JBiSE  Vol.2 No.6 , October 2009
A MCMC strategy for group-specific 16S rRNA probe design
Abstract: Revealing biodiversity in microbial communities is essential in metagenomics researches. With thousands of sequenced 16S rRNA gene available, and advancements in oligonucleotide microarray technology, the detection of microor-ganisms in microbial communities consisting of hundreds of species may be possible. Many of the existing strategies developed for oligonucleotide probe design are dependent on the result of global multiple sequences alignment, which is a time-consuming task. We present a novel program named OligoSampling that uses MCMC method to design group-specific oli-gonucleotide probes. The probes generated by OligoSampling are group specific with weak crosshybridization potentials. Furthermore a high coverage of target sequences can be obtained. Our method does not need to globally align target sequences. Locally aligning target sequences iteratively based on a Gibbs sampling strategy has the same effect as globally aligning sequences in the process of seeking group-specific probes. OligoSampling provides more flexibility and speed than other software programs based on global multiple sequences alignment.
Cite this paper: nullWu, Y. , Yan, L. , Liu, H. , Sun, H. and Xie, H. (2009) A MCMC strategy for group-specific 16S rRNA probe design. Journal of Biomedical Science and Engineering, 2, 412-418. doi: 10.4236/jbise.2009.26059.

[1]   S. R. Gill, M. Pop, R. T. Deboy, P. B. Eckburg, P. J. Turn-baugh, B. S. Samuel, J. I. Gordon, D. A. Relman, C. M. Fra-ser-Liggett, and K. E. Nelson, (2006) Metagenomic analysis of the human distal gut microbiome, Science, 312, 1355–1359.

[2]   E. Pennisi, (2007) Metagenomics, massive microbial sequence project proposed, Science, 315, 1781. A. Jurkowski, A. H. Reid, and J. B. Labov, (2007) Metage-nomics: A call for bringing a new science into the classroom (while it’s still new), CBE Life Sci. Educ., 6, 260–265.

[3]   P. J. Turnbaugh, R. E. Ley, M. Hamady, C. M. Fraser-Liggett, R. Knight, and J. I. Gordon, (2007) The human microbiome project, Nature, 449, 804–810.

[4]   P. B. Eckburg, E. M. Bik, C. N. Bernstein, E. Purdom, L. Dethlefsen, M. Sargent, S. R. Gill, K. E. Nelson, and D. A. Relman, (2005) Diversity of the human intestinal microbial flora, Science, 308, 1635–1638.

[5]   S. C. Lau and W. T. Liu, (2007) Recent advances in molecular techniques for the detection of phylogenetic markers and func-tional genes in microbial communities, FEMS Microbiol Lett., 275, 183–190.

[6]   S. P. Fodor, J. L. Read, M. C. Pirrung, L. Stryer, A. T. Lu, and D. Solas, (1991) Light-directed, spatially addressable parallel chemical synthesis, Science, 251, 767–773.

[7]   S. P. Fodor, R. P. Rava, X. C. Huang, A. C. Pease, C. P. Holmes, and C. L. Adams, (1993) Multiplexed biochemical assays with biological chips, Nature, 364, 555– 556.

[8]   A. C. Pease, D. Solas, E. J. Sullivan, M. T. Cronin, C. P. Holmes, and S. P. Fodor, (1994) Light-generated oligonucleo-tide arrays for rapid DNA sequence analysis, Proc. Natl. Acad. Sci., USA, 91, 5022–5026.

[9]   R. W. Ye, T. Wang, L. Bedzyk, and K. M. Croker, (2001) Ap-plications of DNA microarrays in microbial systems, J. Micro-biol Methods, 47, 257–272.

[10]   A. E. Warsen, M. J. Krug, S. LaFrentz, D. R. Stanek, F. J. Loge, and D. R. Call, (2004) Simultaneous discrimination between 15 fish pathogens by using 16S ribosomal DNA PCR and DNA microarrays, Appl. Environ. Microbiol., 70, 4216–4221.

[11]   D. Z. Jin, S. Y. Wen, S. H. Chen, F. Lin, and S. Q. Wang, (2006) Detection and identification of intestinal pathogens in clinical specimens using DNA microarrays, Mol Cell Probes, 20, 337–347.

[12]   D. Harmsen, C. Singer, J. Rothganger, T. Tonjum, G. S. de Hoog, H. Shah, J. Albert, and M. Frosch, (2001) Diagnostics of neisseriaceae and moraxellaceae by ribosomal DNA sequenc-ing: Ribosomal differentiation of medical microorganisms, J. Clin. Microbiol., 39, 936– 942.

[13]   C. P. Sun, J. C. Liao, Y. H. Zhang, V. Gau, M. Mastali, J. T. Babbitt, W. S. Grundfest, B. M. Churchill, E. R. McCabe, and D. A. Haake, (2005) Rapid, species-specific detection of uro-pathogen 16S rDNA and rRNA at ambient temperature by dot-blot hybridization and an electrochemical sensor array, Mol. Genet. Metab., 84, 90– 99.

[14]   J. K. Loy, F. E. Dewhirst, W. Weber, P. F. Frelier, T. L. Garbar, S. I. Tasca, and J. W. Templeton, (1996) Molecular phylogeny and in situ detection of the etiologic agent of necrotizing hepa-topancreatitis in shrimp, Appl. Environ. Microbiol., 62, 3439–3445.

[15]   B. X. Hong, L. F. Jiang, Y. S. Hu, D.Y. Fang, and H. Y. Guo, (2004) Application of oligonucleotide array technology for the rapid detection of pathogenic bacteria of foodborne infections, J. Microbiol Methods, 58, 403– 411.

[16]   W. Deng, D. Xi, H. Mao, and M. Wanapat, (2007) The use of molecular techniques based on ribosomal RNA and DNA for rumen microbial ecosystem studies: A review, Mol. Biol. Rep.

[17]   G. Taroncher-Oldenburg and B. B. Ward, (2007) Oligonucleo-tide microarrays for the study of coastal microbial communi-ties, Methods Mol. Biol., 353, 301–315.

[18]   C. R. Kuske, S. M. Barns, C. C. Grow, L. Merrill, and J. Dun-bar, (2006) Environmental survey for four pathogenic bacteria and closely related species using phylogenetic and functional genes, J. Forensic. Sci., 51, 548–558.

[19]   D. R. Call, (2005) Challenges and opportunities for pathogen detection using DNA microarrays, Crit. Rev. Microbiol., 31, 91–99.

[20]   T. Mohammadi, P. H. Savelkoul, R. N. Pietersz, and H. W. Reesink, (2006) Applications of real-time PCR in the screening of platelet concentrates for bacterial contamination, Expert Rev. Mol. Diagn., 6, 865–872.

[21]   L. Bodrossy and A. Sessitsch, (2004) Oligonucleotide mi-croarrays in microbial diagnostics, Curr. Opin. Microbiol., 7, 245–254.

[22]   K. Lemarchand, L. Masson, and R. Brousseau, (2004) Mo-lecular biology and DNA microarray technology for microbial quality monitoring of water, Crit. Rev. Microbiol., 30, 145–172.

[23]   L. Kaderali and A. Schliep, (2002) Selecting signature oli-gonucleotides to identify organisms using DNA arrays. Bioin-formatics, 18, 1340–1349.

[24]   A. Loy, M. Horn, and M. Wagner, (2003) ProbeBase: An online resource for rRNA-targeted oligonucleotide probes, Nucleic. Acids. Res., 31, 514–516.

[25]   Y. Kumar, R. Westram, P. Kipfer, H. Meier, and W. Ludwig, (2006) Evaluation of sequence alignments and oligonucleotide probes with respect to three-dimensional structure of ribosomal RNA using ARB software package, BMC Bioinformatics, 7, 240.

[26]   T. Z. DeSantis, I. Dubosarskiy, S. R. Murray, and G. L. Ander-sen, (2003) Comprehensive aligned sequence construction for automated design of effective probes (CASCADE-P) using 16S Rdna, Bioinformatics, 19, 1461– 1468.

[27]   T. Z. DeSantis, P. Hugenholtz, K. Keller, E. L. Brodie, N. Lar-sen, Y. M. Piceno, R. Phan, and G. L. Andersen, (2006) NAST: A multiple sequence alignment server for comparative analysis of 16S rRNA genes, Nucleic. Acids. Res., 34, 394–399.

[28]   C. E. Lawrence, S. F. Altschul, M. S. Boguski, J. S. Liu, A. F. Neuwald, and J. C. Wootton, (1993) Detecting subtle sequence signals: A gibbs sampling strategy for multiple alignment, Sci-ence, 262, 208–214.

[29]   B. L. Maidak, J. R. Cole, T. G. Lilburn, C. T. Parker, P. R. Saxman, R. J. Farris, G. M. Garrity, G. J. Olsen, T. M. Schmidt, and J. M. Tiedje, (2001) The RDP-II (Ribosomal Database Project), Nucleic. Acids. Res., 29, 173– 174

[30]   A. Pozhitkov, P. A. Noble, T. Domazet-Loso, A. W. Nolte, R. Sonnenberg, P. Staehler, M. Beier, and D. Tautz, (2006) Tests of rRNA hybridization to microarrays suggest that hybridiza-tion characteristics of oligonucleotide probes for species dis-crimination cannot be predicted, Nucleic. Acids. Res., 34, 66.