Detecting unknown sequences with DNA microarrays: Explorative probe design strategies

Environmental Microbiology

Volumn 14, Issue 2, 2012, Pages 356-371

  Dugat Bony, Eric ^a,b   Peyretaillade, Eric ^a,b   Parisot, Nicolas ^a,b   Biderre Petit, Corinne ^a,b   Jaziri, Faouzi ^a,c   Hill, David ^a,c   Rimour, Sébastien ^a,b   Peyret, Pierre ^a,b  

^a UNIVERSITÉ CLERMONT AUVERGNE   (France)

^b UNIVERSITÉ BLAISE PASCAL   (France)

^c UNIVERSITÉ BLAISE PASCAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ARCHAEON; BACTERIUM; CLASSIFICATION; DNA MICROARRAY; DNA PROBE; FUNGUS; GENE EXPRESSION PROFILING; GENETICS; METHODOLOGY; PHYLOGENY; REVIEW; SENSITIVITY AND SPECIFICITY;

ARCHAEA; BACTERIA; DNA PROBES; FUNGI; GENE EXPRESSION PROFILING; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PHYLOGENY; SENSITIVITY AND SPECIFICITY;

EID: 83655202427     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2011.02559.x     Document Type: Review

References (139)

1. Albert, T.J., Molla, M.N., Muzny, D.M., Nazareth, L., Wheeler, D., Song, X., etal. (2007) Direct selection of human genomic loci by microarray hybridization. Nat Methods 4: 903-905.
2. Amann, R., Ludwig, W., and Schleifer, K. (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143-169.
3. Ashelford, K.E., Weightman, A.J., and Fry, J.C. (2002) PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database. Nucleic Acids Res 30: 3481-3489.
4. Bae, J.W., and Park, Y.H. (2006) Homogeneous versus heterogeneous probes for microbial ecological microarrays. Trends Biotechnol 24: 318-323.
5. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., and Sayers, E.W. (2011) GenBank. Nucleic Acids Res 39: D32-D37.
6. Bers, K., Sniegowski, K., Albers, P., Breugelmans, P., Hendrickx, L., De Mot, R., and Springael, D. (2011) A molecular toolbox to estimate the number and diversity of Variovorax in the environment: application in soils treated with the phenylurea herbicide linuron. FEMS Microbiol Ecol 76: 14-25.
7. Blaskovic, D., and Barak, I. (2005) Oligo-chip based detection of tick-borne bacteria. FEMS Microbiol Lett 243: 473-478.
8. Bodrossy, L., Stralis-Pavese, N., Murrell, J.C., Radajewski, S., Weilharter, A., and Sessitsch, A. (2003) Development and validation of a diagnostic microbial microarray for methanotrophs. Environ Microbiol 5: 566-582.
9. Boeckaert, C., Vlaeminck, B., Fievez, V., Maignien, L., Dijkstra, J., and Boon, N. (2008) Accumulation of trans C18:1 fatty acids in the rumen after dietary algal supplementation is associated with changes in the Butyrivibrio community. Appl Environ Microbiol 74: 6923-6930.
10. van den Bogert, B., de Vos, W.M., Zoetendal, E.G., and Kleerebezem, M. (2011) Microarray Analysis and Barcoded Pyrosequencing Provide Consistent Microbial Profiles Depending on the Source of Human Intestinal Samples. Appl Environ Microbiol 77: 2071-2080.
11. Bommarito, S., Peyret, N., and SantaLucia, J., Jr (2000) Thermodynamic parameters for DNA sequences with dangling ends. Nucleic Acids Res 28: 1929-1934.
12. Bontemps, C., Golfier, G., Gris-Liebe, C., Carrere, S., Talini, L., and Boivin-Masson, C. (2005) Microarray-based detection and typing of the Rhizobium nodulation gene nodC: potential of DNA arrays to diagnose biological functions of interest. Appl Environ Microbiol 71: 8042-8048.
13. Boyce, R., Chilana, P., and Rose, T.M. (2009) iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences. Nucleic Acids Res 37: W222-W228.
14. Bozdech, Z., Zhu, J., Joachimiak, M.P., Cohen, F.E., Pulliam, B., and DeRisi, J.L. (2003) Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray. Genome Biol 4: R9.
15. Brodie, E.L., Desantis, T.Z., Joyner, D.C., Baek, S.M., Larsen, J.T., Andersen, G.L., etal. (2006) Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidation. Appl Environ Microbiol 72: 6288-6298.
16. Brodie, E.L., DeSantis, T.Z., Parker, J.P., Zubietta, I.X., Piceno, Y.M., and Andersen, G.L. (2007) Urban aerosols harbor diverse and dynamic bacterial populations. Proc Natl Acad Sci USA 104: 299-304.
17. Candela, M., Consolandi, C., Severgnini, M., Biagi, E., Castiglioni, B., Vitali, B., etal. (2010) High taxonomic level fingerprint of the human intestinal microbiota by ligase detection reaction - universal array approach. BMC Microbiol 10: 116.
18. Castiglioni, B., Rizzi, E., Frosini, A., Sivonen, K., Rajaniemi, P., Rantala, A., etal. (2004) Development of a universal microarray based on the ligation detection reaction and 16S rrna gene polymorphism to target diversity of cyanobacteria. Appl Environ Microbiol 70: 7161-7172.
19. Chandler, D.P., and Jarrell, A.E. (2005) Taking arrays from the lab to the field: trying to make sense of the unknown. Biotechniques 38: 591-600.
20. Chou, C.C., Chen, C.H., Lee, T.T., and Peck, K. (2004) Optimization of probe length and the number of probes per gene for optimal microarray analysis of gene expression. Nucleic Acids Res 32: e99.
21. Chung, W.-H., Rhee, S.-K., Wan, X.-F., Bae, J.-W., Quan, Z.-X., and Park, Y.-H. (2005) Design of long oligonucleotide probes for functional gene detection in a microbial community. Bioinformatics 21: 4092-4100.
22. Claesson, M.J., O'Sullivan, O., Wang, Q., Nikkilä, J., Marchesi, J.R., Smidt, H., etal. (2009) Comparative Analysis of Pyrosequencing and a Phylogenetic Microarray for Exploring Microbial Community Structures in the Human Distal Intestine. PLoS ONE 4: e6669.
23. Cochrane, G., Akhtar, R., Bonfield, J., Bower, L., Demiralp, F., Faruque, N., etal. (2009) Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res 37: D19-D25.
24. Cole, J.R., Wang, Q., Cardenas, E., Fish, J., Chai, B., Farris, R.J., etal. (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37: D141-D145.
25. Cruz-Martinez, K., Suttle, K.B., Brodie, E.L., Power, M.E., Andersen, G.L., and Banfield, J.F. (2009) Despite strong seasonal responses, soil microbial consortia are more resilient to long-term changes in rainfall than overlying grassland. ISME J 3: 738-744.
26. Curtis, T.P., Sloan, W.T., and Scannell, J.W. (2002) Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 99: 10494-10499.
27. Darling, A., Carey, L., and Feng, W. (2003) The Design, Implementation, and Evaluation of mpiBLAST. In: 4th International Conference on Linux Clusters: The HPC Revolution 2003. San Jose, California
28. DeAngelis, K.M., Brodie, E.L., DeSantis, T.Z., Andersen, G.L., Lindow, S.E., and Firestone, M.K. (2009) Selective progressive response of soil microbial community to wild oat roots. ISME J 3: 168-178.
29. Delmont, T.O., Robe, P., Cecillon, S., Clark, I.M., Constancias, F., Simonet, P., etal. (2011) Accessing the soil metagenome for studies of microbial diversity. Appl Environ Microbiol 77: 1315-1324.
30. DeSantis, T.Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E.L., Keller, K., etal. (2006) Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB. Appl Environ Microbiol 72: 5069-5072.
31. DeSantis, T.Z., Brodie, E.L., Moberg, J.P., Zubieta, I.X., Piceno, Y.M., and Andersen, G.L. (2007) High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb Ecol 53: 371-383.
32. Duc, L., Neuenschwander, S., Rehrauer, H., Wagner, U., Sobek, J., Schlapbach, R., and Zeyer, J. (2009) Development and experimental validation of a nifH oligonucleotide microarray to study diazotrophic communities in a glacier forefield. Environ Microbiol 11: 2179-2189.
33. Dufva, M. (2005) Fabrication of high quality microarrays. Biomol Eng 22: 173-184.
34. Dugat-Bony, E., Missaoui, M., Peyretaillade, E., Biderre-Petit, C., Bouzid, O., Gouinaud, C., etal. (2011) HiSpOD: probe design for functional DNA microarrays. Bioinformatics 27: 641-648.
35. Ehrenreich, A. (2006) DNA microarray technology for the microbiologist: an overview. Appl Microbiol Biotechnol 73: 255-273.
36. Emrich, S.J., Lowe, M., and Delcher, A.L. (2003) PROBEmer: A web-based software tool for selecting optimal DNA oligos. Nucleic Acids Res 31: 3746-3750.
37. Evertsz, E.M., Au-Young, J., Ruvolo, M.V., Lim, A.C., and Reynolds, M.A. (2001) Hybridization cross-reactivity within homologous gene families on glass cDNA microarrays. Biotechniques 31: 1182. 1184, 1186 passim.
38. Feldhaar, H., Straka, J., Krischke, M., Berthold, K., Stoll, S., Mueller, M.J., and Gross, R. (2007) Nutritional upgrading for omnivorous carpenter ants by the endosymbiont Blochmannia. BMC Biol 5: 48.
39. Feng, S., and Tillier, E.R.M. (2007) A fast and flexible approach to oligonucleotide probe design for genomes and gene families. Bioinformatics 23: 1195-1202.
40. Flanagan, J.L., Brodie, E.L., Weng, L., Lynch, S.V., Garcia, O., Brown, R., etal. (2007) Loss of bacterial diversity during antibiotic treatment of intubated patients colonized with Pseudomonas aeruginosa. J Clin Microbiol 45: 1954-1962.
41. Franke-Whittle, I.H., Goberna, M., Pfister, V., and Insam, H. (2009) Design and development of the ANAEROCHIP microarray for investigation of methanogenic communities. J Microbiol Methods 79: 279-288.
42. Fraune, S., Augustin, R., Anton-Erxleben, F., Wittlieb, J., Gelhaus, C., Klimovich, V.B., etal. (2010) In an early branching metazoan, bacterial colonization of the embryo is controlled by maternal antimicrobial peptides. Proc Natl Acad Sci USA 107: 18067-18072.
43. Gans, J., Wolinsky, M., and Dunbar, J. (2005) Computational improvements reveal great bacterial diversity and high metal toxicity in soil. Science 309: 1387-1390.
44. Gardner, M.K., Feng, W.-C., Archuleta, J., Lin, H., and Ma, X. (2006) Parallel genomic sequence-searching on an ad-hoc grid: experiences, lessons learned, and implications. In Proceedings of the 2006 ACM/IEEE Conference on Supercomputing. SC Conference (ed.). Tampa, Florida: ACM, pp. 22.
45. Gentry, T., Wickham, G., Schadt, C., He, Z., and Zhou, J. (2006) Microarray Applications in Microbial Ecology Research. Microb Ecol 52: 159-175.
46. Gittel, A., Sorensen, K.B., Skovhus, T.L., Ingvorsen, K., and Schramm, A. (2009) Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment. Appl Environ Microbiol 75: 7086-7096.
47. Guerrero, R., and Berlanga, M. (2006) Life's unity and flexibility: the ecological link. Int Microbiol 9: 225-235.
48. He, Z., Gentry, T.J., Schadt, C.W., Wu, L., Liebich, J., Chong, S.C., etal. (2007) GeoChip: a comprehensive microarray for investigating biogeochemical, ecological and environmental processes. ISME J 1: 67-77.
49. He, Z., Deng, Y., Van Nostrand, J.D., Tu, Q., Xu, M., Hemme, C.L., etal. (2010) GeoChip 3.0 as a high-throughput tool for analyzing microbial community composition, structure and functional activity. ISME J 4: 1167-1179.
50. He, Z., Van Nostrand, J.D., Deng, Y., and Zhou, J.Z. (2011) Development and applications of functional gene microarrays in the analysis of the functional diversity, composition, and structure of microbial communities. Front Environ Sci Engin China 5: 1-20.
51. He, Z.L., Van Nostrand, J.D., Wu, L.Y., and Zhou, J.Z. (2008) Development and application of functional gene arrays for microbial community analysis. Trans Nonferrous Met Soc China 18: 1319-1327.
52. Hughes, T.R., Mao, M., Jones, A.R., Burchard, J., Marton, M.J., Shannon, K.W., etal. (2001) Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer. Nat Biotechnol 19: 342-347.
53. Huyghe, A., Francois, P., Charbonnier, Y., Tangomo-Bento, M., Bonetti, E.-J., Paster, B.J., etal. (2008) Novel Microarray Design Strategy To Study Complex Bacterial Communities. Appl Environ Microbiol 74: 1876-1885.
54. Kaminuma, E., Kosuge, T., Kodama, Y., Aono, H., Mashima, J., Gojobori, T., etal. (2011) DDBJ progress report. Nucleic Acids Res 39: D22-D27.
55. Kane, M.D., Jatkoe, T.A., Stumpf, C.R., Lu, J., Thomas, J.D., and Madore, S.J. (2000) Assessment of the sensitivity and specificity of oligonucleotide (50mer) microarrays. Nucleic Acids Res 28: 4552-4557.
56. Kang, S., Denman, S.E., Morrison, M., Yu, Z., Dore, J., Leclerc, M., and McSweeney, C.S. (2010) Dysbiosis of fecal microbiota in Crohn's disease patients as revealed by a custom phylogenetic microarray. Inflamm Bowel Dis 16: 2034-2042.
57. Kawasaki, E.S. (2006) The end of the microarray Tower of Babel: will universal standards lead the way? J Biomol Tech 17: 200-206.
58. Kelly, J.J., Siripong, S., McCormack, J., Janus, L.R., Urakawa, H., El Fantroussi, S., etal. (2005) DNA microarray detection of nitrifying bacterial 16S rRNA in wastewater treatment plant samples. Water Res 39: 3229-3238.
59. Kelly, L.C., Cockell, C.S., Piceno, Y.M., Andersen, G.L., Thorsteinsson, T., and Marteinsson, V. (2010) Bacterial diversity of weathered terrestrial Icelandic volcanic glasses. Microb Ecol 60: 740-752.
60. Klitgaard, K., Boye, M., Capion, N., and Jensen, T.K. (2008) Evidence of multiple Treponema phylotypes involved in bovine digital dermatitis as shown by 16S rRNA gene analysis and fluorescence in situ hybridization. J Clin Microbiol 46: 3012-3020.
61. Koltai, H., and Weingarten-Baror, C. (2008) Specificity of DNA microarray hybridization: characterization, effectors and approaches for data correction. Nucleic Acids Res 36: 2395-2405.
62. Kyselkova, M., Kopecky, J., Felfoldi, T., Cermak, L., Omelka, M., Grundmann, G.L., etal. (2008) Development of a 16S rRNA gene-based prototype microarray for the detection of selected actinomycetes genera. Antonie Van Leeuwenhoek 94: 439-453.
63. Lee, M.L., Kuo, F.C., Whitmore, G.A., and Sklar, J. (2000) Importance of replication in microarray gene expression studies: statistical methods and evidence from repetitive cDNA hybridizations. Proc Natl Acad Sci USA 97: 9834-9839.
64. Lehner, A., Loy, A., Behr, T., Gaenge, H., Ludwig, W., Wagner, M., and Schleifer, K.H. (2005) Oligonucleotide microarray for identification of Enterococcus species. FEMS Microbiol Lett 246: 133-142.
65. Leinonen, R., Akhtar, R., Birney, E., Bower, L., Cerdeno-Tarraga, A., Cheng, Y., etal. (2011) The European Nucleotide Archive. Nucleic Acids Res 39: D28-D31.
66. Lemoine, S., Combes, F., and Le Crom, S. (2009) An evaluation of custom microarray applications: the oligonucleotide design challenge. Nucleic Acids Res 37: 1726-1739.
67. Leparc, G.G., Tuchler, T., Striedner, G., Bayer, K., Sykacek, P., Hofacker, I.L., and Kreil, D.P. (2009) Model-based probe set optimization for high-performance microarrays. Nucleic Acids Res 37: e18.
68. Letowski, J., Brousseau, R., and Masson, L. (2004) Designing better probes: effect of probe size, mismatch position and number on hybridization in DNA oligonucleotide microarrays. J Microbiol Methods 57: 269-278.
69. Li, F., and Stormo, G.D. (2001) Selection of optimal DNA oligos for gene expression arrays. Bioinformatics 17: 1067-1076.
70. Li, X., He, Z., and Zhou, J. (2005) Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation. Nucleic Acids Res 33: 6114-6123.
71. Liebich, J., Schadt, C.W., Chong, S.C., He, Z., Rhee, S.K., and Zhou, J. (2006) Improvement of oligonucleotide probe design criteria for functional gene microarrays in environmental applications. Appl Environ Microbiol 72: 1688-1691.
72. Liles, M.R., Turkmen, O., Manske, B.F., Zhang, M., Rouillard, J.-M., George, I., etal. (2010) A phylogenetic microarray targeting 16S rRNA genes from the bacterial division Acidobacteria reveals a lineage-specific distribution in a soil clay fraction. Soil Biol Biochem 42: 739-747.
73. Lipshutz, R.J., Fodor, S.P., Gingeras, T.R., and Lockhart, D.J. (1999) High density synthetic oligonucleotide arrays. Nat Genet 21: 20-24.
74. Loy, A., and Bodrossy, L. (2006) Highly parallel microbial diagnostics using oligonucleotide microarrays. Clin Chim Acta 363: 106-119.
75. Loy, A., Lehner, A., Lee, N., Adamczyk, J., Meier, H., Ernst, J., etal. (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.
76. Loy, A., Schulz, C., Lucker, S., Schopfer-Wendels, A., Stoecker, K., Baranyi, C., etal. (2005) 16S rRNA gene-based oligonucleotide microarray for environmental monitoring of the betaproteobacterial order 'Rhodocyclales'. Appl Environ Microbiol 71: 1373-1386.
77. Ludwig, W., Amann, R., Martinez-Romero, E., Schönhuber, W., Bauer, S., Neef, A., and Schleifer, K.-H. (1998) rRNA based identification and detection systems for rhizobia and other bacteria. Plant Soil 204: 1-19.
78. Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Kumar, Y., etal. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 1363-1371.
79. Marcelino, L.A., Backman, V., Donaldson, A., Steadman, C., Thompson, J.R., Preheim, S.P., etal. (2006) Accurately quantifying low-abundant targets amid similar sequences by revealing hidden correlations in oligonucleotide microarray data. Proc Natl Acad Sci USA 103: 13629-13634.
80. Militon, C., Rimour, S., Missaoui, M., Biderre, C., Barra, V., Hill, D., etal. (2007) PhylArray: phylogenetic probe design algorithm for microarray. Bioinformatics 23: 2550-2557.
81. Muhling, M., Woolven-Allen, J., Murrell, J.C., and Joint, I. (2008) Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities. ISME J 2: 379-392.
82. Neufeld, J.D., Mohn, W.W., and de Lorenzo, V. (2006) Composition of microbial communities in hexachlorocyclohexane (HCH) contaminated soils from Spain revealed with a habitat-specific microarray. Environ Microbiol 8: 126-140.
83. Nordberg, E.K. (2005) YODA: selecting signature oligonucleotides. Bioinformatics 21: 1365-1370.
84. Øvreås, L. (2000) Population and community level approaches for analysing microbial diversity in natural environments. Ecol Lett 3: 236-251.
85. Pace, N.R. (1997) A Molecular View of Microbial Diversity and the Biosphere. Science 276: 734-740.
86. Paliy, O., Kenche, H., Abernathy, F., and Michail, S. (2009) High-throughput quantitative analysis of the human intestinal microbiota with a phylogenetic microarray. Appl Environ Microbiol 75: 3572-3579.
87. Palmer, C., Bik, E.M., Eisen, M.B., Eckburg, P.B., Sana, T.R., Wolber, P.K., etal. (2006) Rapid quantitative profilingof complex microbial populations. Nucleic Acids Res 34: e5.
88. Pariset, L., Chillemi, G., Bongiorni, S., Romano Spica, V., and Valentini, A. (2009) Microarrays and high-throughput transcriptomic analysis in species with incomplete availability of genomic sequences. Nat Biotechnol 25: 272-279.
89. Peplies, J., Lau, S.C.K., Pernthaler, J., Amann, R., and Glöckner, F.O. (2004) Application and validation of DNA microarrays for the 16S rRNA-based analysis of marine bacterioplankton. Environ Microbiol 6: 638-645.
90. Pozhitkov, A., Noble, P.A., Domazet-Loso, T., Nolte, A.W., Sonnenberg, R., Staehler, P., etal. (2006) Tests of rRNA hybridization to microarrays suggest that hybridization characteristics of oligonucleotide probes for species discrimination cannot be predicted. Nucleic Acids Res 34: e66.
91. Pozhitkov, A.E., Tautz, D., and Noble, P.A. (2007) Oligonucleotide microarrays: widely applied - poorly understood. Brief Funct Genomic Proteomic 6: 141-148.
92. Pruesse, E., Quast, C., Knittel, K., Fuchs, B.M., Ludwig, W., Peplies, J., and Glöckner, F.O. (2007) SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB. Nucleic Acids Res 35: 7188-7196.
93. Quince, C., Curtis, T.P., and Sloan, W.T. (2008) The rational exploration of microbial diversity. ISME J 2: 997-1006.
94. Rajilic-Stojanovic, M., Heilig, H.G., Molenaar, D., Kajander, K., Surakka, A., Smidt, H., and de Vos, W.M. (2009) Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults. Environ Microbiol 11: 1736-1751.
95. Rastogi, G., Osman, S., Vaishampayan, P.A., Andersen, G.L., Stetler, L.D., and Sani, R.K. (2010a) Microbial diversity in uranium mining-impacted soils as revealed by high-density 16S microarray and clone library. Microb Ecol 59: 94-108.
96. Rastogi, G., Osman, S., Kukkadapu, R., Engelhard, M., Vaishampayan, P.A., Andersen, G.L., and Sani, R.K. (2010b) Microbial and mineralogical characterizations of soils collected from the deep biosphere of the former Homestake gold mine, South Dakota. Microb Ecol 60: 539-550.
97. Rastogi, G., Barua, S., Sani, R.K., and Peyton, B.M. (2011) Investigation of Microbial Populations in the Extremely Metal-Contaminated Coeur d'Alene River Sediments. Microb Ecol 62: 1-13.
98. Relogio, A., Schwager, C., Richter, A., Ansorge, W., and Valcarcel, J. (2002) Optimization of oligonucleotide-based DNA microarrays. Nucleic Acids Res 30: e51.
99. Reymond, N., Charles, H., Duret, L., Calevro, F., Beslon, G., and Fayard, J.M. (2004) ROSO: optimizing oligonucleotide probes for microarrays. Bioinformatics 20: 271-273.
100. 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.
101. Rimour, S., Hill, D., Militon, C., and Peyret, P. (2005) GoArrays: highly dynamic and efficient microarray probe design. Bioinformatics 21: 1094-1103.
102. Rinta-Kanto, J.M., Burgmann, H., Gifford, S.M., Sun, S., Sharma, S., del Valle, D.A., etal. (2011) Analysis of sulfur-related transcription by Roseobacter communities using a taxon-specific functional gene microarray. Environ Microbiol 13: 453-467.
103. Roh, S.W., Abell, G.C.J., Kim, K.-H., Nam, Y.-D., and Bae, J.-W. (2010) Comparing microarrays and next-generation sequencing technologies for microbial ecology research. Trends Biotechnol 28: 291-299.
104. Rose, T.M., Schultz, E.R., Henikoff, J.G., Pietrokovski, S., McCallum, C.M., and Henikoff, S. (1998) Consensus-degenerate hybrid oligonucleotide primers for amplification of distantly related sequences. Nucleic Acids Res 26: 1628-1635.
105. Rose, T.M., Henikoff, J.G., and Henikoff, S. (2003) CODEHOP (COnsensus-DEgenerate Hybrid Oligonucleotide Primer) PCR primer design. Nucleic Acids Res 31: 3763-3766.
106. Rouillard, J.M., Zuker, M., and Gulari, E. (2003) OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach. Nucleic Acids Res 31: 3057-3062.
107. Rusch, A., and Amend, J.P. (2004) Order-specific 16S rRNA-targeted oligonucleotide probes for (hyper)thermophilic archaea and bacteria. Extremophiles 8: 357-366.
108. Sagaram, U.S., DeAngelis, K.M., Trivedi, P., Andersen, G.L., Lu, S.E., and Wang, N. (2009) Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing. Appl Environ Microbiol 75: 1566-1574.
109. Sanguin, H., Sarniguet, A., Gazengel, K., Moenne-Loccoz, Y., and Grundmann, G.L. (2009) Rhizosphere bacterial communities associated with disease suppressiveness stages of take-all decline in wheat monoculture. New Phytol 184: 694-707.
110. SantaLucia, J., Jr, Allawi, H.T., and Seneviratne, P.A. (1996) Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35: 3555-3562.
111. Schadt, E.E., Linderman, M.D., Sorenson, J., Lee, L., and Nolan, G.P. (2010) Computational solutions to large-scale data management and analysis. Nat Rev Genet 11: 647-657.
112. Schliep, A., and Rahmann, S. (2006) Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree. Bioinformatics 22: e424-e430.
113. Schonmann, S., Loy, A., Wimmersberger, C., Sobek, J., Aquino, C., Vandamme, P., etal. (2009) 16S rRNA gene-based phylogenetic microarray for simultaneous identification of members of the genus Burkholderia. Environ Microbiol 11: 779-800.
114. Severgnini, M., Cremonesi, P., Consolandi, C., Caredda, G., De Bellis, G., and Castiglioni, B. (2009) ORMA: a tool for identification of species-specific variations in 16S rRNA gene and oligonucleotides design. Nucleic Acids Res 37: e109.
115. Shawkey, M.D., Firestone, M.K., Brodie, E.L., and Beissinger, S.R. (2009) Avian incubation inhibits growth and diversification of bacterial assemblages on eggs. PLoS ONE 4: e4522.
116. Simon, C., and Daniel, R. (2009) Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 85: 265-276.
117. Spruill, S.E., Lu, J., Hardy, S., and Weir, B. (2002) Assessing sources of variability in microarray gene expression data. Biotechniques 33: 916-920. 922-913.
118. Stralis-Pavese, N., Sessitsch, A., Weilharter, A., Reichenauer, T., Riesing, J., Csontos, J., etal. (2004) Optimization of diagnostic microarray for application in analysing landfill methanotroph communities under different plant covers. Environ Microbiol 6: 347-363.
119. Suzuki, M.T., and Giovannoni, S.J. (1996) Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol 62: 625-630.
120. Taroncher-Oldenburg, G., Griner, E.M., Francis, C.A., and Ward, B.B. (2003) Oligonucleotide microarray for the study of functional gene diversity in the nitrogen cycle in the environment. Appl Environ Microbiol 69: 1159-1171.
121. Terrat, S., Peyretaillade, E., Goncalves, O., Dugat-Bony, E., Gravelat, F., Mone, A., etal. (2010) Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development. BMC Bioinformatics 11: 478.
122. Thompson, J.D., Higgins, D.G., and Gibson, T.J. (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
123. Thorsen, O., Smith, B., Sosa, C.P., Jiang, K., Lin, H., Peters, A., and Feng, W.-C. (2007) Parallel genomic sequence-search on a massively parallel system. In Proceedings of the 4th International Conference on Computing Frontiers. ACM (ed.). Ischia, Italy: ACM, pp. 59-68.
124. Tiquia, S.M., Wu, L., Chong, S.C., Passovets, S., Xu, D., Xu, Y., and Zhou, J. (2004) Evaluation of 50-mer oligonucleotide arrays for detecting microbial populations in environmental samples. Biotechniques 36: 664-670.
125. Torsvik, V., and Øvreås, L. (2002) Microbial diversity and function in soil: from genes to ecosystems. Curr Opin Microbiol 5: 240-245.
126. Vora, G.J., Meador, C.E., Stenger, D.A., and Andreadis, J.D. (2004) Nucleic acid amplification strategies for DNA microarray-based pathogen detection. Appl Environ Microbiol 70: 3047-3054.
127. Wagner, M., Smidt, H., Loy, A., and Zhou, J. (2007) Unravelling Microbial Communities with DNA-Microarrays: Challenges and Future Directions. Microb Ecol 53: 498-506.
128. Wang, X., and Seed, B. (2003) Selection of oligonucleotide probes for protein coding sequences. Bioinformatics 19: 796-802.
129. Weinert, N., Piceno, Y., Ding, G.C., Meincke, R., Heuer, H., Berg, G., etal. (2011) PhyloChip hybridization uncovered an enormous bacterial diversity in the rhizosphere of different potato cultivars: many common and few cultivar-dependent taxa. FEMS Microbiol Ecol 75: 497-506.
130. Wernersson, R., and Nielsen, H.B. (2005) OligoWiz 2.0 - integrating sequence feature annotation into the design of microarray probes. Nucleic Acids Res 33: W611-W615.
131. Whitman, W.B., Coleman, D.C., and Wiebe, W.J. (1998) Prokaryotes: The unseen majority. Proc Natl Acad Sci USA 95: 6578-6583.
132. Wilson, K.H., Wilson, W.J., Radosevich, J.L., DeSantis, T.Z., Viswanathan, V.S., Kuczmarski, T.A., and Andersen, G.L. (2002) High-Density Microarray of Small-Subunit Ribosomal DNA Probes. Appl Environ Microbiol 68: 2535-2541.
133. Woese, C.R., Kandler, O., and Wheelis, M.L. (1990) Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 87: 4576-4579.
134. Xu, J. (2006) Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances. Mol Ecol 15: 1713-1731.
135. Yergeau, E., Schoondermark-Stolk, S.A., Brodie, E.L., Dejean, S., DeSantis, T.Z., Goncalves, O., etal. (2009) Environmental microarray analyses of Antarctic soil microbial communities. ISME J 3: 340-351.
136. Yu, Y., Lee, C., Kim, J., and Hwang, S. (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89: 670-679.
137. Zhou, J. (2003) Microarrays for bacterial detection and microbial community analysis. Curr Opin Microbiol 6: 288-294.
138. Zhou, Z., Dou, Z.-X., Zhang, C., Yu, H.-Q., Liu, Y.-J., Zhang, C.-Z., and Cao, Y.-J. (2007) A strategy to optimize the oligo-probes for microarray-based detection of viruses. Virol Sin 22: 326-335.
139. Zuker, M. (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406-3415.