Chapter 18
Functional Intestinal Metagenomics
Bartholomeus van den Bogert,
Milkha M. Leimena,
Willem M. de Vos,
Erwin G. Zoetendal,
Michiel Kleerebezem,
Bartholomeus van den Bogert
Top Institute Food and Nutrition, Wageningen, The Netherlands
Wageningen University, Wageningen, The Netherlands
Search for more papers by this authorMilkha M. Leimena
Top Institute Food and Nutrition, Wageningen, The Netherlands
Wageningen University, Wageningen, The Netherlands
Search for more papers by this authorWillem M. de Vos
Wageningen University, Wageningen, The Netherlands
University of Helsinki, Helsinki, Finland
Search for more papers by this authorErwin G. Zoetendal
Top Institute Food and Nutrition, Wageningen, The Netherlands
Wageningen University, Wageningen, The Netherlands
Search for more papers by this authorMichiel Kleerebezem
Top Institute Food and Nutrition, Wageningen, The Netherlands
Wageningen University, Wageningen, The Netherlands
Search for more papers by this authorBartholomeus van den Bogert,
Milkha M. Leimena,
Willem M. de Vos,
Erwin G. Zoetendal,
Michiel Kleerebezem,
Bartholomeus van den Bogert
Top Institute Food and Nutrition, Wageningen, The Netherlands
Wageningen University, Wageningen, The Netherlands
Search for more papers by this authorMilkha M. Leimena
Top Institute Food and Nutrition, Wageningen, The Netherlands
Wageningen University, Wageningen, The Netherlands
Search for more papers by this authorWillem M. de Vos
Wageningen University, Wageningen, The Netherlands
University of Helsinki, Helsinki, Finland
Search for more papers by this authorErwin G. Zoetendal
Top Institute Food and Nutrition, Wageningen, The Netherlands
Wageningen University, Wageningen, The Netherlands
Search for more papers by this authorMichiel Kleerebezem
Top Institute Food and Nutrition, Wageningen, The Netherlands
Wageningen University, Wageningen, The Netherlands
Search for more papers by this authorBook Editor(s):Frans J. de Bruijn,
Frans J. de Bruijn
Laboratory of Plant Micro-organism Interaction, CNRS-INRA, Castanet Tolosan, France
Search for more papers by this authorSummary
This chapter contains sections titled:
-
Introduction
-
Characterization of the Gastrointestinal Microbiota
-
The Human Gastrointestinal Microbiota
-
Metagenomic Approaches to Study Microbial Communities
-
Metagenomics Library Analysis: Screening Approaches
-
Complementary “Meta-Omics” Approaches to Study Microbial Communities
-
Concluding Remarks and Future Perspectives
-
Internet Resources
-
References
INTERNET RESOURCES
- Ribosomal database project (http://rdp.cme.msu.edu/)
- REFERENCES
- Ahmed S, Macfarlane GT, Fite A, McBain AJ, Gilbert P, Macfarlane S. 2007. Mucosa-associated bacterial diversity in relation to human terminal ileum and colonic biopsy samples. Appl. Environ. Microbiol. 73: 7435–7442.
- Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59: 143–169.
- Andersson AF, Lindberg M, Jakobsson H, Backhed F, Nyren P, Engstrand L. 2008. Comparative analysis of human gut microbiota by barcoded pyrosequencing. PloS One 3: e2836.
- Ashelford KE, Chuzhanova NA, Fry JC, Jones AJ, Weightman AJ. 2005. At least 1 in 20 16S rRNA sequence records currently held in public repositories is estimated to contain substantial anomalies. Appl. Environ. Microbiol. 71: 7724–7736.
- Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. 2005. Host–bacterial mutualism in the human intestine. Science 307: 1915–1920.
- Baker GC, Smith JJ, Cowan DA. 2003. Review and re-analysis of domain-specific 16S primers. J. Microbiol. Methods 55: 541–555.
- Berridge BR, Fuller JD, de Azavedo J, Low DE, Bercovier H, Frelier PF. 1998. Development of specific nested oligonucleotide PCR primers for the Streptococcus iniae 16S-23S ribosomal DNA intergenic spacer. J. Clin. Microbiol. 36: 2778–2781.
- Bik EM, Eckburg PB, Gill SR, Nelson KE, Purdom EA, et al. 2006. Molecular analysis of the bacterial microbiota in the human stomach. Proc. Natl. Acad. Sci. USA 103: 732–737.
- Booijink CC. 2009. Analysis of Diversity and Function of the Human Small Intestinal Microbiota. Wageningen University, Wageningen, The Netherlands.
- Booijink CC, Zoetendal EG, Kleerebezem M, de Vos WM. 2007. Microbial communities in the human small intestine: Coupling diversity to metagenomics. Future Microbiol. 2: 285–295.
- Booijink CC, El-Aidy SF, Rajilić-Stojanović M, Heilig HG, Troost FJ, et al. 2010. High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol. 12: 3213–3227.
- Breitbart M, Hewson I, Felts B, Mahaffy JM, Nulton J, et al. 2003. Metagenomic analyses of an uncultured viral community from human feces. J. Bacteriol. 185: 6220–6223.
- Case RJ, Boucher Y, Dahllof I, Holmstrom C, Doolittle WF, Kjelleberg S. 2007. Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies. Appl. Environ. Microbiol. 73: 278–288.
- Chen K, Pachter L. 2005. Bioinformatics for whole-genome shotgun sequencing of microbial communities. PLoS Comput. Biol. 1: 106–112.
- Claesson MJ, O'Sullivan O, Wang Q, Nikkila J, Marchesi JR, et al. 2009. Comparative analysis of pyrosequencing and a phylogenetic microarray for exploring microbial community structures in the human distal intestine. PloS One 4: e6669.
- Cloonan N, Grimmond SM. 2008. Transcriptome content and dynamics at single-nucleotide resolution. Genome biology 9: 234.
- Collins MD, Lawson PA, Willems A, Cordoba JJ, FernandezGarayzabal J, et al. 1994. The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int. J. Syst. Bacteriol. 44: 812–826.
- Darby AC, Hall N. 2008. Fast forward genetics. Nat. Biotechnol. 26: 1248–1249.
- DeSantis TZ, Brodie EL, Moberg JP, Zubieta IX, Piceno YM, Andersen GL. 2007. High-density universal 16S rRNA microarray analysis reveals broader diversity than typical clone library when sampling the environment. Microb. Ecol. 53: 371–383.
- Dethlefsen L, Huse S, Sogin ML, Relman DA. 2008. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol. 6: e280.
- Dridi B, Henry M, El Khechine A, Raoult D, Drancourt M. 2009. High prevalence of Methanobrevibacter smithii and Methanosphaera stadtmanae detected in the human gut using an improved DNA detection protocol. PloS One 4: e7063.
- Duerkop BA, Vaishnava S, Hooper LV. 2009. Immune responses to the microbiota at the intestinal mucosal surface. Immunity 31: 368–376.
- Duncan SH, Louis P, Flint HJ. 2004. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl. Environ. Microbiol. 70: 5810–5817.
- Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, et al. 2005. Diversity of the human intestinal microbial flora. Science 308: 1635–8.
- Emrich SJ, Barbazuk WB, Li L, Schnable PS. 2007. Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res. 17: 69–73.
- Fang F, Li Y, Bumann M, Raftis EJ, Casey PG, Cooney JC, et al. 2009. Allelic variation of bile salt hydrolase genes in Lactobacillus salivarius does not determine bile resistance levels. J. Bacteriol. 191: 5743–5757.
- Gloux K, Leclerc M, Iliozer H, L'Haridon R, Manichanh C, etal. 2007. Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth. Appl. Environ. Microbiol. 73: 3734–3737.
- Guarner F. 2006. Enteric flora in health and disease. Digestion 73(Suppl.) 1: 5–12.
- Hamady M, Knight R. 2009. Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res. 19: 1141–1152.
- Handelsman J, Liles M, Mann D, Riesenfeld C, Goodman RM. 2002. Cloning the metagenome: Culture-independent access to the diversity and functions of the uncultivated microbial world. InWren B, Dorell N, ed. Methods in Microbiology, Vol. 33. Academic Press, pp. 241–255.
- Handelsman J. 2004. Metagenomics: application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68: 669–685.
- Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, et al. 2009. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc. Natl. Acad. Sci. USA 106: 17187–17192.
- Hayashi H, Takahashi R, Nishi T, Sakamoto M, Benno Y. 2005. Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism. J. Med. Microbiol. 54: 1093–1101.
- Henne A, Schmitz RA, Bomeke M, Gottschalk G, Daniel R. 2000. Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli. Appl. Environ. Microbiol. 66: 3113–6.
- Hooper LV. 2009. Do symbiotic bacteria subvert host immunity ? Nat. Rev. Microbiol. 7: 367–374.
- Horz HP, Vianna ME, Gomes BP, 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: 5332–5337.
- Huse SM, Huber JA, Morrison HG, Sogin ML, Welch DM. 2007. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol. 8: R143.
- Huys G, Vanhoutte T, Vandamme P. 2008. Application of sequence-dependent electrophoresis fingerprinting in exploring biodiversity and population dynamics of human intestinal microbiota: What can be revealed? Interdisciplin. Perspect. Infect. Dis. 2008: 597603.
- Ingham CJ, Sprenkels A, Bomer J, Molenaar D, van den Berg A, et al. 2007. The micro-Petri dish, a million-well growth chip for the culture and high-throughput screening of microorganisms. Proc. Natl. Acad. Sci. USA 104: 18217–18222.
- Jacobs DM, Gaudier E, van Duynhoven J, Vaughan EE. 2009. Non-digestible food ingredients, colonic microbiota and the impact on gut health and immunity: A role for metabolomics. Curr. Drug. Metab. 10: 41–54.
-
Jarvie T, Harkins T. 2008. Transcriptome sequencing with the Genome Sequencer FLX system. Nat. Methods 5: vi–vii.
10.1038/nmeth.f.220 Google Scholar
- Jones BV, Marchesi JR. 2007a. Accessing the mobile metagenome of the human gut microbiota. Mol. Biosyst. 3: 749–758.
- Jones BV, Marchesi JR. 2007b. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat. Methods 4: 55–61.
- Jones BV, Begley M, Hill C, Gahan CG, Marchesi JR. 2008. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc. Natl. Acad. Sci. USA 105: 13580–13585.
- Juncker AS, Jensen LJ, Pierleoni A, Bernsel A, Tress ML, et al. 2009. Sequence-based feature prediction and annotation of proteins. Genome Biol. 10: 206.
- Kaddurah-Daouk R, Kristal BS, Weinshilboum RM. 2008. Metabolomics: a global biochemical approach to drug response and disease. Annu. Rev. Pharmacol. Toxicol. 48: 653–683.
- Keijser BJ, Zaura E, Huse SM, van der Vossen JM, Schuren FH, et al. 2008. Pyrosequencing analysis of the oral microflora of healthy adults. J. Dental Res. 87: 1016–1020.
-
Kimura N. 2006. Metagenomics: Access to unculturable microbes in the environment. Microbes Environ. 21: 201–215.
10.1264/jsme2.21.201 Google Scholar
- Kitano H. 2002a. Systems biology: A brief overview. Science 295: 1662–1664.
- Kitano H. 2002b. Computational systems biology. Nature 420: 206–210.
- Klaassens ES. 2007. Exploring the Functionality of Intestinal Bifidobacteria: A Post-Genomics Approach. Wageningen University, Wageningen.
- Klaassens ES, de Vos WM, Vaughan EE. 2007. Metaproteomics approach to study the functionality of the microbiota in the human infant gastrointestinal tract. Appl. Environ. Microbiol. 73: 1388–1392.
- Klaassens ES, Boesten RJ, Haarman M, Knol J, Schuren FH, et al. 2009. Mixed-species genomic microarray analysis of fecal samples reveals differential transcriptional responses of bifidobacteria in breast- and formula-fed infants. Appl. Environ. Microbiol. 75: 2668–2676.
- Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, et al. 2007. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res. 14: 169–181.
- Lambert JM, Bongers RS, de Vos WM, Kleerebezem M. 2008a. Functional analysis of four bile salt hydrolase and penicillin acylase family members in Lactobacillus plantarum WCFS1. Appl. Environ. Microbiol. 74: 4719–4726.
- Lambert JM, Siezen RJ, de Vos WM, Kleerebezem M. 2008b. Improved annotation of conjugated bile acid hydrolase superfamily members in gram-positive bacteria. Microbiology (Reading, England) 154: 2492–500.
- Lepage P, Seksik P, Sutren M, de la Cochetiere MF, Jian R, et al. 2005. Biodiversity of the mucosa-associated microbiota is stable along the distal digestive tract in healthy individuals and patients with IBD. Inflamm. Bowel Dis. 11: 473–480.
- Leser TD and Molbak L. 2009. Better living through microbial action: The benefits of the mammalian gastrointestinal microbiota on the host. Environ. Microbiol. 11: 2194–2206.
- Ley RE, Hamady M, Lozupone C, Turnbaugh PJ, Ramey RR, et al. 2008a. Evolution of mammals and their gut microbes. Science 320: 1647–1651.
- Ley RE, Lozupone CA, Hamady M, Knight R, Gordon JI. 2008b. Worlds within worlds: evolution of the vertebrate gut microbiota. Nat. Rev. Microbiol. 6: 776–788.
- Li M, Wang B, Zhang M, Rantalainen M, Wang S, et al. 2008. Symbiotic gut microbes modulate human metabolic phenotypes. Proc. Natl. Acad. Sci. USA 105: 2117–2122.
- Liu YQ, Pan YJ. 2009. Application of FT-ICR MS for the study of protein complexes. Appl. Spectrosc. Rev. 44: 231–244.
- Louis P, Flint HJ. 2007. Development of a semiquantitative degenerate real-time pcr-based assay for estimation of numbers of butyrylcoenzyme A (CoA) CoA transferase genes in complex bacterial samples. Appl. Environ. Microbiol. 73: 2009–2012.
- Louis P, Young P, Holtrop G, Flint HJ. 2009. Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene. Environ. Microbiol. 00: 000–000.
- Macpherson AJ, Harris NL. 2004. Interactions between commensal intestinal bacteria and the immune system. Nat. Rev. Immunol. 4: 478–485.
- Mane SP, Evans C, Cooper KL, Crasta OR, Folkerts O, et al. 2009. Transcriptome sequencing of the microarray quality control (MAQC) RNA reference samples using next generation sequencing. BMC Genomics 10: 264.
- Maron PA, Ranjard L, Mougel C, Lemanceau P. 2007. Metaproteomics: A new approach for studying functional microbial ecology. Microb. Ecol. 53: 486–493.
- Martin FP, Sprenger N, Yap IK, Wang Y, Bibiloni R, et al. 2009. Panorganismal gut microbiome–host metabolic crosstalk. J. Proteome Res. 8: 2090–2105.
- Matsuki T, Watanabe K, Fujimoto J, Takada T, 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: 7220–7228.
- Morozova O, Hirst M, Marra MA. 2009. Applications of new sequencing technologies for transcriptome analysis. Annu. Rev. Genomics Hum. Genet. 10: 135–151.
- Neish AS. 2009. Microbes in gastrointestinal health and disease. Gastroenterology 136: 65–80.
- Nicholson JK, Lindon JC. 2008. Systems biology: Metabonomics. Nature 455: 1054–1056.
- O'Farrell PH. 1975. High resolution two-dimensional electrophoresis of proteins. J. Biol. Chem. 250: 4007–4021.
- Oresic M. 2009. Metabolomics, a novel tool for studies of nutrition, metabolism and lipid dysfunction. Nutr. Metab. Cardiovasc. Dis. 19: 816–824.
- Ozsolak F, Platt AR, Jones DR, Reifenberger JG, Sass LE, et al. 2009. Direct RNA sequencing. Nature 461: 814–818.
- Paliy O, Kenche H, Abernathy F, Michail S. 2009. High-throughput quantitative analysis of the human intestinal micro-biota with a phylogenetic microarray. Appl. Environ. Microbiol. 75: 3572–3579.
- Palmer C, Bik EM, Eisen MB, Eckburg PB, Sana TR, et al. 2006. Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res. 34: e5.
- Park SJ, Kang CH, Chae JC, Rhee SK. 2008. Metagenome microarray for screening of fosmid clones containing specific genes. FEMS Microbiol. Lett. 284: 28–34.
- Passalacqua KD, Varadarajan A, Ondov BD, Okou DT, Zwick ME, Bergman NH. 2009. Structure and complexity of a bacterial transcriptome. J. Bacteriol. 191: 3203–3211.
- Peterson J, Garges S, Giovanni M, McInnes P, Wang L, et al. 2009. The NIH Human Microbiome Project. Genome Res. 19: 2317–2323.
- Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, et al. 2010. A human gut microbial gene catalog established by deep metagenomic sequencing. Nature 464: 59–65.
- Raes J, Bork P. 2008. Molecular eco-systems biology: Towards an understanding of community function. Nat. Rev. Microbiol. 6: 693–699.
- Rajilić-Stojanović M. 2007. Diversity of Human Gastrointestinal Microbiota—Novel Perspectives from High Throughput Analyses. Wageningen University, Wageningen, The Netherlands.
- Rajilić-Stojanović M, Smidt H, de Vos WM. 2007. Diversity of the human gastrointestinal tract microbiota revisited. Environ. Microbiol. 9: 2125–2136.
- Rajilić-Stojanović M, Heilig HG, Molenaar D, Kajander K, Surakka A, et al. 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.
- Riesenfeld CS, Schloss PD, Handelsman J. 2004. Metagenomics: genomic analysis of microbial communities. Annu. Rev. Genet. 38: 525–552.
- Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, et al. 2000. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66: 2541–2547.
- Scanlan PD and Marchesi JR. 2008. Micro-eukaryotic diversity of the human distal gut microbiota: Qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J. 2: 1183–1193.
- Schmeisser C, Steele H, Streit WR. 2007. Metagenomics, biotechnology with non-culturable microbes. Appl. Microbiol. Biotechnol. 75: 955–962.
- Sebat JL, Colwell FS, Crawford RL. 2003. Metagenomic profiling: Microarray analysis of an environmental genomic library. Appl. Environ. Microbiol. 69: 4927–4934.
- Seow KT, Meurer G, Gerlitz M, Wendt-Pienkowski E, Hutchinson CR, Davies J. 1997. A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: A means to access and use genes from uncultured microorganisms. J. Bacteriol. 179: 7360–7368.
- Suau A, Bonnet R, Sutren M, Godon JJ, Gibson GR, et al. 1999. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl. Environ. Microbiol. 65: 4799–4807.
- Swann J, Wang Y, Abecia L, Costabile A, Tuohy K, et al. 2009. Gut microbiome modulates the toxicity of hydrazine: A metabonomic study. Mol. Biosyst. 5: 351–355.
- Tap J, Mondot S, Levenez F, Pelletier E, Caron C, et al. 2009. Towards the human intestinal microbiota phylogenetic core. Environ. Microbiol. 11: 2574–2584.
- Taroncher-Oldenburg G. 2009. RNA direct. SciBX 2: 1–2.
- Tartar A, Wheeler MM, Zhou X, Coy MR, Boucias DG, Scharf ME. 2009. Parallel metatranscriptome analyses of host and symbiont gene expression in the gut of the termite Reticulitermes flavipes. Biotechnol. Biofuels 2: 25.
- Tjaden B, Saxena RM, Stolyar S, Haynor DR, Kolker E, Rosenow C. 2002. Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res. 30: 3732–3738.
- Turnbaugh PJ, Gordon JI. 2008. An invitation to the marriage of metagenomics and metabolomics. Cell 134: 708–713.
- Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. 2007. The human microbiome project. Nature 449: 804–810.
- Turnbaugh PJ, Backhed F, Fulton L, Gordon JI. 2008. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe 3: 213–223.
- Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, et al. 2009. A core gut microbiome in obese and lean twins. Nature 457: 480–484.
- Uchiyama T, Abe T, Ikemura T, Watanabe K. 2005. Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. Nat. Biotechnol. 23: 88–93.
- Uchiyama T, Watanabe K. 2008. Substrate-induced gene expression (SIGEX) screening of metagenome libraries. Nat. Protoc. 3: 1202–1212.
- Van den Bogert B, De Vos WM, Zoetendal EG, 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.
- Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science 304: 66–74.
- Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, et al. 2009. Shotgun metaproteomics of the human distal gut micro-biota. ISME J. 3: 179–189.
- Wang M, Ahrne S, Jeppsson B, Molin G. 2005. Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes. FEMS Microbiol. Ecol. 54: 219–231.
- Warnecke F, Hess M. 2009. A perspective: metatranscriptomics as a tool for the discovery of novel biocatalysts. J. Biotechnol. 142: 91–95.
- Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, et al. 2009. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc. Natl. Acad. Sci. USA 106: 3698–3703.
- Williamson LL, Borlee BR, Schloss PD, Guan C, Allen HK, Handelsman J. 2005. Intracellular screen to identify metagenomic clones that induce or inhibit a quorum-sensing biosensor. Appl. Environ. Microbiol. 71: 6335–6344.
- Wilmes P, Bond PL. 2006. Metaproteomics: Studying functional gene expression in microbial ecosystems. Trends Microbiol. 14: 92–97.
- Yoder-Himes DR, Chain PS, Zhu Y, Wurtzel O, Rubin EM, et al. 2009. Mapping the Burkholderia cenocepacia niche response via high-throughput sequencing. Proc. Natl. Acad. Sci. USA 106: 3976–3981.
- Yun J, Ryu S. 2005. Screening for novel enzymes from metagenome and SIGEX, as a way to improve it. Microb. Cell Factories 4: 8.
- Zoetendal EG, Akkermans AD, de Vos WM. 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: 3854–3859.
- Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans AD, de Vos WM. 2002. Mucosa-associated bacteria in the human gastrointestinal tract are uniformly distributed along the colon and differ from the community recovered from feces. Appl. Environ. Microbiol. 68: 3401–3407.
- Zoetendal EG, Collier CT, Koike S, Mackie RI, Gaskins HR. 2004. Molecular ecological analysis of the gastrointestinal microbiota: A review. J. Nutr. 134: 465–472.
- Zoetendal EG, Booijink CC, Klaassens ES, Heilig HG, Kleerebezem M, et al. 2006. Isolation of RNA from bacterial samples of the human gastrointestinal tract. Nat. Protoc. 1: 954–959.
- Zoetendal EG, Rajilić-Stojanović M, de Vos WM. 2008. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 57: 1605–1615.
