The host selects mucosal and luminal associations of coevolved gut microorganisms: A novel concept

FEMS Microbiology Reviews

Volumn 35, Issue 4, 2011, Pages 681-704

  Van den Abbeele, Pieter ^a   Van de Wiele, Tom ^a   Verstraete, Willy ^a   Possemiers, Sam ^a  

^a GHENT UNIVERSITY   (Belgium)

Author keywords

Colon; Crohn's disease; Gastrointestinal; Microbial communities; Symbiotic bacteria

Indexed keywords

CASPASE RECRUITMENT DOMAIN PROTEIN 4; DECTIN 1; DEFENSIN; DNA DEPENDENT ACTIVATOR OF INTERFERON REGULATORY FACTOR; G PROTEIN COUPLED RECEPTOR; MUCIN; NUCLEOTIDE BINDING OLIGOMERIZATION DOMAIN LIKE RECEPTOR; TOLL LIKE RECEPTOR; TRANSCRIPTION FACTOR; TUMOR NECROSIS FACTOR ALPHA; UNCLASSIFIED DRUG;

ADAPTIVE IMMUNITY; ANTIGEN PRESENTING CELL; ARTICLE; BACTEROIDES FRAGILIS; BACTEROIDES THETAIOTAOMICRON; CROHN DISEASE; ENTERITIS; FAECALIBACTERIUM PRAUSNITZII; FIRMICUTES; GASTROINTESTINAL TRACT; GENE; HELICOBACTER PYLORI; HOST PATHOGEN INTERACTION; HOST RESISTANCE; HUMAN; IMMUNOCOMPETENT CELL; INNATE IMMUNITY; INTESTINE EPITHELIUM CELL; INTESTINE FLORA; LACTOBACILLUS ACIDOPHILUS; LACTOBACILLUS RHAMNOSUS; MELANOMA DIFFERENTIATION ASSOCIATED GENE 5; MICROBIAL COLONIZATION; MICROBIAL COMMUNITY; MICROORGANISM; MUCUS; NONHUMAN; NUTRIENT; OBESITY; PHYLOGENETIC TREE; PROTEIN EXPRESSION; PROTEIN SECRETION; RETINOIC ACID INDUCIBLE GENE I; SALMONELLA TYPHIMURIUM; SQUID; T LYMPHOCYTE; VERTEBRATE; VIBRIO FISCHERI;

ANIMALS; ASTHMA; BIOLOGICAL EVOLUTION; GASTROINTESTINAL TRACT; HOST-PATHOGEN INTERACTIONS; HUMANS; HYPERSENSITIVITY; IMMUNITY, INNATE; IMMUNITY, MUCOSAL; INFLAMMATORY BOWEL DISEASES; INTESTINAL MUCOSA; MODELS, BIOLOGICAL; OBESITY; SYMBIOSIS; VERTEBRATES;

BACTERIA (MICROORGANISMS);

EID: 79958056338     PISSN: 01686445     EISSN: 15746976     Source Type: Journal    
DOI: 10.1111/j.1574-6976.2011.00270.x     Document Type: Article

References (209)

1. Adlercreutz H (2007) Lignans and human health. Crit Rev Cl Lab Sci 44: 483-525.
2. Akira S, Uematsu S & Takeuchi O (2006) Pathogen recognition and innate immunity. Cell 124: 783-801.
3. Alander M, Satokari R, Korpela R, Saxelin M, Vilpponen-Salmela T, Mattila-Sandholm T & von Wright A (1999) Persistence of colonization of human colonic mucosa by a probiotic strain, Lactobacillus rhamnosus GG, after oral consumption. Appl Environ Microb 65: 351-354.
4. Alexopoulou L, Holt AC, Medzhitov R & Flavell RA (2001) Recognition of double-stranded RNA and activation of NF-kappaB by Toll-like receptor 3. Nature 413: 732-738.
5. Armelagos GJ & Harper KN (2005) Genomics at the origins of agriculture, part two. Evol Anthropol 14: 109-121.
6. Atuma C, Strugala V, Allen A & Holm L (2001) The adherent gastrointestinal mucus gel layer: thickness and physical state in vivo. Am J Physiol-Gastr L 280: G922-G929.
7. Ayabe T, Ashida T, Kohgo Y & Kono T (2004) The role of Paneth cells and their antimicrobial peptides in innate host defense. Trends Microbiol 12: 394-398.
8. Backhed F, Ley RE, Sonnenburg JL, Peterson DA & Gordon JI (2005) Host-bacterial mutualism in the human intestine. Science 307: 1915-1920.
9. Barnes P (2001) Th2 cytokines and asthma: an introduction. Respir Res 2: 64-65.
10. Bates JM, Akerlund J, Mittge E & Guillemin K (2007) Intestinal alkaline phosphatase detoxifies lipopolysaccharide and prevents inflammation in zebrafish in response to the gut microbiota. Cell Host Microbe 2: 371-382.
11. Belenguer A, Duncan SH, Calder AG, Holtrop G, Louis P, Lobley GE & Flint HJ (2006) Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microb 72: 3593-3599.
12. Benson AK, Kelly SA, Legge R et al. (2010) Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors. P Natl Acad Sci USA 107: 18933-18938.
13. Bernet MF, Brassart D, Neeser JR & Servin AL (1994) Lactobacillus acidophilus LA-1 binds to cultured human intestinal-cell lines and inhibits cell attachment and cell invasion by enterovirulent bacteria. Gut 35: 483-489.
14. Biedermann T & Rocken M (1999) Th1/Th2 balance in atopy. Springer Semin Immun 21: 295-316.
15. Bjorksten B, Naaber P, Sepp E & Mikelsaar M (1999) The intestinal microflora in allergic Estonian and Swedish 2-year-old children. Clin Exp Allergy 29: 342-346.
16. Blaser MJ (2006) Who are we? Indigenous microbes and the ecology of human diseases. EMBO Rep 7: 956-960.
17. Blaser MJ & Kirschner D (2007) The equilibria that allow bacterial persistence in human hosts. Nature 449: 843-849.
18. Blaser MJ, Chen Y & Reibman J (2008) Does Helicobacter pylori protect against asthma and allergy? Gut 57: 561-567.
19. Bomba A, Kastel R, Gancarcikova S, Nemcova R, Herich R & Cizek M (1996) The effect of lactobacilli inoculation on organic acid levels in the mucosal film and the small intestine contents in gnotobiotic pigs. Berl Munch Tierarztl 109: 428-430.
20. Bornside GH, Donovan WE & Myers MB (1976) Intracolonic tensions of oxygen and carbon dioxide in germfree, conventional, and gnotobiotic rats. P Soc Exp Biol Med 151: 437-441.
21. Boyden ED & Dietrich WF (2006) Nalp1b controls mouse macrophage susceptibility to anthrax lethal toxin. Nat Genet 38: 240-244.
22. Brandtzaeg P & Pabst R (2004) Let's go mucosal: communication on slippery ground. Trends Immunol 25: 570-577.
23. Buhnik K, Danin-Poleg Y & Kashi Y (2010) Effect of host genotype on gut microflora in mice. Proceedings of the International Scientific Conference on Probiotics and Prebiotics, 978-80-970168-4-5.
24. Busch R, Doebele RC, Patil NS, Pashine A & Mellins ED (2000) Accessory molecules for MHC class II peptide loading. Curr Opin Immunol 12: 99-106.
25. Cani PD, Amar J, Iglesias MA et al. (2007) Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 56: 1761-1772.
26. Cani PD, Possemiers S, Van de Wiele T et al. (2009) Changes in gut microbiota control inflammation in obese mice through a mechanism involving GLP-2-driven improvement of gut permeability. Gut 58: 1091-1103.
27. Cario E & Podolsky DK (2000) Differential alteration in intestinal epithelial cell expression of toll-like receptor 3 (TLR3) and TLR4 in inflammatory bowel disease. Infect Immun 68: 7010-7017.
28. Carneiro L, Magalhaes JG, Tattoli I, Philpott DJ & Travassos LH (2008) Nod-like proteins in inflammation and disease. J Pathol 214: 136-148.
29. Carroll MC (2004) The complement system in regulation of adaptive immunity. Nat Immunol 5: 981-986.
30. Chamaillard M, Hashimoto M, Horie Y et al. (2003) An essential role for NOD1 in host recognition of bacterial peptidoglycan containing diaminopimelic acid. Nat Immunol 4: 702-707.
31. Cheesman SE & Guillemin K (2007) We know you are in there: conversing with the indigenous gut microbiota. Res Microbiol 158: 2-9.
32. Cho JH (2008) The genetics and immunopathogenesis of inflammatory bowel disease. Nat Rev Immunol 8: 458-466.
33. Claesson MJ, Cusack S, O'Sullivan O et al. (2010) Composition, variability, and temporal stability of the intestinal microbiota of the elderly. P Natl Acad Sci USA. DOI: DOI: 10.1073/pnas.1000097107.
34. Clavel T, Dore J & Blaut M (2006) Bioavailability of lignans in human subjects. Nutr Res Rev 19: 187-196.
35. Collado MC, Gonzalez A, Gonzalez R, Hernandez M, Ferrus MA & Sanz Y (2005) Antimicrobial peptides are among the antagonistic metabolites produced by Bifidobacterium against Helicobacter pylori. Int J Antimicrob Ag 25: 385-391.
36. Cooper MD & Alder MN (2006) The evolution of adaptive immune systems. Cell 124: 815-822.
37. Dabbagh K, Dahl ME, Stepick-Biek P & Lewis DB (2002) Toll-like receptor 4 is required for optimal development of Th2 immune responses: role of dendritic cells. J Immunol 168: 4524-4530.
38. Danin-Poleg Y, Buhnik Y, Matsko V & Kashi Y (2010) Characterization of Lactobacillus johnsonii isolated from various hosts. Proceedings of the International Scientific Conference on Probiotics and Prebiotics, 978-80-970168-4-5.
39. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, Collini S, Pieraccini G & Lionetti P (2010) Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. P Natl Acad Sci USA 107: 14691-14696.
40. De La Cochetiere MF, Durand T, Lepage P, Bourreille A, Galmiche JP & Dore J (2005) Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol 43: 5588-5592.
41. Derrien M, Vaughan EE, Plugge CM & de Vos WM (2004) Akkermansia muciniphila gen. nov., sp. nov., a human intestinal mucin-degrading bacterium. Int J Syst Evol Micr 54: 1469-1476.
42. Dethlefsen L, Eckburg PB, Bik EM & Relman DA (2006) Assembly of the human intestinal microbiota. Trends Ecol Evol 21: 517-523.
43. 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.
44. Didierlaurent A, Sirard J, Kraehenbuhl J & Neutra MR (2002) How the gut senses its content. Cell Microbiol 4: 61-72.
45. Duncan SH, Hold GL, Harmsen HJM, Stewart CS & Flint HJ (2002) Growth requirements and fermentation products of Fusobacterium prausnitzii, and a proposal to reclassify it as Faecalibacterium prausnitzii gen. nov., comb. nov. Int J Syst Evol Micr 52: 2141-2146.
46. Duncan SH, Louis P & Flint HJ (2004) Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microb 70: 5810-5817.
47. Duncan SH, Belenguer A, Holtrop G, Johnstone AM, Flint HJ & Lobley GE (2007) Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microb 73: 1073-1078.
48. Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P & Flint HJ (2008) Human colonic microbiota associated with diet, obesity and weight loss. Int J Obesity 32: 1720-1724.
49. Ebersbach T, Jorgensen JB, Heegaard PM, Lahtinen SJ, Ouwehand AC, Poulsen M, Frokiaer H & Licht TR (2009) Certain dietary carbohydrates promote Listeria infection in a guinea pig model, while others prevent it. Int J Food Microbiol 140: 218-224.
50. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE & Relman DA (2005) Diversity of the human intestinal microbial flora. Science 308: 1635-1638.
51. Egert M, de Graaf AA, Smidt H, de Vos WM & Venema K (2006) Beyond diversity: functional microbiomics of the human colon. Trends Microbiol 14: 86-91.
52. Epstein J, Eichbaum Q, Sheriff S & Ezekowitz RAB (1996) The collectins in innate immunity. Curr Opin Immunol 8: 29-35.
53. Falony G, Vlachou A, Verbrugghe K & De Vuyst L (2006) Cross-feeding between Bifidobacterium longum BB536 and acetate-converting, butyrate-producing colon bacteria during growth on oligofructose. Appl Environ Microb 72: 7835-7841.
54. Flint HJ, Bayer EA, Rincon MT, Lamed R & White BA (2008) Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis. Nat Rev Microbiol 6: 121-131.
55. Frank DN, St.Amand AL, Feldman RA, Boedeker EC, Harpaz N & Pace NR (2007) Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. P Natl Acad Sci USA 104: 13780-13785.
56. Fritz JH, Ferrero RL, Philpott DJ & Girardin SE (2006) Nod-like proteins in immunity, inflammation and disease. Nat Immunol 7: 1250-1257.
57. Fritz JH, Le Bourhis L, Sellge G et al. (2007) Nod1-mediated innate immune recognition of peptidoglycan contributes to the onset of adaptive immunity. Immunity 26: 445-459.
58. Gaboriau-Routhiau V, Rakotobe S, Lecuyer E et al. (2009) The key role of segmented filamentous bacteria in the coordinated maturation of gut helper T cell responses. Immunity 31: 677-689.
59. Garima G & Avadhesha S (2007) Collectins: sentinels of innate immunity. Bioessays 29: 452-464.
60. Garrett WS, Lord GM, Punit S, Lugo-Villarino G, Mazmanian Sarkis K, Ito S, Glickman JN & Glimcher LH (2007) Communicable ulcerative colitis induced by T-bet deficiency in the innate immune system. Cell 131: 33-45.
61. Garrett WS, Gallini CA, Yatsunenko T et al. (2010) Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe 8: 292-300.
62. Gaskins HR (1997) Immunological aspects of host/microbiota interactions at the intestinal epithelium. Gastrointestinal Microbiology, Vol. 2 (Mackie RI, White BA & Isaacson RE, eds), pp. 537-587. Chapman and Hall, New York.
63. Gewirtz AT, Navas TA, Lyons S, Godowski PJ & Madara JL (2001) Cutting edge: bacterial flagellin activates basolaterally expressed TLR5 to induce epithelial proinflammatory gene expression. J Immunol 167: 1882-1885.
64. Girardin SE, Tournebize R, Mavris M et al. (2001) CARD4/Nod1 mediates NF-kappa B and JNK activation by invasive Shigella flexneri. EMBO Rep 2: 736-742.
65. Girardin SE, Boneca IG, Carneiro LAM et al. (2003a) Nod1 detects a unique muropeptide from gram-negative bacterial peptidoglycan. Science 300: 1584-1587.
66. Girardin SE, Boneca IG, Viala J, Chamaillard M, Labigne A, Thomas G, Philpott DJ & Sansonetti PJ (2003b) Nod2 is a general sensor of peptidoglycan through muramyl dipeptide (MDP) detection. J Biol Chem 278: 8869-8872.
67. Glimcher LH (2007) Trawling for treasure: tales of T-bet. Nat Immunol 8: 448-450.
68. Gutcher I & Becher B (2007) APC-derived cytokines and T cell polarization in autoimmune inflammation. J Clin Invest 117: 1119-1127.
69. Hackstein JHP & Stumm CK (1994) Methane production in terrestrial arthropods. P Natl Acad Sci USA 91: 5441-5445.
70. Hackstein JHP & van Alen TA (1996) Fecal methanogens and vertebrate evolution. Evolution 50: 559-572.
71. Harrington SM, Sheikh J, Henderson IR, Ruiz-Perez F, Cohen PS & Nataro JP (2009) The Pic protease of enteroaggregative Escherichia coli promotes intestinal colonization and growth in the presence of mucin. Infect Immun 77: 2465-2473.
72. Hayashi F, Smith KD, Ozinsky A, Hawn TR, Yi EC, Goodlett DR, Eng JK, Akira S, Underhill DM & Aderem A (2001) The innate immune response to bacterial flagellin is mediated by Toll-like receptor 5. Nature 410: 1099-1103.
73. Heil F, Hemmi H, Hochrein H, Ampenberger F, Kirschning C, Akira S, Lipford G, Wagner H & Bauer S (2004) Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8. Science 303: 1526-1529.
74. Hemmi H, Takeuchi O, Kawai T et al. (2000) A toll-like receptor recognizes bacterial DNA. Nature 408: 740-745.
75. Holmes E, Loo RL, Stamler J et al. (2008) Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 453: 396-400.
76. Hooper LV (2009) Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol 7: 367-374.
77. Hooper LV, Xu J, Falk PG, Midtvedt T & Gordon JI (1999) A molecular sensor that allows a gut commensal to control its nutrient foundation in a competitive ecosystem. P Natl Acad Sci USA 96: 9833-9838.
78. Hooper LV, Midtvedt T & Gordon JI (2002) How host-microbial interactions shape the nutrient environment of the mammalian intestine. Annu Rev Nutr 22: 283-307.
79. Hooper LV, Stappenbeck TS, Hong CV & Gordon JI (2003) Angiogenins: a new class of microbicidal proteins involved in innate immunity. Nat Immunol 4: 269-273.
80. Hopkins MJ, Sharp R & Macfarlane GT (2001) Age and disease related changes in intestinal bacterial populations assessed by cell culture, 16S rRNA abundance, and community cellular fatty acid profiles. Gut 48: 198-205.
81. Hoshino K, Takeuchi O, Kawai T, Sanjo H, Ogawa T, Takeda Y, Takeda K & Akira S (1999) Cutting edge: toll-like receptor 4 (TLR4)-deficient mice are hyporesponsive to lipopolysaccharide: evidence for TLR4 as the Lps gene product. J Immunol 162: 3749-3752.
82. Infante-Duarte C & Kamradt T (1999) Th1/Th2 balance in infection. Springer Semin Immun 21: 317-338.
83. Ivanov II, McKenzie BS, Zhou L, Tadokoro CE, Lepelley A, Lafaille JJ, Cua DJ & Littman DR (2006) The orphan nuclear receptor ROR gamma t directs the differentiation program of proinflammatory IL-17(+) T helper cells. Cell 126: 1121-1133.
84. Ivanov II, Frutos RD, Manel N, Yoshinaga K, Rifkin DB, Sartor RB, Finlay BB & Littman DR (2008) Specific microbiota direct the differentiation of IL-17-producing T-helper cells in the mucosa of the small intestine. Cell Host Microbe 4: 337-349.
85. Ivanov II, Atarashi K, Manel N et al. (2009) Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 139: 485-498.
86. Iwasaki A & Medzhitov R (2004) Toll-like receptor control of the adaptive immune responses. Nat Immunol 5: 987-995.
87. Johansson MEV, Phillipson M, Petersson J, Velcich A, Holm L & Hansson GC (2008) The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. P Natl Acad Sci USA 105: 15064-15069.
88. Johansson MEV, Gustafsson JK, Sjöberg KE, Petersson J, Holm L, Sjövall H & Hansson GC (2010) Bacteria penetrate the inner mucus layer before inflammation in the dextran sulfate colitis model. PLoS One 5: e12238.
89. Kankainen M, Paulin L, Tynkkynen S et al. (2009) Comparative genomic analysis of Lactobacillus rhamnosus GG reveals pili containing a human-mucus binding protein. P Natl Acad Sci USA 106: 17193-17198.
90. Kaparakis M, Philpott DJ & Ferrero RL (2007) Mammalian NLR proteins; discriminating foe from friend. Immunol Cell Biol 85: 495-502.
91. Kapsenberg ML (2003) Dendritic-cell control of pathogen-driven T-cell polarization. Nat Rev Immunol 3: 984-993.
92. Karasov WH & Martinez del Rio C (2007) Physiological Ecology: How Animals Process Energy, Nutrients, and Toxins. Princeton University Press, NJ.
93. Kirk E (1949) The quantity and composition of human colonic flatus. Gastroenterology 12: 782-794.
94. Koeppel A, Perry EB, Sikorski J et al. (2008) Identifying the fundamental units of bacterial diversity: a paradigm shift to incorporate ecology into bacterial systematics. P Natl Acad Sci USA 105: 2504-2509.
95. Konstantinov SR, Smidt H, de Vos WM et al. (2008) S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions. P Natl Acad Sci USA 105: 19474-19479.
96. Kovatcheva-Datchary P, Egert M, Maathuis A, Rajilić-Stojanović M, De Graaf AA, Smidt H, De Vos WM & Venema K (2009) Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 11: 914-926.
97. Lederberg J (2000) Infectious history. Science 288: 287-293.
98. Lepage P, Seksik P, Sutren M, de la Cochetière MF, Jian R, Marteau P & Doré J (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.
99. Le Poul E, Loison C, Struyf S et al. (2003) Functional characterization of human receptors for short chain fatty acids and their role in polymorphonuclear cell activation. J Biol Chem 278: 25481-25489.
100. Ley RE, Turnbaugh PJ, Klein S & Gordon JI (2006) Microbial ecology: human gut microbes associated with obesity. Nature 444: 1022-1023.
101. Ley RE, Hamady M, Lozupone C et al. (2008) Evolution of mammals and their gut microbes. Science 320: 1647-1651.
102. Li M, Wang B, Zhang M et al. (2008) Symbiotic gut microbes modulate human metabolic phenotypes. P Natl Acad Sci USA 105: 2117-2122.
103. Lievin-Le Moal V & Servin AL (2006) The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota. Clin Microbiol Rev 19: 315-337.
104. Louis P & Flint HJ (2009) Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett 294: 1-8.
105. Louis P, Scott KP, Duncan SH & Flint HJ (2007) Understanding the effects of diet on bacterial metabolism in the large intestine. J Appl Microbiol 102: 1197-1208.
106. Luckey TD (1972) Introduction to intestinal microecology. Am J Clin Nutr 25: 1292-1294.
107. Macfarlane GT & Macfarlane S (1997) Human colonic microbiota: ecology, physiology and metabolic potential of intestinal bacteria. Scand J Gastroentero 32: 3-9.
108. Macfarlane S & Macfarlane GT (2003) Regulation of short-chain fatty acid production. P Nutr Soc 62: 67-72.
109. Macpherson AJ & Uhr T (2004) Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303: 1662-1665.
110. Mandel M, Wollenberg M, Stabb E, Visick K & Ruby E (2009) A single regulatory gene is sufficient to alter bacterial host range. Nature 458: 215-218.
111. Margarita M-M, Xavier A, Ferran G-H, Doroteo A & Garcia-Gil LJ (2006) Abnormal microbiota composition in the ileocolonic mucosa of Crohn's disease patients as revealed by polymerase chain reaction-denaturing gradient gel electrophoresis. Inflamm Bowel Dis 12: 1136-1145.
112. Mariathasan S, Weiss DS, Newton K, McBride J, O'Rourke K, Roose-Girma M, Lee WP, Weinrauch Y, Monack DM & Dixit VM (2006) Cryopyrin activates the inflammasome in response to toxins and ATP. Nature 440: 228-232.
113. Martens EC, Chiang HC & Gordon JI (2008) Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 4: 447-457.
114. Martens EC, Koropatkin NM, Smith TJ & Gordon JI (2009) Complex glycan catabolism by the human gut microbiota: the Bacteroidetes sus-like paradigm. J Biol Chem 284: 24673-24677.
115. Martin FPJ, Dumas ME, Wang YL et al. (2007) A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol 3: 112.
116. Martinon F, Petrilli V, Mayor A, Tardivel A & Tschopp J (2006) Gout-associated uric acid crystals activate the NALP3 inflammasome. Nature 440: 237-241.
117. Mazmanian SK, Liu CH, Tzianabos AO & Kasper DL (2005) An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 122: 107-118.
118. Mazmanian SK, Round JL & Kasper DL (2008) A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 453: 620-625.
119. McFall-Ngai M (2007) Adaptive immunity: care for the community. Nature 445: 153.
120. McFall-Ngai MJ & Ruby EG (1991) Symbiont recognition and subsequent morphogenesis as early events in an animal-bacterial mutualism. Science 254: 1491-1494.
121. Medzhitov R & Janeway CA (1997) Innate immunity: the virtues of a nonclonal system of recognition. Cell 91: 295-298.
122. Medzhitov R & Janeway CA Jr (2002) Decoding the patterns of self and nonself by the innate immune system. Science 296: 298-300.
123. Meyer-Hoffert U, Hornef MW, Henriques-Normark B, Axelsson LG, Midtvedt T, Putsep K & Andersson M (2008) Secreted enteric antimicrobial activity localises to the mucus surface layer. Gut 57: 764-771.
124. Miller TL & Wolin MJ (1985) Methanosphaera stadtmaniae gen. nov., sp. nov. - a species that forms methane by reducing methanol with hydrogen. Arch Microbiol 141: 116-122.
125. Mokdad AH, Bowman BA, Ford ES, Vinicor F, Marks JS & Koplan JP (2001) The continuing epidemics of obesity and diabetes in the United States. J Am Med Assoc 286: 1195-1200.
126. Molofsky AB, Byrne BG, Whitfield NN, Madigan CA, Fuse ET, Tateda K & Swanson MS (2006) Cytosolic recognition of flagellin by mouse macrophages restricts Legionella pneumophila infection. J Exp Med 203: 1093-1104.
127. Montalto M, Maggiano N, Ricci R, Curigliano V, Santoro L, Di Nicuolo F, Vecchio FM, Gasbarrini A & Gasbarrini G (2004) Lactobacillus acidophilus protects tight junctions from aspirin damage in HT-29 cells. Digestion 69: 225-229.
128. Mukherjee S, Vaishnava S & Hooper L (2008) Multi-layered regulation of intestinal antimicrobial defense. Cell Mol Life Sci 65: 3019-3027.
129. Mulder IE, Schmidt B, Stokes CR et al. (2009) Environmentally-acquired bacteria influence microbial diversity and natural innate immune responses at gut surfaces. BMC Biol 7: 79.
130. Nash J (1951) Non-cooperative games. Ann Math 54: 286-295.
131. Neutra MR (1998) V. Role of M cells in transepithelial transport of antigens and pathogens to the mucosal immune system. Am J Physiol-Gastr L 274: G785-G791.
132. Niedergang F & Kweon M-N (2005) New trends in antigen uptake in the gut mucosa. Trends Microbiol 13: 485-490.
133. Niess JH, Brand S, Gu X et al. (2005) CX3CR1-mediated dendritic cell access to the intestinal lumen and bacterial clearance. Science 307: 254-258.
134. Nishiguchi MK, Ruby EG & McFall-Ngai MJ (1998) Competitive dominance among strains of luminous bacteria provides an unusual form of evidence for parallel evolution in sepiolid squid-vibrio symbioses. Appl Environ Microb 64: 3209-3213.
135. Nuding S, Zabel LT, Enders C, Porter E, Fellermann K, Wehkamp J, Mueller HAG & Stange EF (2009) Antibacterial activity of human defensins on anaerobic intestinal bacterial species: a major role of HBD-3. Microbes Infect 11: 384-393.
136. Ogura Y, Lala S, Xin W et al. (2003) Expression of NOD2 in Paneth cells: a possible link to Crohn's ileitis. Gut 52: 1591-1597.
137. O'Hara AM & Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7: 688-693.
138. Oh PL, Benson AK, Peterson DA, Patil PB, Moriyama EN, Roos S & Walter J (2010) Diversification of the gut symbiont Lactobacillus reuteri as a result of host-driven evolution. ISME J 4: 377-387.
139. Ozinsky A, Underhill DM, Fontenot JD, Hajjar AM, Smith KD, Wilson CB, Schroeder L & Aderem A (2000) The repertoire for pattern recognition of pathogens by the innate immune system is defined by cooperation between Toll-like receptors. P Natl Acad Sci USA 97: 13766-13771.
140. Palm NW & Medzhitov R (2009) Pattern recognition receptors and control of adaptive immunity. Immunol Rev 227: 221-233.
141. Pamer E & Cresswell P (1998) Mechanisms of MHC class I-restricted antigen processing. Annu Rev Immunol 16: 323-358.
142. Petersen A, Heegaard PMH, Pedersen AL, Andersen JB, Sorensen RB, Frokiaer H, Lahtinen SJ, Ouwehand AC, Poulsen M & Licht TR (2009) Some putative prebiotics increase the severity of Salmonella enterica serovar Typhimurium infection in mice. BMC Microbiol 9: 245.
143. Porcelli SA & Modlin RL (1999) THE CD1 SYSTEM: antigen-presenting molecules for T cell recognition of lipids and glycolipids. Annu Rev Immunol 17: 297-329.
144. Pretzer G, Snel J, Molenaar D, Wiersma A, Bron PA, Lambert J, de Vos WM, van der Meer R, Smits MA & Kleerebezem M (2005) Biodiversity-based identification and functional characterization of the mannose-specific adhesin of Lactobacillus plantarum. J Bacteriol 187: 6128-6136.
145. Pryde SE, Duncan SH, Hold GL, Stewart CS & Flint HJ (2002) The microbiology of butyrate formation in the human colon. FEMS Microbiol Lett 217: 133-139.
146. Qi H, Egen JG, Huang AYC & Germain RN (2006) Extrafollicular activation of lymph node B cells by antigen-bearing dendritic cells. Science 312: 1672-1676.
147. Qin J, Li R, Raes J et al. (2010) A human gut microbial gene catalogue established by metagenomic sequencing. Nature 464: 59-65.
148. Rammensee HG, Bachmann J, Emmerich NPN, Bachor OA & Stevanović S (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics 50: 213-219.
149. Rawls JF, Mahowald MA, Ley RE & Gordon JI (2006) Reciprocal gut microbiota transplants from zebrafish and mice to germ-free recipients reveal host habitat selection. Cell 127: 423-433.
150. Reid DM, Gow NAR & Brown GD (2009) Pattern recognition: recent insights from dectin-1. Curr Opin Immunol 21: 30-37.
151. Rescigno M, Urbano M, Valzasina B, Francolini M, Rotta G, Bonasio R, Granucci F, Kraehenbuhl J-P & Ricciardi-Castagnoli P (2001) Dendritic cells express tight junction proteins and penetrate gut epithelial monolayers to sample bacteria. Nat Immunol 2: 361-367.
152. Rijkers GT, Bengmark S, Enck P et al. (2010) Guidance for substantiating the evidence for beneficial effects of probiotics: current status and recommendations for future research. J Nutr 140: 671S-676S.
153. Romagnani S (1992) Human Th1 and Th2 subsets - regulation of differentiation and role in protection and immunopathology. Int Arch Allergy Imm 98: 279-285.
154. Roncarolo MG & Levings MK (2000) The role of different subsets of T regulatory cells in controlling autoimmunity. Curr Opin Immunol 12: 676-683.
155. Rook GAW (2007) The hygiene hypothesis and the increasing prevalence of chronic inflammatory disorders. T Roy Soc Trop Med H 101: 1072-1074.
156. Rook GAW (2009) Review series on helminths, immune modulation and the hygiene hypothesis: the broader implications of the hygiene hypothesis. Immunology 126: 3-11.
157. Roos S & Jonsson H (2002) A high-molecular-mass cell-surface protein from Lactobacillus reuteri 1063 adheres to mucus components. Microbiology 148: 433-442.
158. Ruas-Madiedo P, Gueimonde M, Fernandez-Garcia M, de los Reyes-Gavilan CG & Margolles A (2008) Mucin degradation by Bifidobacterium strains isolated from the human intestinal microbiota. Appl Environ Microb 74: 1936-1940.
159. Rubio S, Lacaze-Masmonteil T, Chailley-Heu B, Kahn A, Bourbon JR & Ducroc R (1995) Pulmonary surfactant protein A (SP-A) is expressed by epithelial cells of small and large intestine. J Biol Chem 270: 12162-12169.
160. Salyers AA, Vercellotti JR, West SEH & Wilkins TD (1977a) Fermentation of mucin and plant polysaccharides by strains of Bacteroides from human colon. Appl Environ Microb 33: 319-322.
161. Salyers AA, West SEH, Vercellotti JR & Wilkins TD (1977b) Fermentation of mucins and plant polysaccharides by anaerobic bacteria from human colon. Appl Environ Microb 34: 529-533.
162. Samuel BS, Shaito A, Motoike T et al. (2008) Effects of the gut microbiota on host adiposity are modulated by the short-chain fatty-acid binding G protein-coupled receptor, Gpr41. P Natl Acad Sci USA 105: 16767-16772.
163. Sartor RB (2006) Mechanisms of disease: pathogenesis of Crohn's disease and ulcerative colitis. Nat Clin Pract Gastr 3: 390-407.
164. Scheppach W & Weiler F (2004) The butyrate story: old wine in new bottles? Curr Opin Clin Nutr 7: 563-567.
165. Schreiber O (2010) Microcirculation, Mucus and Microbiota in Inflammatory Bowel Disease. Acta Universitatis Upsaliensis, Uppsala.
166. Schwiertz A, Taras D, Schafer K, Beijer S, Bos NA, Donus C & Hardt PD (2010) Microbiota and SCFA in lean and overweight healthy subjects. Obesity 18: 190-195.
167. Sekirov I, Tam NM, Jogova M, Robertson ML, Li Y, Lupp C & Finlay BB (2008) Antibiotic-induced perturbations of the intestinal microbiota alter host susceptibility to enteric infection. Infect Immun 76: 4726-4736.
168. Seth A, Yan F, Polk DB & Rao RK (2008) Probiotics ameliorate the hydrogen peroxide-induced epithelial barrier disruption by a PKC- and MAP kinase-dependent mechanism. Am J Physiol-Gastr L 294: G1060-G1069.
169. Shapiro JA (1998) Thinking about bacterial populations as multicellular organisms. Annu Rev Microbiol 52: 81-104.
170. Shevach EM (2002) CD4(+)CD25(+) suppressor T cells: more questions than answers. Nat Rev Immunol 2: 389-400.
171. Sokol H, Pigneur B, Watterlot L et al. (2008) Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. P Natl Acad Sci USA 105: 16731-16736.
172. Stappenbeck TS, Hooper LV & Gordon JI (2002) Developmental regulation of intestinal angiogenesis by indigenous microbes via Paneth cells. P Natl Acad Sci USA 99: 15451-15455.
173. Stecher B & Hardt W-D (2008) The role of microbiota in infectious disease. Trends Microbiol 16: 107-114.
174. Stewart PS & Costerton JW (2001) Antibiotic resistance of bacteria in biofilms. Lancet 358: 135-138.
175. Strachan DP (1989) Hay-fever, hygiene, and household size. Brit Med J 299: 1259-1260.
176. Strugala V, Dettmar PW & Pearson JP (2008) Thickness and continuity of the adherent colonic mucus barrier in active and quiescent ulcerative colitis and Crohn's disease. Int J Clin Pract 62: 762-769.
177. Swidsinski A, Ladhoff A, Pernthaler A et al. (2002) Mucosal flora in inflammatory bowel disease. Gastroenterology 122: 44-54.
178. Szabo SJ, Kim ST, Costa GL, Zhang X, Fathman CG & Glimcher LH (2000) A novel transcription factor, T-bet, directs Th1 lineage commitment. Cell 100: 655-669.
179. Takaoka A, Wang Z, Choi MK et al. (2007) DAI (DLM-1/ZBP1) is a cytosolic DNA sensor and an activator of innate immune response. Nature 448: 501-505.
180. Takeda K & Akira S (2004) TLR signaling pathways. Semin Immunol 16: 3-9.
181. Takeda K, Kaisho T & Akira S (2003) Toll-like receptors. Annu Rev Immunol 21: 335-376.
182. Takeuchi O & Akira S (2008) MDA5/RIG-I and virus recognition. Curr Opin Immunol 20: 17-22.
183. Takeuchi O, Kawai T, Muhlradt PF, Morr M, Radolf JD, Zychlinsky A, Takeda K & Akira S (2001) Discrimination of bacterial lipoproteins by Toll-like receptor 6. Int Immunol 13: 933-940.
184. Takeuchi O, Sato S, Horiuchi T, Hoshino K, Takeda K, Dong Z, Modlin RL & Akira S (2002) Cutting edge: role of toll-like receptor 1 in mediating immune response to microbial lipoproteins. J Immunol 169: 10-14.
185. Tap J, Mondot S, Levenez F et al. (2009) Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 11: 2574-2584.
186. Ten Bruggencate SJM, Bovee-Oudenhoven IMJ, Lettink-Wissink MLG & Van der Meer R (2003) Dietary fructo-oligosaccharides dose-dependently increase translocation of Salmonella in rats. J Nutr 133: 2313-2318.
187. Tenovuo J (2002) Clinical applications of antimicrobial host proteins lactoperoxidase, lysozyme and lactoferrin in xerostomia: efficacy and safety. Oral Dis 8: 23-29.
188. Ting JPY, Kastner DL & Hoffman HM (2006) CATERPILLERs, pyrin and hereditary immunological disorders. Nat Rev Immunol 6: 183-195.
189. Ting JPY, Lovering RC, Alnemri ES et al. (2008) The NLR gene family: a standard nomenclature. Immunity 28: 285-287.
190. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER & Gordon JI (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444: 1027-1131.
191. Turnbaugh PJ, Bäckhed 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.
192. Turnbaugh PJ, Hamady M, Yatsunenko T et al. (2009) A core gut microbiome in obese and lean twins. Nature 457: 480-484.
193. Vaishnava S, Behrendt CL, Ismail AS, Eckmann L & Hooper LV (2008) Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface. P Natl Acad Sci USA 105: 20858-20863.
194. van Vliet MJ, Tissing WJE, Dun CAJ, Meessen NEL, Kamps WA, de Bont E & Harmsen HJM (2009) Chemotherapy treatment in pediatric patients with acute myeloid leukemia receiving antimicrobial prophylaxis leads to a relative increase of colonization with potentially pathogenic bacteria in the gut. Clin Infect Dis 49: 262-270.
195. Vasquez N, Mangin I, Lepage P et al. (2007) Patchy distribution of mucosal lesions in ileal Crohn's disease is not linked to differences in the dominant mucosa-associated bacteria: a study using fluorescence in situ hybridization and temporal temperature gradient gel electrophoresis. Inflamm Bowel Dis 13: 684-692.
196. Visick KL, Foster J, Doino J, McFall-Ngai M & Ruby EG (2000) Vibrio fischeri lux genes play an important role in colonization and development of the host light organ. J Bacteriol 182: 4578-4586.
197. von Hertzen LC (2000) Puzzling associations between childhood infections and the later occurrence of asthma and atopy. Ann Med 32: 397-400.
198. Walker AW, Duncan SH, Leitch ECM, Child MW & Flint HJ (2005) pH and peptide supply can radically alter bacterial populations and short-chain fatty acid ratios within microbial communities from the human colon. Appl Environ Microb 71: 3692-3700.
199. Whitman WB, Coleman DC & Wiebe WJ (1998) Prokaryotes: the unseen majority. P Natl Acad Sci USA 95: 6578-6583.
200. Willing B, Halfvarson J, Dicksved J, Rosenquist M, Järnerot G, Engstrand L, Tysk C & Jansson JK (2009) Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease. Inflamm Bowel Dis 15: 653-660.
201. Xu J, Xu X & Verstraete W (2001) Quantitative measurement of the nitrate reductase activity in the human oral cavity. Food Chem Toxicol 39: 393-400.
202. Yarovinsky F, Hieny S & Sher A (2008) Recognition of toxoplasma gondii by TLR11 prevents parasite-induced immunopathology. J Immunol 181: 8478-8484.
203. Ye Z & Ting JP-Y (2008) NLR, the nucleotide-binding domain leucine-rich repeat containing gene family. Curr Opin Immunol 20: 3-9.
204. Zaneveld J, Turnbaugh PJ, Lozupone C, Ley RE, Hamady M, Gordon JI & Knight R (2008) Host-bacterial coevolution and the search for new drug targets. Curr Opin Chem Biol 12: 109-114.
205. Zhang D, Zhang G, Hayden MS, Greenblatt MB, Bussey C, Flavell RA & Ghosh S (2004) A toll-like receptor that prevents infection by uropathogenic bacteria. Science 303: 1522-1526.
206. Zheng W-P & Flavell RA (1997) The transcription factor GATA-3 is necessary and sufficient for Th2 cytokine gene expression in CD4 T cells. Cell 89: 587-596.
207. Zoetendal EG, Akkermans ADL & 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 Microb 64: 3854-3859.
208. Zoetendal EG, Akkermans ADL, Akkermans-van Vliet WM, de Visser JAGM & de Vos WM (2001) The host genotype affects the bacterial community in the human gastrointestinal tract. Microb Ecol Health D 13: 129-134.
209. Zoetendal EG, von Wright A, Vilpponen-Salmela T, Ben-Amor K, Akkermans ADL & 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 Microb 68: 3401-3407.