References
- Bae, J. W., S. K. Rhee, J. R. Park, W. H. Chung, Y. D. Nam, I. Lee, H. Kim, and Y. H. Park. 2005. Development and evaluation of genome-probing microarrays for monitoring lactic acid bacteria. Appl. Environ. Microbiol. 71: 8825- 8835 https://doi.org/10.1128/AEM.71.12.8825-8835.2005
- Brenner, D. J., G. R. Fanning, F. J. Skerman, and S. Falkow. 1972. Polynucleotide sequence divergence among strains of Escherichia coli and closely related organisms. J. Bacteriol. 3: 953-965
- Crosa, J. H., D. J. Brenner, W. H. Ewing, and S. Falkow. 1973. Molecular relationships among the Salmonelleae. J. Bacteriol. 115: 307-315
- Dorris, D. R., R. Ramakrishnan, D. Trakas, F. Dudzik, R. Belval, C. Zhao, A. Nguyen, M. Domanus, and A. Mazumder. 2002. A highly reproducible, linear, and automated sample preparation method for DNA microarrays. Genome Res. 12: 976-984 https://doi.org/10.1101/gr.227402
- Fukushima, M., K. Kakinuma, H. Hayashi, H. Nagai, K. Ito, and R. Kawaguchi. 2003. Detection and identification of Mycobacterium species isolates by DNA microarray. J. Clin. Microbiol. 41: 2605-2615 https://doi.org/10.1128/JCM.41.6.2605-2615.2003
- Girke, T., J. Todd, S. Ruuska, J. White, C. Benning, and J. Ohlrogge. 2000. Microarray analysis of developing Arabidopsis seeds. Plant Physiol. 124: 1570-1581 https://doi.org/10.1104/pp.124.4.1570
- Gogarten, J. P. and J. P. Townsend. 2005. Horizontal gene transfer, genome innovation and evolution. Nat. Rev. Microbiol. 3: 679-687 https://doi.org/10.1038/nrmicro1204
- Grimont, P. A. D., M. Y. Popoff, F. Grimont, C. Coynault, and M. Lemelin. 1980. Reproducibility and correlation study of three deoxyribonucleic acid hybridization procedures. Curr. Microbiol. 4: 325-330 https://doi.org/10.1007/BF02605371
- Hwang, K. O. and J. C. Cho. 2006. Evaluation of DNA microarray approach for identifying strain-specific genes. J. Microbiol. Biotechnol. 16:1773-1777
- Kim, B. S., S. J. Kang, S. B. Lee, W. Hwang, and K. S. Kim. 2005. Simple method to correct gene-specific dye bias from partial dye swap information of a DNA microarray experiment. J. Microbiol. Biotechnol. 15: 1377-1383
- Kim, I. S., H. S. Yun, H. Shimisu, E. Kitagawa, H. Iwahashi, and I. Jin. 2005. Elucidation of copper and asparagine transport systems in Saccharomyces cerevisiae KNU5377 through genome-wide transcriptional analysis. J. Microbiol. Biotechnol. 15: 1240-1249
- Konstantinidis, K. T. and J. M. Tiedje. 2005. Towards a genome-based taxonomy for prokaryotes. J. Bacteriol. 187: 6258-6264 https://doi.org/10.1128/JB.187.18.6258-6264.2005
- Loy, A., A. Lehner, N. Lee, J. Adamczyk, H. Meier, J. Ernst, K. H. Schleifer, and M. Wagner. 2002. Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl. Environ. Microbiol. 68: 5064-5081 https://doi.org/10.1128/AEM.68.10.5064-5081.2002
- Maynard, S. J. 1995. Do Bacteria Have Population Genetics? Cambridge University Press, Cambridge
- Oh, M. K., M. J. Cha, S. G. Lee, L. Rohlin, and J. C. Liao. 2006. Dynamic gene expression profiling of Escherichia coli in carbon source transition from glucose to acetate. J. Microbiol. Biotechnol. 14: 543-549
- Paster, B. J. and F. E. Dewhirst. 1988. Phylogeny of campylobacters, wolinellas, Bacteroides gracilis, and Bacteroides ureolyticus by 16S ribosomal ribonucleic acid sequencing. Int. J. Syst. Bacteriol. 38: 56-62 https://doi.org/10.1099/00207713-38-1-56
- Qi, J., B. Wang, and B. I. Hao. 2004. Whole proteome prokaryote phylogeny without sequence alignment: A Kstring composition approach. J. Mol. Evol. 58: 1-11 https://doi.org/10.1007/s00239-003-2493-7
- Rhee, S. K., X. Liu, L. Wu, S. C. Chong, X. Wan, and J. Zhou. 2004. Detection of genes involved in biodegradation and biotransformation in microbial communities by using 50-mer oligonucleotide microarrays. Appl. Environ. Microbiol. 70: 4303-4317 https://doi.org/10.1128/AEM.70.7.4303-4317.2004
- Rocap, G., F. W. Larimer, J. Lamerdin, S. Malfatti, P. Chain, N. A. Ahlgren, A. Arellano, M. Coleman, L. Hauser, W. R. Hess, Z. I. Johnson, M. Land, D. Lindell, A. F. Post, W. Regala, M. Shah, S. L. Shaw, C. Steglich, M. B. Sullivan, C. S. Ting, A. Tolonen, E. A. Webb, E. R. Zinser, and S. W. Chisholm. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047 https://doi.org/10.1038/nature01947
- Roop, R. M., R. M. Smibert, J. L. Johnson, and N. R. Krieg. 1984. Differential characteristics of catalase-positive campylobacters correlated with DNA homology groups. Can. J. Microbiol. 30: 938-951 https://doi.org/10.1139/m84-147
- Roop, R. M., R. M. Smibert, J. L. Johnson, and N. R. Krieg. 1994. DNA homology studies of the catalase-negative campylobacters and Campylobacter fecalis, an emended description of Campylobacter sputorum, and proposal of the neotype strain of Campylobacter sputorum. Can. J. Microbiol. 31: 846-849
- Rossello-Mora, R. and R. Amann. 2001. The species concept for prokaryotes. FEMS Microbiol. Rev. 25: 39-67 https://doi.org/10.1111/j.1574-6976.2001.tb00571.x
- Somerville, H. J. and M. L. Jones. 1972. DNA competition studies within the Bacillus cereus group of bacilli. J. Gen. Microbiol. 73: 257-265 https://doi.org/10.1099/00221287-73-2-257
- Stackebrandt, E. and B. M. Goebel. 1994. Taxonomic note: 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 https://doi.org/10.1099/00207713-44-4-846
- Taroncher-Oldenburg, G., E. M. Griner, C. A. Francis, and B. B. Ward. 2003. Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl. Environ. Microbiol. 69: 1159-1171 https://doi.org/10.1128/AEM.69.2.1159-1171.2003
- Ursing, J., M. Walder, and K. Sandstedt. 1983. Base composition and sequence homology of deoxyribonucleic acid of thermotolerant Campylobacter from human and animal sources. Curr. Microbiol. 8: 307-310 https://doi.org/10.1007/BF01577733
- Vandamme, P., E. Falsen, R. Rossau, B. Hoste, P. Segers, R. Tytgat, and J. D. Ley. 1991. Revision of Campylobacter, Helicobacter, and Wolinella taxonomy: Emendation of generic descriptions and proposal of Arcobacter gen. nov. Int. J. Syst. Bacteriol. 41: 88-103 https://doi.org/10.1099/00207713-41-1-88
- Wayne, L.G., D. J. Brenner, R. R. Colwell, P. A. D. Grimont, O. Kandler, M. I. Krichevsky, L. H. Moore, W. E. C. Moore, R. G. E. Murray, E. Stackebrandt, M. P. Starr, and H. G. Trüper. 1987. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int. J. Syst. Bacteriol. 37: 463-464 https://doi.org/10.1099/00207713-37-4-463
- Wu, L., D. K. Thompson, G. Li, R. A. Hurt, J. M. Tiedje, and J. Zhou. 2001. Development and evaluation of functional gene arrays for detection of selected genes in the environment. Appl. Environ. Microbiol. 67: 5780-5790 https://doi.org/10.1128/AEM.67.12.5780-5790.2001
- Wu, L., D. K. Thompson, X. Liu, M. W. Fields, C. E. Bagwell, J. M. Tiedje, and J. Zhou. 2004. Development and evaluation of microarray-based whole-genome hybridization for detection of microorganisms within the context of environmental applications. Environ. Sci. Technol. 38: 6775- 6782 https://doi.org/10.1021/es049508i
- Wu, X., X. F. Wan, G. Wu, D. Xu, and G. Lin. 2006. Whole genome phylogeny via complete composition vectors. Int. J. Bioinform. Res. Applic. 2: 219-248 https://doi.org/10.1504/IJBRA.2006.010602
- Xu, W., S. Bak, A. Decker, S. M. Paquette, R. Feyereisen, and D. W. Galbraith. 2001. Microarray-based analysis of gene expression in very large gene families: The cytochrome P450 gene superfamily of Arabidopsis thaliana. Gene 272: 61-74 https://doi.org/10.1016/S0378-1119(01)00516-9
- Zhang, L., U. Srinivasan, C. F. Marrs, D. Ghosh, J. R. Gilsdorf, and B. Foxman. 2004. Library on a slide for bacterial comparative genomics. BMC Microbiol. 4: 12 https://doi.org/10.1186/1471-2180-4-12
- Zhou, J. and D. K. Thompson. 2002. Challenges in applying microarrays to environmental studies. Curr. Opin. Biotechnol. 13: 204-207 https://doi.org/10.1016/S0958-1669(02)00319-1