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  • Acinas, S.G., Sarma-Rupavtarm, R., Klepac-Ceraj, V., and Polz, M.F. (2005) PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol 71: 89668969.
  • Altschul, S.F., Gish, W., Miller, W., Meyers, E.W., and Lipman, D.J. (1990) Basic Local Alignment Search Tool. J Mol Biol 215: 403410.
  • Andersson, A.F., Lindberg, M., Jakobsson, H., Backhed, F., Nyren, P., and Engstrand, L. (2008) Comparative analysis of human gut microbiota by barcoded pyrosequencing. PLoS ONE 3: e2836.
  • Bäckhed, F., Ley, R.E., Sonnenburg, J.L., Peterson, D.A., and Gordon, J.I. (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915–.
  • Bauer, D.F. (1972) Constructing confidence sets using rank statistics. J Am Stat Assoc 67: 687690.
  • Ben-Amor, K., Heilig, H.G., Smidt, H., Vaughan, E.E., Abee, T., and De Vos, W.M. (2005) Genetic diversity of viable, injured, and dead fecal bacteria assessed by fluorescence-activated cell sorting and 16S rRNA gene analysis. Appl Environ Microbiol 71: 46794689.
  • Bertilsson, S., Cavanaugh, C.M., and Polz, M.F. (2002) Sequencing-independent method to generate oligonucleotide probes targeting a variable region in bacterial 16S rRNA by PCR with deatachable primers. Appl Environ Microbiol 68: 60776086.
  • Blanchard, A.P., Kaiser, R.J., and Hood, L.E. (1996) High-density oligonucleotide arrays. Biosens Bioelectron 11: 687690.
  • Bodrossy, L., and Sessitsch, A. (2004) Oligonucleotide microarrays in microbial diagnostics. Curr Opin Microbiol 7: 245254.
  • 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: 566582.
  • Bolstad, B.M., Irizarry, R.A., Astrand, M., and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185193.
  • Bonnet, R., Suau, A., Doré, J., Gibson, G.R., and Collins, M.D. (2002) Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs. Int J Syst Evol Microbiol 52: 757763.
  • Ter Braak, C.J.F., and Šmilauer, P. (2002) canoco Reference Manual and CanoDraw for Windows User's Guide: Software for Canonical Community Ordination, version 4.5. Ithaca, NY, USA: Microcomputer Power.
  • Button, D.K., and Robertson, B.R. (2001) Determination of DNA content of aquatic bacteria by flow cytometry. Appl Environ Microbiol 67: 16361645.
  • Chee, M., Yang, R., Hubbell, E., Berno, A., Huang, X.C., Stern, D., et al. (1996) Accessing genetic information with high-density DNA arrays. Science 274: 610614.
  • Cleveland, W.S., Grosse, E., and Shyu, W.M. (1992) Local regression models. In Statistical Models in S. Chambers, J.M., and Hastie, T.J. (eds). Cole, USA: Wadsworth & Brooks/Cole Computer Science Series, pp. 309376.
  • Collins, M., Lawson, P., Willems, A., Cordoba, J., Fernandez-Garayzabal, J., Garcia, P., et al. (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44: 812826.
  • 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: 371383.
  • Dethlefsen, L., Eckburg, P.B., Bik, E.M., and Relman, D.A. (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21: 517523.
  • Dixon, W.J. (1950) Analysis of extreme values. Ann Math Stat 21: 488506.
  • Eckburg, P.B., Bik, E.M., Bernstein, C.N., Purdom, E., Dethlefsen, L., Sargent, M., et al. (2005) Diversity of the human intestinal microbial flora. Science 308: 16351638.
  • 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: 37463750.
  • Favier, C.F., Vaughan, E.E., De Vos, W.M., and Akkermans, A.D.L. (2002) Molecular monitoring of succession of bacterial communities in human neonates. Appl Environ Microbiol 68: 219226.
  • Fogarty, L.R., and Voytek, M.A. (2005) Comparison of Bacteroides-Prevotella 16S rRNA genetic markers for fecal samples from different animal species. Appl Environ Microbiol 71: 59996007.
  • Gentry, T.J., Wickham, G.S., Schadt, C.W., He, Z., and Zhou, J. (2006) Microarray applications in microbial ecology research. Microb Ecol 52: 159175.
  • Gill, S.R., Pop, M., Deboy, R.T., Eckburg, P.B., Turnbaugh, P.J., Samuel, B.S., et al. (2006) Metagenomic analysis of the human distal gut microbiome. Science 312: 13551359.
  • Guschin, D.Y., Mobarry, B.K., Proudnikov, D., Stahl, D.A., Rittmann, B.E., and Mirzabekov, A.D. (1997) Oligonucleotide microchips as genosensors for determinative and environmental studies in microbiology. Appl Environ Microbiol 63: 23972402.
  • Heuer, H., Hartung, K., Wieland, G., Kramer, I., and Smalla, K. (1999) Polynuclotide probes that target a hypervariable region of 16S rRNA genes to identify bacterial isolates corresponding to bands of community fingerprints. Appl Environ Microbiol 65: 10451049.
  • Horz, H.P., Vianna, M.E., Gomes, B.P.F.A., and Conrads, G. (2005) Evaluation of universal probes and primer sets for assessing total bacterial load in clinical samples: general implications and practical use in endodontic antimicrobial therapy. J Clin Microbiol 43: 53325337.
  • Hugenholtz, P., Pitulle, C., Hershberger, K.L., and Pace, N.R. (1998) Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 180: 366376.
  • Klappenbach, J.A., Saxman, P.R., Cole, J.R., and Schmidt, T.M. (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29: 181184.
  • Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., et al. (2007) Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 14: 169181.
  • Lane, D.J. (1991) 16S/23S rRNA sequencing. In Nucleic Acid Techniques in Bacterial Systematics. Stackebrandt, E., and Goodfellow, M. (eds). Chichester, UK: J. Wiley & Sons, pp. 115175.
  • Larkin, J.E., Frank, B.C., Gavras, H., Sultana, R., and Quackenbush, J. (2005) Independence and reproducibility across microarray platforms. Nat Methods 2: 337344.
  • Lay, C., Rigottier-Gois, L., Holmstrom, K., Rajilic, M., Vaughan, E.E., De Vos, W.M., et al. (2005) Colonic microbiota signatures across five Northern European countries. Appl Environ Microbiol 71: 41534155.
  • Leitch, E.C., Walker, A.W., Duncan, S.H., Holtrop, G., and Flint, H.J. (2007) Selective colonization of insoluble substrates by human faecal bacteria. Environ Microbiol 9: 667679.
  • Lepš, J., and Šmilauer, P. (2003) Multivariate Analysis of Ecological Data Using CANOCO. Cambridge, UK: Cambridge University Press.
  • Ley, R.E., Turnbaugh, P.J., Klein, S., and Gordon, J.I. (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 10221023.
  • Li, M., Wang, B., Zhang, M., Rantalainen, M., Wang, S., Zhou, H., et al. (2008) Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci U S A 105: 21172122.
  • 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: 61146123.
  • Loy, A., Lehner, A., Lee, N., Adamczyk, J., Meier, H., Ernst, J., et al. (2002) Oligonucleotide microarray for 16S rRNA gene-based detection of all recognized lineages of sulfate-reducing prokaryotes in the environment. Appl Environ Microbiol 68: 50645081.
  • Ludwig, W., Strunk, O., Westram, R., Richter, L., Meier, H., Yadhukumar, et al. (2004) ARB: a software environment for sequence data. Nucleic Acids Res 32: 13631371.
  • McCartney, A.L., Wenzhi, W., and Tannock, G.W. (1996) Molecular analysis of the composition of the bifidobacterial and lactobacillus microflora of humans. Appl Environ Microbiol 62: 46084613.
  • Matsuki, T., Watanabe, K., Fujimoto, J., Miyamoto, Y., Takada, T., Matsumoto, K., et al. (2002) Development of 16S rRNA-gene-targeted group-specific primers for the detection and identification of predominant bacteria in human feces. Appl Environ Microbiol 68: 54455451.
  • Matsuki, T., Watanabe, K., Fujimoto, J., Takada, T., and Tanaka, R. (2004) Use of 16S rRNA gene-targeted group-specific primers for real-time PCR analysis of predominant bacteria in human feces. Appl Environ Microbiol 70: 72207228.
  • Mitsuoka, T. (1992) Intestinal flora and aging. Nutr Rev 50: 438446.
  • Mueller, S., Saunier, K., Hanisch, C., Norin, E., Alm, L., Midtvedt, T., et al. (2006) Differences in fecal microbiota in different European study populations in relation to age, gender, and country: a cross-sectional study. Appl Environ Microbiol 72: 10271033.
  • Myllyluoma, E., Veijola, L., Ahlroos, T., Tynkkynen, S., Kankuri, E., Vapaatalo, H., et al. (2005) Probiotic supplementation improves tolerance to Helicobacter pylori eradication therapy – a placebo-controlled, double-blind randomized pilot study. Aliment Pharmacol Ther 21: 12631272.
  • Nicholson, J.K., Holmes, E., and Wilson, I.D. (2005) Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 3: 431438.
  • Nübel, U., Engelen, B., Felske, A., Snaidr, J., Wieshuber, A., Amann, R.I., et al. (1996) Sequence heterogeneities of genes encoding 16S rRNAs in Paenibacillus polymyxa detected by temperature gradient gel electrophoresis. J Bacteriol 178: 56365643.
  • Palmer, C., Bik, E.M., Eisen, M.B., Eckburg, P.B., Sana, T.R., Wolber, P.K., et al. (2006) Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res 34: e5.
  • Palmer, C., Bik, E.M., Digiulio, D.B., Relman, D.A., and Brown, P.O. (2007) Development of the human infant intestinal microbiota. PLoS Biol 5: e177.
  • Panjkovich, A., and Melo, F. (2004) Comparison of different melting temperature calculation methods for short DNA sequences. Bioinformatics 21: 711722.
  • Panjkovich, A., and Melo, F. (2005) Comparison of different melting temperature calculation methods for short DNA sequences. Bioinformatics 21: 711712.
  • Possemiers, S., Verthé, K., Uyttendaele, S., and Verstraete, W. (2004) PCR-DGGE-based quantification of stability of the microbial community in a simulator of the human intestinal microbial ecosystem. FEMS Microbiol Ecol 49: 495507.
  • Pozhitkov, A., Noble, P.A., Domazet-Loso, T., Nolte, A.W., Sonnenberg, R., Staehler, P., et al. (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.
  • Rajilić-Stojanović, M., Smidt, H., and De Vos, W.M. (2007) Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 9: 21252136.
  • Roest, K.C. (2007) Microbial community analysis in sludge of anaerobic wastewater treatment systems. In Laboratory of Microbiology. De Vos, W.M., and Stams, A.J.M. (eds). Wageningen, the Netherlands: Wageningen University, p. 174.
  • Royston, P. (1982) An extension of Shapiro and Wilk's W test for normality to large samples. Appl Stat 31: 115124.
  • Sacchi, C.T., Alber, D., Dull, P., Mothershed, E.A., Whitney, A.M., Barnett, G.A., et al. (2005) High level of sequence diversity in the 16S rRNA genes of Haemophilus influenzae isolates is useful for molecular subtyping. J Clin Microbiol 43: 37343742.
  • Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989a) Calculating melting temperatures for perfectly matched hybrids between oligonucleotides and their target sequences. In Molecular Cloning – A Laboratory Manual. Sambrook, J., Fritsch, E.F., and Maniatis, T. (eds). Cold Spring Habour, NY, USA: Cold Spring Habour Laboratory Press, p. 11.46.
  • Sambrook, J., Fritsch, E.F., and Maniatis, T. (1989b) Preparation of reagents and buffers used in molecular cloning. In Molecular Cloning – A Laboratory Manual. Sambrook, J., Fritsch, E.F., and Maniatis, T. (eds). Cold Spring Habour, NY, USA: Cold Spring Habour Habour Laboratory Press, p. B.13.
  • SantaLucia, J., Jr. (1998) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95: 14601465.
  • Scanlan, P.D., Shanahan, F., Clune, Y., Collins, J.K., O'Sullivan, G.C., O'Riordan, M., et al. (2008) Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol 10: 789798.
  • Schloss, P.D., and Handelsman, J. (2004) Status of the microbial census. Microbiol Mol Biol Rev 68: 686691.
  • Shen, J., Zhang, B., Wei, G., Pang, X., Wei, H., Li, M., et al. (2006) Molecular profiling of the clostridium leptum subgroup in human fecal microflora by PCR-denaturing gradient gel electrophoresis and clone library analysis. Appl Environ Microbiol 72: 52325238.
  • Suau, A., Bonnet, R., Sutren, M., Godon, J.-J., Gibson, G.R., Collins, M.D., and Doré, J. (1999) Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 65: 47994807.
  • Surakka, A., Kajander, K., Rajilić-Stojanović, M., Karjalainen, H., Hatakka, K., Vapaatalo, H., et al. (2009) Yoghurt containing galactooligosaccharides facilitates defecation among elderly subjects and selectively Increases the number of bifidobacteria. Int J Prob Preb 4: 6574.
  • Tan, P.K., Downey, T.J., Spitznagel, E.L., Jr, Xu, P., Fu, D., Dimitrov, D.S., et al. (2003) Evaluation of gene expression measurements from commercial microarray platforms. Nucleic Acids Res 31: 56765684.
  • Turnbaugh, P.J., Hamady, M., Yatsunenko, T., Cantarel, B.L., Duncan, A., Ley, R.E., et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480484.
  • Vanhoutte, T., Huys, G., Brandt, E., and Swings, J. (2004) Temporal stability analysis of the microbiota in human feces by denaturing gradient gel electrophoresis using universal and group-specific 16S rRNA gene primers. FEMS Microbiol Ecol 48: 437446.
  • Wagner, M., Smidt, H., Loy, A., and Zhou, J. (2007) Unravelling microbial communities with DNA-microarrays: challenges and future directions. Microb Ecol 53: 498506.
  • Watanabe, K., Kodama, Y., and Harayama, S. (2001) Design and evaluation of PCR primers to amplify bacterial 16S ribosomal DNA fragments used for community fingerprinting. J Microbiol Methods 44: 253262.
  • Weis, B.K., and Consortium, M.O.T.T.R. (2005) Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods 2: 351356.
  • 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: 25352541.
  • Zoetendal, E.G., Akkermans, A.D., and De Vos, W.M. (1998) Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 64: 38543859.
  • Zoetendal, E.G., Collier, C.T., Koike, S., Mackie, R.I., and Gaskins, H.R. (2004) Molecular ecological analysis of the gastrointestinal microbiota: a review. J Nutr 134: 465472.
  • Zoetendal, E.G., Vaughan, E.E., and De Vos, W.M. (2006a) A microbial world within us. Mol Microbiol 59: 16391650.
  • Zoetendal, E.G., Heilig, H.G.H.J., Klaassens, E.S., Booijink, C.C.G.M., Kleerebezem, M., Smidt, H., and De Vos, W.M. (2006b) Isolation of DNA from bacterial samples of the human gastrointestinal tract. Nat Protocols 1: 870873.
  • Zoetendal, E.G., Rajilić-Stojanović, M., and De Vos, W.M. (2008) High throughput diversity und functionality analysis of the gastrointestinal tract microbiota. Gut 57: 16051615.