbiol 107, 131 137.
17. Chihib, N.E. Tholozan, J.L. (1999) Effect of rapid cooling and acidic pH on cellular homeostasis of Pectinatus frisingensis, a strictly anaerobic beer-spoilage bacterium. Int J Food Microbiol 48, 191 202.
18. Cho, J.C. Tiedje, J.M. (2001) Bacterial species determination from DNA-DNA hybridization by using genome fragments and DNA microarrays. Appl Environ Microbiol 67, 3677 3682.
19. De Man, J.C., Rogosa, M. Sharpe, M.E. (1960) A medium for the cultivation of lactobacilli. J Appl Bacteriol 23, 130 135.
20. Doktycz, M.J., Morris, M.D., Dormady, S.J., Beattie, K.L. Jacobson, K.B. (1995) Optical melting of 128 octamer DNA duplexes. Effects of base pair location and nearest neighbors on thermal stability. J Biol Chem 270, 8439 8445.
21. Drobyshev, A., Mologina, N., Shik, V., Pobedimskaya, D., Yershov, G. Mirzabekov, A. (1997) Sequence analysis by hybridization with oligonucleotide microchip: identification of beta-thalassemia mutations. Gene 188, 45 52.
22. Eisen, M.B. Brown, P.O. (1999) DNA arrays for analysis of gene expression. Methods Enzymol 303, 179 205.
23. Engelmann, U., Weiss, N. Mackey, B.M. (1985) Megasphaera cerevisiae sp. nov.: a new gram-negative obligately anaerobic coccus isolated from spoiled beer. Syst Appl Microbiol 6, 287 290.
24. Flint, J.F. Angert, E.R. (2005) Development of a strain-specific assay for detection of viable Lactobacillus sp. HOFG1 after application to cattle feed. J Microbiol Methods 61, 235 243.
25. Forget, B.G. Jordan, B. (1970) 5S RNA synthesized by Escherichia coli in presence of chloramphenicol: different 5'-terminal sequences. Science 167, 382 384.
26. 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.
27. Gurtler, V. Stanisich, V.A. (1996) New approaches to typing and identification of bacteria using the 16S-23S rDNA spacer region. Microbiology 142, 3 16.
28. Heiskanen, M.A., Bittner, M.L., Chen, Y., Khan, J., Adler, K.E., Trent, J.M. Meltzer, P.S. (2000) Detection of gene amplification by genomic hybridization to cDNA microarrays. Cancer Res 60, 799 802.
29. Hurt, R.A., Qiu, X., Wu, L., Roh, Y., Palumbo, A.V., Tiedje, J.M. Zhou, J. (2001) Simultaneous recovery of RNA and DNA from soils and sediments. Appl Environ Microbiol 67, 4495 4503.
30. Jespersen, L. Jakobsen, M. (1996) Specific spoilage organisms in breweries and laboratory media for their detection. Int J Food Microbiol 33, 139 155.
31. Jin, L.Q., Li, J.W., Wang, S.Q., Chao, F.H., Wang, X.W. Yuan, Z.Q. (2005) Detection and identification of intestinal pathogenic bacteria by hybridization to oligonucleotide microarrays. World J Gastroenterol 11, 7615 7619.
32. Keramas, G., Bang, D.D., Lund, M., Madsen, M., Rasmussen, S.E., Bunkenborg, H., Telleman, P. Christensen, C.B. (2003) Development of a sensitive DNA microarray suitable for rapid detection of Campylobacter spp. Mol Cell Probes 17, 187 196.
33. Klein, P.G. Juneja, V.K. (1997) Sensitive detection of viable Listeria monocytogenes by reverse transcription-PCR. Appl Environ Microbiol 63, 4441 4448.
34. Leblond-Bourget, N., Philippe, H., Mangin, I. Decaris, B. (1996) 16S rRNA and 16S to 23S internal transcribed spacer sequence analyses reveal inter- and intraspecific Bifidobacterium phylogeny. Int J Syst Bacteriol 46, 102 111.
35. Lin, M.C., Huang, A.H., Tsen, H.Y., Wong, H.C. Chang, T.C. (2005) Use of oligonucleotide array for identification of six foodborne pathogens and Pseudomonas aeruginosa grown on selective media. J Food Prot 68, 2278 2286.
36. Lindahl, T. (1993) Instability and decay of the primary structure of DNA. Nature 362, 709 715.
37. Liu, W.T., Mirzabekov, A.D. Stahl, D.A. (2001) Optimization of an oligonucleotide microchip for microbial identification studies: a non-equilibrium dissociation approach. Environ Microbiol 3, 619 629.
38. Loughney, K., Lund, E. Dahlberg, J.E. (1982) tRNA genes are found between 16S and 23S rRNA genes in Bacillus subtilis. Nucleic Acids Res 10, 1607 1624.
39. March, C., Manclus, J.J., Abad, A., Navarro, A. Montoya, A. (2005) Rapid detection and counting of viable beer-spoilage lactic acid bacteria using a monoclonal chemiluminescence enzyme immunoassay and a CCD camera. J Immunol Methods 303, 92 104.
40. Masters, C.I., Shallcross, J.A. Mackey, B.M. (1994) Effect of stress treatments on the detection of Listeria monocytogenes and enterotoxigenic Escherichia coli by the polymerase chain reaction. J Appl Bacteriol 77, 73 79.
41. Maynard, C., Berthiaume, F., Lemarchand, K., Harel, J., Payment, P., Bayardelle, P., Masson, L. Brousseau, R. (2005) Waterborne pathogen detection by use of oligonucleotide-based microarrays. Appl Environ Microbiol 71, 8548 8557.
42. McKillip, J.L., Jaykus, L.A. Drake, M. (1998) rRNA stability in heat-killed and UV-irradiated enterotoxigenic Staphylococcus aureus and Escherichia coli O157:H7. Appl Environ Microbiol 64, 4264 4268.
43. Nakagawa, T., Shimada, M., Mukai, H., Asada, K., Kato, I., Fujino, K. Sato, T. (1994) Detection of alcohol-tolerant hiochi bacteria by PCR. Appl Environ Microbiol 60, 637 640.
44. Nelson, P.T., Baldwin, D.A., Scearce, L.M., Oberholtzer, J.C., Tobias, J.W. Mourelatos, Z. (2004) Microarray-based, high-throughput gene expression profiling of microRNAs. Nat Methods 1, 155 161.
45. Nour, M. (1998) 16S-23S and 23S-5S intergenic spacer regions of lactobacilli: nucleotide sequence, secondary structure and comparative analysis. Res Microbiol 149, 433 448.
46. Nubel, U., Schmidt, P.M., Reiss, E., Bier, F., Beyer, W. Naumann, D. (2004) Oligonucleotide microarray for identification of Bacillus anthracis based on intergenic transcribed spacers in ribosomal DNA. FEMS Microbiol Lett 240, 215 223.
47. Oerther, D.B., Pernthaler, J., Schramm, A., Amann, R. Raskin, L. (2000) Monitoring precursor 16S rRNAs of Acinetobacter spp. in activated sludge wastewater treatment systems. Appl Environ Microbiol 66, 2154 2165.
48. Pace, N.R. (1973) Structure and synthesis of the ribosomal ribonucleic acid of prokaryotes. Bacteriol Rev 37, 562 603.
49. Patel, B.K., Banerjee, D.K. Butcher, P.D. (1993) Determination of Mycobacterium leprae viability by polymerase chain reaction amplification of 71-kDa heat-shock protein mRNA. J Infect Dis 168, 799 800.
50. Polen, T. Wendisch, V.F. (2004) Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays. Appl Biochem Biotechnol 118, 215 232.
51. Polen, T., Rittmann, D., Wendisch, V.F. Sahm, H. (2003) DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate. Appl Environ Microbiol 69, 1759 1774.
52. Relogio, A., Schwager, C., Richter, A., Ansorge, W. Valcarcel, J. (2002) Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 30, e51.
53. Rozen, S. Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132, 365 386.
54. Schena, M., Shalon, D., Davis, R.W. Brown, P.O. (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270, 467 470.
55. Schmid, M., Schmitz-Esser, S., Jetten, M. Wagner, M. (2001) 16S-23S rDNA intergenic spacer and 23S rDNA of anaerobic ammonium-oxidizing bacteria: implications for phylogeny and in situ detection. Environ Microbiol 3, 450 459.
56. Schuchhardt, J., Beule, D., Malik, A., Wolski, E., Eickhoff, H., Lehrach, H. Herzel, H. (2000) Normalization strategies for cDNA microarrays. Nucleic Acids Res 28, E47.
57. Shalon, D., Smith, S.J. Brown, P.O. (1996) A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6, 639 645.
58. Sheridan, G.E., Masters, C.I., Shallcross, J.A. MacKey, B.M. (1998) Detection of mRNA by reverse transcription-PCR as an indicator of viability in Escherichia coli cells. Appl Environ Microbiol 64, 1313 1318.
59. Small, J., Call, D.R., Brockman, F.J., Straub, T.M. Chandler, D.P. (2001) Direct detection of 16S rRNA in soil extracts by using oligonucleotide microarrays. Appl Environ Microbiol 67, 4708 4716.
60. Song, Y., Kato, N., Liu, C., Matsumiya, Y., Kato, H. Watanabe, K. (2000) Rapid identification of 11 human intestinal Lactobacillus species by multiplex PCR assays using group- and species-specific primers derived from the 16S-23S rRNA intergenic spacer region and its flanking 23S rRNA. FEMS Microbiol Lett 187, 167 173.
61. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. Higgins, D.G. (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25, 4876 4882.
62. Weiler, J., Gausepohl, H., Hauser, N., Jensen, O.N. Hoheisel, J.D. (1997) Hybridisation based DNA screening on peptide nucleic acid (PNA) oligomer arrays. Nucleic Acids Res 25, 2792 2799.
63. Wildsmith, S.E., Archer, G.E., Winkley, A.J., Lane, P.W. Bugelski, P.J. (2001) Maximization of signal derived from cDNA microarrays. Biotechniques 30, 202 206.
64. Yansanjav, A., Svec, P., Sedlacek, I., Hollerova, I. Nemec, M. (2003) Ribotyping of lactobacilli isolated from spoiled beer. FEMS Microbiol Lett 229, 141 144.
65. Yershov, G., Barsky, V., Belgovskiy, A., Kirillov, E., Kreindlin, E., Ivanov, I., Parinov, S., Guschin, D. et al. (1996) DNA analysis and diagnostics on oligonucleotide microchips. Proc Natl Acad Sci USA 93, 4913 4918.
66. Zheng, D., Alm, E.W., Stahl, D.A. Raskin, L. (1996) Characterization of universal small-subunit rRNA hybridization probes for quantitative molecular microbial ecology studies. Appl Environ Microbiol 62, 4504 4513.
67. Zhou, J., Bruns, M.A. Tiedje, J.M. (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62, 316 322.