A metagenomic insight into our gut's microbiome

Gut

Volumn 62, Issue 1, 2013, Pages 146-158

  Lepage, Patricia ^a   Leclerc, Marion C ^a   Joossens, Marie ^b,c,d   Mondot, Stanislas ^e   Blottière, Hervé M ^a   Raes, Jeroen ^b,c   Ehrlich, Dusko ^a   Doré, Joel ^a  

^a UMR1319 MICALIS   (France)

^b DEPARTMENT OF PLANT SYSTEMS BIOLOGY   (Belgium)

^c VRIJE UNIVERSITEIT BRUSSEL   (Belgium)

^d UNIVERSITY OF LEUVEN   (Belgium)

^e CSIRO   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL GENOME; DNA LIBRARY; ENTEROPATHY; EUROPE; GENE FUNCTION; GENE SEQUENCE; HUMAN; INTESTINE FLORA; INTESTINE FUNCTION; METAGENOMICS; MICROBIOME; NONHUMAN; OPEN READING FRAME; PRIORITY JOURNAL; QUORUM SENSING; REVIEW; SEQUENCE ANALYSIS; SIGNAL TRANSDUCTION;

BACTERIOPHAGES; HUMANS; INFLAMMATORY BOWEL DISEASES; INTESTINES; METAGENOME; METAGENOMICS;

EID: 84871124415     PISSN: 00175749     EISSN: 14683288     Source Type: Journal    
DOI: 10.1136/gutjnl-2011-301805     Document Type: Review

References (94)

1. Davies J. In a map for human life, count the microbes, too. Science 2001;291:2316. (Pubitemid 32231773)
2. Berg RD. The indigenous gastrointestinal microflora. Trends Microbiol 1996;4:430-5. (Pubitemid 26373240)
3. Savage DC. Microorganisms associated with epithelial surfaces and stability of the indigenous gastrointestinal microflora. Nahrung 1987;31:383-95.
4. Edwards DP. The roles of tolerance in the evolution, maintenance and breakdown of mutualism. Naturwissenschaften 2009;96:1137-45.
5. Gaboriau-Routhiau V, Rakotobe S, Lecuyer E, et al. The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 2009;31:677-89.
6. Neish AS. Microbes in gastrointestinal health and disease. Gastroenterology 2009;136:65-80.
7. Round JL, Mazmanian SK. The gut microbiota shapes intestinal immune responses during health and disease. Nat Rev Immunol 2009;9:313-23.
8. Bocci V. The neglected organ: bacterial flora has a crucial immunostimulatory role. Perspect Biol Med 1992;35:251-60.
9. Backhed F, Ley RE, Sonnenburg JL, et al. Hostebacterial mutualism in the human intestine. Science 2005;307:1915-20.
10. Cummings JH. Microbial digestion of complex carbohydrates in man. Proc Nutr Soc 1984;43:35-44.
11. Hooper LV, Midtvedt T, Gordon JI. How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr 2002;22:283-307. (Pubitemid 35221463)
12. Kelly D, Campbell JI, King TP, et al. Commensal anaerobic gut bacteria attenuate inflammation by regulating nuclear-cytoplasmic shuttling of PPAR-gamma and RelA. Nat Immunol 2004;5:104-12. (Pubitemid 38081475)
13. Willing BP, Van Kessel AG. Enterocyte proliferation and apoptosis in the caudal small intestine is influenced by the composition of colonizing commensal bacteria in the neonatal gnotobiotic pig. J Anim Sci 2007;85:3256-66. (Pubitemid 350247377)
14. Suau A, Bonnet R, Sutren M, et al. Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut. Appl Environ Microbiol 1999;65:4799-807.
15. Zoetendal EG, Rajilic-Stojanovic M, de Vos WM. High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota. Gut 2008;57:1605-15.
16. Koenig JE, Spor A, Scalfone N, et al. Succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci U S A 2011;108(Suppl 1):4578-85.
17. Mackie RI, Sghir A, Gaskins HR. Developmental microbial ecology of the neonatal gastrointestinal tract. Am J Clin Nutr 1999;69:1035S-45S. (Pubitemid 29205082)
18. De La Cochetiere MF, Durand T, Lepage P, et al. Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol 2005;43:5588-92. (Pubitemid 41612335)
19. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A 2011;108 (Suppl 1):4554-61.
20. Frank DN, St Amand AL, Feldman RA, et al. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 2007; 104:13780-5. (Pubitemid 350003397)
21. Tap J, Mondot S, Levenez F, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 2009;11:2574-84.
22. Dethlefsen L, Eckburg PB, Bik EM, et al. Assembly of the human intestinal microbiota. Trends Ecol Evol 2006;21:517-23. (Pubitemid 44233957)
23. Ley RE, Hamady M, Lozupone C, et al. Evolution of mammals and their gut microbes. Science 2008;320:1647-51. (Pubitemid 351931256)
24. Backhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci U S A 2004;101:15718-23. (Pubitemid 39473554)
25. Frank DN, Robertson CE, Hamm CM, et al. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis 2011;17:179-84.
26. Lepage P, Hasler R, Spehlmann ME, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011;141:227-36.
27. Ley RE, Backhed F, Turnbaugh P, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 2005;102:11070-5. (Pubitemid 41105994)
28. Ley RE, Turnbaugh PJ, Klein S, et al. Microbial ecology: human gut microbes associated with obesity. Nature 2006; 444:1022-3. (Pubitemid 46018512)
29. Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach. Gut 2006;55:205-11. (Pubitemid 43117279)
30. Mondot S, Kang S, Furet JP, et al. Highlighting new phylogenetic specificities of Crohn's disease microbiota. Inflamm Bowel Dis 2011;17:185-92.
31. Seksik P, Sokol H, Lepage P, et al. Review article: the role of bacteria in onset and perpetuation of inflammatory bowel disease. Aliment Pharmacol Ther 2006;24(Suppl 3):11-18. (Pubitemid 44326413)
32. Sartor RB. Intestinal microflora in human and experimental inflammatory bowel disease. Curr Opin Gastroenterol 2001;17:324-30. (Pubitemid 32619973)
33. Nagalingam NA, Lynch SV. Role of the microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. Published Online First: 20 September 2011. doi:10.1002/ibd.21866
34. Tamboli CP, Neut C, Desreumaux P, et al. Dysbiosis as a prerequisite for IBD. Gut 2004;53:1057.
35. Handelsman J, Rondon MR, Brady SF, et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem Biol 1998;5:R245-9. (Pubitemid 29000111)
36. Rondon MR, Raffel SJ, Goodman RM, et al. Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. Proc Natl Acad Sci U S A 1999;96:6451-5. (Pubitemid 29256686)
37. Niedringhaus TP, Milanova D, Kerby MB, et al. Landscape of next-generation sequencing technologies. Anal Chem 2011;83:4327-41.
38. Pope PB, Smith W, Denman SE, et al. Isolation of Succinivibrionaceae implicated in low methane emissions from Tammar wallabies. Science 2011;333:646-8.
39. Tyson GW, Chapman J, Hugenholtz P, et al. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004;428:37-43. (Pubitemid 38332350)
40. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65.
41. Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science 2006;312:1355-9. (Pubitemid 43839542)
42. Kurokawa K, Itoh T, Kuwahara T, et al. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 2007;14:169-81.
43. Manichanh C, Chapple CE, Frangeul L, et al. A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res 2008;36:5180-8.
44. Davenport CF, Tummler B. Abundant oligonucleotides common to most bacteria. PLoS One 2010;5:e9841.
45. Gabor EM, Alkema WB, Janssen DB. Quantifying the accessibility of the metagenome by random expression cloning techniques. Environ Microbiol 2004;6:879-86. (Pubitemid 39123242)
46. Handelsman J. Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 2004; 68:669-85. (Pubitemid 39628532)
47. Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009;457:480-4.
48. Turnbaugh PJ, Henrissat B, Gordon JI. Viewing the human microbiome through three-dimensional glasses: integrating structural and functional studies to better define the properties of myriad carbohydrate-active enzymes. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010;66:1261-4.
49. Li LL, McCorkle SR, Monchy S, et al. Bioprospecting metagenomes: glycosyl hydrolases for converting biomass. Biotechnol Biofuels 2009;2:10.
50. Tasse L, Bercovici J, Pizzut-Serin S, et al. Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes. Genome Res 2010;20:1605-12.
51. Jones BV, Begley M, Hill C, et al. Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome. Proc Natl Acad Sci U S A 2008; 105:13580-5.
52. Gloux K, Berteau O, El Oumami H, et al. A metagenomic beta-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci U S A 2011;108 (Suppl 1):4539-46.
53. Gloux K, Leclerc M, Iliozer H, et al. Development of high-throughput phenotyping of metagenomic clones from the human gut microbiome for modulation of eukaryotic cell growth. Appl Environ Microbiol 2007;73:3734-7. (Pubitemid 46871466)
54. Lakhdari O, Cultrone A, Tap J, et al. Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-kappaB modulation in the human gut. PLoS One 2010;5:pii: e13092.
55. Jones BV, Marchesi JR. Transposon-aided capture (TRACA) of plasmids resident in the human gut mobile metagenome. Nat Methods 2007;4:55-61. (Pubitemid 46029477)
56. Smillie CS, Smith MB, Friedman J, et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 2011;480:241-4.
57. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature 2011;473:174-80.
58. Wu GD, Chen J, Hoffmann C, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011;334:105-8.
59. Horvath K, Papadimitriou JC, Rabsztyn A, et al. Gastrointestinal abnormalities in children with autistic disorder. J Pediatr 1999;135:559-63. (Pubitemid 30180444)
60. Collins SM, Bercik P. The relationship between intestinal microbiota and the central nervous system in normal gastrointestinal function and disease. Gastroenterology 2009;136:2003-14.
61. Gonzalez A, Stombaugh J, Lozupone C, et al. The mind-body-microbial continuum. Dialogues Clin Neurosci 2011;13:55-62.
62. Heijtz RD, Wang S, Anuar F, et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci U S A 2011;108:3047-52.
63. Neufeld KM, Kang N, Bienenstock J, et al. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol Motil 2011;23:255-64, e119.
64. Sharon G, Segal D, Ringo JM, et al. Commensal bacteria play a role in mating preference of Drosophila melanogaster. Proc Natl Acad Sci U S A 2010;107:20051-6.
65. Frias-Lopez J, Shi Y, Tyson GW, et al. Microbial community gene expression in ocean surface waters. Proc Natl Acad Sci U S A 2008;105:3805-10. (Pubitemid 351723480)
66. Gosalbes MJ, Durban A, Pignatelli M, et al. Metatranscriptomic approach to analyze the functional human gut microbiota. PLoS One 2011;6:e17447.
67. O Cuiv P, Aguirre de Carcer D, Jones M, et al. The effects from DNA extraction methods on the evaluation of microbial diversity associated with human colonic tissue. Microb Ecol 2011;61:353-62.
68. Verberkmoes NC, Russell AL, Shah M, et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J 2009;3:179-89.
69. Turnbaugh PJ, Gordon JI. An invitation to the marriage of metagenomics and metabolomics. Cell 2008;134:708-13.
70. Marchesi JR, Holmes E, Khan F, et al. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 2007;6:546-51. (Pubitemid 46340158)
71. Jansson J, Willing B, Lucio M, et al. Metabolomics reveals metabolic biomarkers of Crohn's disease. PLoS One 2009;4:e6386.
72. Le Gall G, Noor SO, Ridgway K, et al. Metabolomics of fecal extracts detects altered metabolic activity of gut microbiota in ulcerative colitis and irritable bowel syndrome. J Proteome Res 2011;10:4208-18.
73. Breitbart M, Hewson I, Felts B, et al. Metagenomic analyses of an uncultured viral community from human feces. J Bacteriol 2003;185:6220-3. (Pubitemid 37248478)
74. Reyes A, Haynes M, Hanson N, et al. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010;466:334-8.
75. Minot S, Sinha R, Chen J, et al. The human gut virome: inter-individual variation and dynamic response to diet. Genome Res 2011;21:1616-25.
76. Lepage P, Colombet J, Marteau P, et al. Dysbiosis in inflammatory bowel disease: a role for bacteriophages? Gut 2008;57:424-5. (Pubitemid 351288109)
77. Paterson S, Vogwill T, Buckling A, et al. Antagonistic coevolution accelerates molecular evolution. Nature 2010;464:275-8.
78. Riley PA. Bacteriophages in autoimmune disease and other inflammatory conditions. Med Hypotheses 2004;62:493-8. (Pubitemid 38453348)
79. Alexopoulou L, Holt AC, Medzhitov R, et al. Recognition of double-stranded RNA and activation of NF-kappaB by toll-like receptor 3. Nature 2001;413:732-8. (Pubitemid 33009951)
80. Shi Z, Cai Z, Sanchez A, et al. A novel toll-like receptor that recognizes vesicular stomatitis virus. J Biol Chem 2011;286:4517-24.
81. D'Herelle F. On an invisible microbe antagonistic toward dysenteric bacilli: brief note by Mr. F. D'Herelle, presented by Mr. Roux. 1917. Res Microbiol 2007;158:553-4.
82. d'Herelle F. Bacteriophage as a treatment in acute medical and surgical infections. Bull N Y Acad Med 1931; 7:329-48.
83. Pirnay JP, De Vos D, Verbeken G, et al. The phage therapy paradigm: pret-a-porter or sur-mesure? Pharm Res 2011;28:934-7.
84. Kutateladze M, Adamia R. Phage therapy experience at the Eliava Institute. Med Mal Infect 2008;38:426-30.
85. Sulakvelidze A, Alavidze Z, Morris JG Jr. Bacteriophage therapy. Antimicrob Agents Chemother 2001;45:649-59. (Pubitemid 32182003)
86. Bruttin A, Brussow H. Human volunteers receiving Escherichia coli phage T4 orally: a safety test of phage therapy. Antimicrob Agents Chemother 2005;49:2874-8. (Pubitemid 40917605)
87. Gill JJ, Hyman P. Phage choice, isolation, and preparation for phage therapy. Curr Pharm Biotechnol 2010;11:2-14.
88. Raes J, Letunic I, Yamada T, et al. Toward molecular trait-based ecology through integration of biogeochemical, geographical and metagenomic data. Mol Syst Biol 2011;7:473.
89. Wang Y, Antonopoulos DA, Zhu X, et al. Laser capture microdissection and metagenomic analysis of intact mucosa-associated microbial communities of human colon. Appl Microbiol Biotechnol 2010;88:1333-42.
90. Mondot S, Barreau F, Al Nabhani Z, et al. Altered gut microbiota composition in immune-impaired Nod2-/- mice. Gut. Published Online First: 25 August 2011. doi:10.1136/gutjnl-2011-300478
91. Petnicki-Ocwieja T, Hrncir T, Liu YJ, et al. Nod2 is required for the regulation of commensal microbiota in the intestine. Proc Natl Acad Sci U S A 2009;106:15813-18.
92. Rehman A, Sina C, Gavrilova O, et al. Nod2 is essential for temporal development of intestinal microbial communities. Gut 2011;60:1354-62.
93. Joossens M, Huys G, Cnockaert M, et al. Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 2011;60:631-7.
94. Van de Merwe JP, Stegeman JH, Hazenberg MP. The resident faecal flora is determined by genetic characteristics of the host. Implications for Crohn's disease? Antonie Van Leeuwenhoek 1983;49:119-24. (Pubitemid 13045727)