Generation of subspecies level-specific microbial diagnostic microarrays using genes amplified from subtractive suppression hybridization as microarray probes

Nucleic Acids Research

Volumn 33, Issue 13, 2005, Pages 1-8

  Bae, Jin Woo ^a   Rhee, Sung Keun ^b   Nam, Young Do ^a   Park, Yong Ha ^a  

^a Korea Research Institute of Bioscience and Biotechnology (KRIBB)   (South Korea)

^b Chungbuk National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIUM CULTURE; DNA MICROARRAY; DNA PROBE; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE SEQUENCE; GENOME ANALYSIS; HIGH THROUGHPUT SCREENING; METHODOLOGY; MICROBIAL IDENTIFICATION; PHYLOGENY; PRIORITY JOURNAL; SALMONELLA; SEQUENCE ANALYSIS; SPECIES DIFFERENTIATION; STRAIN DIFFERENCE; SUPPRESSION SUBTRACTIVE HYBRIDIZATION; VALIDATION PROCESS; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL INFECTION; BACTERIUM IDENTIFICATION; CLASSIFICATION; DIAGNOSTIC PROCEDURE; EVALUATION; GENETICS; ISOLATION AND PURIFICATION; NUCLEIC ACID HYBRIDIZATION; POLYMERASE CHAIN REACTION; SPECIES DIFFERENCE;

BACTERIA (MICROORGANISMS); SALMONELLA;

BACTERIAL INFECTIONS; BACTERIAL TYPING TECHNIQUES; DNA PROBES; GENES, BACTERIAL; GENOME, BACTERIAL; MOLECULAR DIAGNOSTIC TECHNIQUES; NUCLEIC ACID HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; POLYMERASE CHAIN REACTION; SALMONELLA; SPECIES SPECIFICITY;

EID: 27144530664     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gni112     Document Type: Article

References (44)

1. Bodrossy,L. and Sessitsch,A. (2004) Oligonucleotide microarrays in microbial diagnostics. Curr. Opin. Microbiol., 7, 245-254.
2. Zhou,J. (2003) Microarrays for bacterial detection and microbial community analysis. Curr. Opin. Microbiol., 6, 288-294.
3. Zhou,J. and Thompson,D.K. (2002) Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol., 13, 204-207.
4. Cook,K.L. and Sayler,G.S. (2003) Environmental application of array technology: Promise, problems and practicalities. Curr. Opin. Biotechnol., 14, 311-318.
5. Rebrikov,D.V., Desai,S.M., Siebert,P.D. and Lukyanov,S.A. (2004) Suppression subtractive hybridization. Methods Mol. Biol., 258, 107-134.
6. Lukyanov,S.A., Gurskaya,N.G., Lukyanov,K.A., Tarabykin,V.S. and Sverdlov,E.D. (1994) Highly efficient subtractive hybridization of cDNA. J. Bioorg. Chem., 20, 386-388.
7. Gurskaya,N.G., Diatchenko,L., Chenchik,A., Siebert,P.D., Khaspekov,G.L., Lukyanov,K.A., Vagner,L.L., Ermolaeva,O.D., Lukyanov,S.A. and Sverdlov,E.D. (1996) Equalizing cDNA subtraction based on selective suppression of polymerase chain reaction: Cloning of Jurkat cell transcripts induced by phytohemaglutinin and phorbol 12-myristate 13-acetate. Anal. Biochem., 240, 90-97.
8. Diatchenko,L., Lau,Y.F., Campbell,A.P., Chenchik,A., Moqadam,F., Huang,B., Lukyanov,S., Lukyanov,K., Gurskaya,N., Sverdlov,E.D. and Siebert,P.D. (1996) Suppression subtractive hybridization: A method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proc. Natl Acad. Sci. USA, 93, 6025-6030.
9. Harms,C., Kase,M. and Hildebrandt,A. (2002) Characterization of minute differences between genomes of strains of Penicillium nal giovense using subtractive suppression hybridization without cloning. Lett. Appl. Microbiol., 35, 113-116.
10. Stocki,S.L., Babiuk,L.A., Rawlyk,N.A., Potter,A.A. and Allan,B.J. (2002) Identification of genomic differences between Escherichia coli strains pathogenic for poultry and E.coli K-12MG1655 using suppression subtractive hybridization analysis. Microb. Pathog., 33, 289-298.
11. Harakava,R. and Gabriel,D.W. (2003) Genetic differences between two strains of Xylella fastidiosa revealed by suppression subtractive hybridization. Appl. Environ. Microbiol., 69, 1315-1319.
12. Dai,Z., Mao,X., Magnuson,J.K. and Lasure,L.L. (2004) Identification of genes associated with morphology in Aspergillus niger by using suppression subtractive hybridization. Appl. Environ. Microbiol., 70, 2474-2485.
13. Hsieh,W.J. and Pan,M.J. (2004) Identification Leptospira santarosai serovar shermani specific sequences by suppression subtractive hybridization. FEMS Microbiol. Lett., 235, 117-124.
14. Galbraith,E.A., Antonopoulos,D.A. and White,B.A. (2004) Suppressive subtractive hybridization as a tool for identifying genetic diversity in an environmental metagenome: The rumen as a model. Environ. Microbiol., 6, 928-937.
15. Rishi,A.S., Munir,S., Kapur,V., Nelson,N.D. and Goyal,A. (2004) Identification and analysis of safener-inducible expressed sequence tags in Populus using a cDNA microarray. Planta, 220, 296-306.
16. Pomati,F., Burns,B.P. and Neilan,B.A. (2004) Identification of an Na(+)-dependent transporter associated with saxitoxin-producing strains of the cyanobacterium Anabaena circinalis. Appl. Environ. Microbiol., 70, 4711-4719.
17. Munir,S., Singh,S., Kaur,K. and Kapur,V. (2004) Suppression subtractive hybridization coupled with microarray analysis to examine differential expression of genes in virus infected cells. Biol. Proced. Online, 6, 94-104.
18. Li,T.X., Wang,J., Bai,Y., Sun,X. and Lu,Z. (2004) A novel method for screening species-specific gDNA probes for species identification. Nucleic Acids Res., 32, e45.
19. Greene,E.A. and Voordouw,G. (2003) Analysis of environmental microbial communities by reverse sample genome probing. J. Microbiol. Methods, 53, 211-219.
20. Dorris,D.R., Ramakrishnan,R., Trakas,D., Dudzik,F., Belval,R., Zhao,C., Nguyen,A., Domanus,M. and Mazumder,A. (2002) A highly reproducible, linear, and automated sample preparation method for DNA microarrays. Genome Res., 12, 976-984.
21. Yeates,C., Gillings,M.R., Davison,A.D., Altavilla,N. and Veal,D.A. (1998) Methods for microbial DNA extraction from soil for PCR amplification. Biol. Proced. Online, 1, 40-47.
22. Chang,Y.-H., Kim,J.-K., Kim,H.-J., Kim,W.-Y., Kim,Y.-B. and Park,Y.-H. (2001) Selection of a potential probiotic Lactobacillus strain and subsequent in vivo studies. Antonie Van Leeuwenhoek, 80, 193-199.
23. Rhee,S.K., Liu,X., Wu,L., Chong,S.C., Wan,X. and Zhou,J. (2004) Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol., 70, 4303-4317.
24. Zong,Y., Wang,Y., Zhang,S. and Shi,Y. (2003) How to evaluate a microarray scanner. In Hardiman,G. (ed.), Microarrays Methods and Applications: Nuts & Bolts. DNA press, LLC, pp. 97-114.
25. Yoon,J.H., Lee,S.T. and Park,Y.H. (1998) Inter- and intraspecific phylogenetic analysis of the genus Nocardioides and related taxa based on 16S rDNA sequences. Int. J. Syst. Bacteriol., 48, 187-194.
26. Yoon,J.H., Kim,H., Kim,I.G., Kang,K.H. and Park,Y.H. (2003) Erythrobacter flavus sp. nov., a slight halophile from the East Sea in Korea. Int. J. Syst. Evol. Microbiol., 53, 1169-1174.
27. Thompson,J.D., Gibson,T.J., Plewniak,F., Jeanmougin,F. and 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.
28. Saitou,N. and Nei,M. (1987) The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol. Biol. Evol., 4, 406-425.
29. Kumar,S., Tamura,K., Jakobsen,I.B. and Nei,M. (2001) MEGA2: Molecular evolutionary genetics analysis software. Bioinformatics, 17, 1244-1245.
30. Ezaki,T., Kawamura,Y. and Yabuuchi,E. (2000) Recognition of nomenclatural standing of Salmonella typhi (Approved Lists 1980), Salmonella enteritidis (Approved Lists 1980) and Salmonella typhimurium (Approved Lists 1980), and conservation of the specific epithets enteritidis and typhimurium. Request for an opinion. Int. J. Syst. Evol. Microbiol., 50, 945-947.
31. Crosa,J.H., Brenner,D.J., Ewing,W.H. and Falkow,S. (1973) Molecular relationship among the Salmonella. J. Bacteriol., 115, 307-315.
32. Christensen,H., Nordentoft,S. and Olsen,J.E. (1998) Phylogenetic relationships of Salmonella based on rRNA sequences. Int. J. Syst. Bacteriol., 48, 605-610.
33. Stoleru,G.H., Le Minor,L. and Lheritier,M. (1976) Polynucleotide sequence divergence among strains of Salmonella subgenus IV and closely related organisms. Ann. Microbiol., 127, 447-486.
34. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
35. Herikstad,H., Motarjemi,Y. and Tauxe,R.V. (2002) Salmonella surveillance: A global survey of public health serotyping. Epidemiol Infect., 129, 1-8.
36. Le Minor,L. (1991) The Genus Salmonella. 2nd edn. Springer-Verlag, NY.
37. Le Minor,L. (1988) Typing of Salmonella species. Eur. J. Clin. Microbiol. Infect. Dis., 7, 214-218.
38. Farber,J.M. (1996) An introduction to the hows and whys of molecular typing. J. Food Prot., 59, 1091-1101.
39. Kuipers,O.P. (1999) Genomics for food biotechnology: Prospects of the use of high-throughput technologies for the improvement of food microorganisms. Curr. Opin. Biotechnol., 10, 511-516.
40. Porwollik,S., Wong,R.M. and McClelland,M. (2002) Evolutionary genomics of Salmonella: Gene acquisitions revealed by microarray analysis. Proc. Natl Acad. Sci. USA, 99, 8956-8961.
41. Panicker,G., Call,D.R., Krug,M.J. and Bej,A.K. (2004) Detection of pathogenic Vibrio spp. in shellfish by using multiplex PCR and DNA microarrays. Appl. Environ. Microbiol., 70, 7436-7444.
42. Call,D.R., Borucki,M.K. and Loge,F.J. (2003) Detection of bacterial pathogens in environmental samples using DNA microarrays. J. Microbiol. Methods, 53, 235-243.
43. Dahllof,I. (2002) Molecular community analysis of microbial diversity. Curr. Opin. Biotechnol., 13, 213-217.
44. Kakinuma,K., Fukushima,M. and Kawaguchi,R. (2003) Detection and identification of Escherichia coli, Shigella, and Salmonella by microarrays using the gyrB gene. Biotechnol. Bioeng., 83, 721-728.