Gut microbiome-host interactions in health and disease

Genome Medicine

Volumn 3, Issue 3, 2011, Pages

  Kinross, James M ^a   Darzi, Ara W ^a   Nicholson, Jeremy K ^b  

^a ST MARY S HOSPITAL   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; RNA 16S;

DRUG EFFICACY; HEALTH CARE FACILITY; HEALTH STATUS; HOST PARASITE INTERACTION; INTESTINE; INTESTINE FLORA; METAGENOMICS; MICROBIOME; MODULATION; NONHUMAN; PRIORITY JOURNAL; REVIEW; TRANSPLANTATION;

EID: 79952712983     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/gm228     Document Type: Review

References (101)

1. Bengmark S. Ecological control of the gastrointestinal tract. The role of probiotic flora. Gut 1998, 42:2-7. 10.1136/gut.42.1.2, 1726957, 9505873.
2. Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, Gordon JI, Relman DA, Fraser-Liggett CM, Nelson KE. Metagenomic analysis of the human distal gut microbiome. Science 2006, 312:1355-1359. 10.1126/science.1124234, 3027896, 16741115.
3. Lederberg J. Infectious history. Science 2000, 288:287-293. 10.1126/science.288.5464.287, 10777411.
4. Dethlefsen L, McFall-Ngai M, Relman DA. An ecological and evolutionary perspective on human-microbe mutualism and disease. Nature 2007, 449:811-818. 10.1038/nature06245, 17943117.
5. Vaughan EE, Schut F, Heilig HG, Zoetendal EG, de Vos WM, Akkermans AD. A molecular view of the intestinal ecosystem. Curr Issues Intest Microbiol 2000, 1:1-12.
6. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, Pons N, Levenez F, Yamada T, Mende DR, Li J, Xu J, Li S, Li D, Cao J, Wang B, Liang H, Zheng H, Xie Y, Tap J, Lepage P, Bertalan M, Batto JM, Hansen T, Le Paslier D, Linneberg A, Nielsen HB, Pelletier E, Renault P, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464:59-65. 10.1038/nature08821, 20203603.
7. Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006, 444:1027-1031. 10.1038/nature05414, 17183312.
8. Holmes E, Loo RL, Stamler J, Bictash M, Yap IK, Chan Q, Ebbels T, De Iorio M, Brown IJ, Veselkov KA, Daviglus ML, Kesteloot H, Ueshima H, Zhao L, Nicholson JK, Elliott P. Human metabolic phenotype diversity and its association with diet and blood pressure. Nature 2008, 453:396-400. 10.1038/nature06882, 18425110.
9. Marchesi JR, Holmes E, Khan F, Kochhar S, Scanlan P, Shanahan F, Wilson ID, Wang Y. Rapid and noninvasive metabonomic characterization of inflammatory bowel disease. J Proteome Res 2007, 6:546-551. 10.1021/pr060470d, 17269711.
10. Finegold SM. Therapy and epidemiology of autism - clostridial spores as key elements. Med Hypotheses 2008, 70:508-511. 10.1016/j.mehy.2007.07.019, 17904761.
11. Clayton TA, Lindon JC, Cloarec O, Antti H, Charuel C, Hanton G, Provost JP, Le Net JL, Baker D, Walley RJ, Everett JR, Nicholson JK. Pharmaco-metabonomic phenotyping and personalized drug treatment. Nature 2006, 440:1073-1077. 10.1038/nature04648, 16625200.
12. Hooper LV, Gordon JI. Commensal host-bacterial relationships in the gut. Science 2001, 292:1115-1118. 10.1126/science.1058709, 11352068.
13. Macpherson AJ, Gatto D, Sainsbury E, Harriman GR, Hengartner H, Zinkernagel RM. A primitive T cell-independent mechanism of intestinal mucosal IgA responses to commensal bacteria. Science 2000, 288:2222-2226. 10.1126/science.288.5474.2222, 10864873.
14. Kinross JM, Alkhamesi N, Barton RH, Silk DB, Yap IK, Darzi AW, Holmes E, Nicholson JK. Global metabolic phenotyping in an experimental laparotomy model of surgical trauma. J Proteome Res 2011, 10:277-287. 10.1021/pr1003278, 21105667.
15. Nicholson JK, Holmes E, Wilson ID. Gut microorganisms, mammalian metabolism and personalized health care. Nat Rev Microbiol 2005, 3:431-438. 10.1038/nrmicro1152, 15821725.
16. Mazmanian SK, Liu CH, Tzianabos AO, Kasper DL. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell 2005, 122:107-118. 10.1016/j.cell.2005.05.007, 16009137.
17. Rakoff-Nahoum S, Paglino J, Eslami-Varzaneh F, Edberg S, Medzhitov R. Recognition of commensal microflora by toll-like receptors is required for intestinal homeostasis. Cell 2004, 118:229-241. 10.1016/j.cell.2004.07.002, 15260992.
18. Wilson ID, Nicholson JK. The role of gut microbiota in drug response. Curr Pharm Des 2009, 15:1519-1523. 10.2174/138161209788168173, 19442168.
19. Ley RE, Knight R, Gordon JI. The human microbiome: eliminating the biomedical/environmental dichotomy in microbial ecology. Environ Microbiol 2007, 9:3-4. 10.1111/j.1462-2920.2006.01222_3.x, 17227400.
20. Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science 2009, 326:1694-1697. 10.1126/science.1177486, 19892944.
21. Manichanh C, Varela E, Martinez C, Antolin M, Llopis M, Dore J, Giralt J, Guarner F, Malagelada JR. The gut microbiota predispose to the pathophysiology of acute postradiotherapy diarrhea. Am J Gastroenterol 2008, 103:1754-1761. 10.1111/j.1572-0241.2008.01868.x, 18564125.
22. Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006, 124:837-848. 10.1016/j.cell.2006.02.017, 16497592.
23. Sartor RB. Therapeutic manipulation of the enteric microflora in inflammatory bowel diseases: antibiotics, probiotics, and prebiotics. Gastroenterology 2004, 126:1620-1633. 10.1053/j.gastro.2004.03.024, 15168372.
24. Raibaud P. Experimental models for studying the microbial ecology in the intestinal tract. Acta Gastroenterol Latinoam 1989, 19:219-226.
25. Jia W, Li H, Zhao L, Nicholson JK. Gut microbiota: a potential new territory for drug targeting. Nat Rev Drug Discov 2008, 7:123-129. 10.1038/nrd2505, 18239669.
26. Palmer C, Bik EM, DiGiulio DB, Relman DA, Brown PO. Development of the human infant intestinal microbiota. PLoS Biol 2007, 5:e177. 10.1371/journal.pbio.0050177, 1896187, 17594176.
27. Zoetendal EG, Akkermans AD, De Vos WM. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 1998, 64:3854-3859. 106569, 9758810.
28. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 2005, 102:11070-11075. 10.1073/pnas.0504978102, 1176910, 16033867.
29. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484. 10.1038/nature07540, 19043404.
30. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, Gill SR, Nelson KE, Relman DA. Diversity of the human intestinal microbial flora. Science 2005, 308:1635-1638. 10.1126/science.1110591, 1395357, 15831718.
31. Kibe R, Sakamoto M, Hayashi H, Yokota H, Benno Y. Maturation of the murine cecal microbiota as revealed by terminal restriction fragment length polymorphism and 16S rRNA gene clone libraries. FEMS Microbiol Lett 2004, 235:139-146. 10.1111/j.1574-6968.2004.tb09578.x, 15158273.
32. Licht TR, Madsen B, Wilcks A. Selection of bacteria originating from a human intestinal microbiota in the gut of previously germ-free rats. FEMS Microbiol Lett 2007, 277:205-209. 10.1111/j.1574-6968.2007.00962.x, 18031341.
33. Kibe R, Sakamoto M, Yokota H, Benno Y. Characterization of the inhabitancy of mouse intestinal bacteria (MIB) in rodents and humans by real-time PCR with group-specific primers. Microbiol Immunol 2007, 51:349-357.
34. Tringe SG, Rubin EM. Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet 2005, 6:805-814. 10.1038/nrg1709, 16304596.
35. von Mering C, Hugenholtz P, Raes J, Tringe SG, Doerks T, Jensen LJ, Ward N, Bork P. Quantitative phylogenetic assessment of microbial communities in diverse environments. Science 2007, 315:1126-1130. 10.1126/science.1133420, 17272687.
36. Riesenfeld CS, Schloss PD, Handelsman J. Metagenomics: genomic analysis of microbial communities. Annu Rev Genet 2004, 38:525-552. 10.1146/annurev.genet.38.072902.091216, 15568985.
37. Kurokawa K, Itoh T, Kuwahara T, Oshima K, Toh H, Toyoda A, Takami H, Morita H, Sharma VK, Srivastava TP, Taylor TD, Noguchi H, Mori H, Ogura Y, Ehrlich DS, Itoh K, Takagi T, Sakaki Y, Hayashi T, Hattori M. Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes. DNA Res 2007, 14:169-181. 10.1093/dnares/dsm018, 2533590, 17916580.
38. Madara JL, Nash S, Moore R, Atisook K. Structure and function of the intestinal epithelial barrier in health and disease. Monogr Pathol 1990, 31:306-324.
39. Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE, Sogin ML, Jones WJ, Roe BA, Affourtit JP, Egholm M, Henrissat B, Heath AC, Knight R, Gordon JI. A core gut microbiome in obese and lean twins. Nature 2009, 457:480-484. 10.1038/nature07540, 2677729, 19043404.
40. Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IK, White BA, Fahey GC. Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice. ISME J
41. MG-RAST. , http://metagenomics.nmpdr.org/
42. Peleg AY, Hogan DA, Mylonakis E. Medically important bacterial-fungal interactions. Nat Rev Microbiol 8:340-349. 10.1038/nrmicro2313, 20348933.
43. Ghannoum MA, Jurevic RJ, Mukherjee PK, Cui F, Sikaroodi M, Naqvi A, Gillevet PM. Characterization of the oral fungal microbiome (mycobiome) in healthy individuals. PLoS Pathog 2010, 6:e1000713. 10.1371/journal.ppat.1000713, 2795202, 20072605.
44. Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F, Gordon JI. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010, 466:334-338. 10.1038/nature09199, 2919852, 20631792.
45. Turroni F, Marchesi JR, Foroni E, Gueimonde M, Shanahan F, Margolles A, van Sinderen D, Ventura M. Microbiomic analysis of the bifidobacterial population in the human distal gut. ISME J 2009, 3:745-751. 10.1038/ismej.2009.19, 19295640.
46. Martin FP, Wang Y, Sprenger N, Yap IK, Rezzi S, Ramadan Z, Pere-Trepat E, Rochat F, Cherbut C, van Bladeren P, Fay LB, Kochhar S, Lindon JC, Holmes E, Nicholson JK. Top-down systems biology integration of conditional prebiotic modulated transgenomic interactions in a humanized microbiome mouse model. Mol Syst Biol 2008, 4:205. 2516362, 18628745.
47. Verberkmoes NC, Russell AL, Shah M, Godzik A, Rosenquist M, Halfvarson J, Lefsrud MG, Apajalahti J, Tysk C, Hettich RL, Jansson JK. Shotgun metaproteomics of the human distal gut microbiota. Isme J 2009, 3:179-189. 10.1038/ismej.2008.108, 18971961.
48. Nicholson JK, Lindon JC, Holmes E. 'Metabonomics': understanding the metabolic responses of living systems to pathophysiological stimuli via multivariate statistical analysis of biological NMR spectroscopic data. Xenobiotica 1999, 29:1181-1189. 10.1080/004982599238047, 10598751.
49. Kanazawa H, Nagino M, Kamiya S, Komatsu S, Mayumi T, Takagi K, Asahara T, Nomoto K, Tanaka R, Nimura Y. Synbiotics reduce postoperative infectious complications: a randomized controlled trial in biliary cancer patients undergoing hepatectomy. Langenbecks Arch Surg 2005, 390:104-113. 10.1007/s00423-004-0536-1, 15711820.
50. Alverdy JC, Chang EB. The re-emerging role of the intestinal microflora in critical illness and inflammation: why the gut hypothesis of sepsis syndrome will not go away. J Leukoc Biol 2008, 83:461-466. 10.1189/jlb.0607372, 18160538.
51. Nicholson JK, Holmes E. Global systems biology and personalized healthcare solutions. Discov Med 2006, 6:63-70.
52. Li M, Wang B, Zhang M, Rantalainen M, Wang S, Zhou H, Zhang Y, Shen J, Pang X, Wei H, Chen Y, Lu H, Zuo J, Su M, Qiu Y, Jia W, Xiao C, Smith LM, Yang S, Holmes E, Tang H, Zhao G, Nicholson JK, Li L, Zhao L. Symbiotic gut microbes modulate human metabolic phenotypes. Proc Natl Acad Sci USA 2008, 105:2117-2122. 10.1073/pnas.0712038105, 2538887, 18252821.
53. Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, Eisen JA. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci USA 2009, 106:17187-17192. 10.1073/pnas.0904847106, 2746123, 19805153.
54. Wikoff WR, Anfora AT, Liu J, Schultz PG, Lesley SA, Peters EC, Siuzdak G. Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites. Proc Natl Acad Sci USA 2009, 106:3698-3703. 10.1073/pnas.0812874106, 2656143, 19234110.
55. Nicholson JK, Connelly J, Lindon JC, Holmes E. Metabonomics: a platform for studying drug toxicity and gene function. Nat Rev Drug Discov 2002, 1:153-161. 10.1038/nrd728, 12120097.
56. Brindle JT, Antti H, Holmes E, Tranter G, Nicholson JK, Bethell HW, Clarke S, Schofield PM, McKilligin E, Mosedale DE, Grainger DJ. Rapid and noninvasive diagnosis of the presence and severity of coronary heart disease using 1H-NMR-based metabonomics. Nat Med 2002, 8:1439-1444. 10.1038/nm802, 12447357.
57. Dumas ME, Wilder SP, Bihoreau MT, Barton RH, Fearnside JF, Argoud K, D'Amato L, Wallis RH, Blancher C, Keun HC, Baunsgaard D, Scott J, Sidelmann UG, Nicholson JK, Gauguier D. Direct quantitative trait locus mapping of mammalian metabolic phenotypes in diabetic and normoglycemic rat models. Nat Genet 2007, 39:666-672. 10.1038/ng2026, 17435758.
58. Stella C, Beckwith-Hall B, Cloarec O, Holmes E, Lindon JC, Powell J, van der Ouderaa F, Bingham S, Cross AJ, Nicholson JK. Susceptibility of human metabolic phenotypes to dietary modulation. J Proteome Res 2006, 5:2780-2788. 10.1021/pr060265y, 17022649.
59. Clayton TA, Baker D, Lindon JC, Everett JR, Nicholson JK. Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism. Proc Natl Acad Sci USA 2009, 106:14728-14733. 10.1073/pnas.0904489106, 2731842, 19667173.
60. Saric J, Wang Y, Li J, Coen M, Utzinger J, Marchesi JR, Keiser J, Veselkov K, Lindon JC, Nicholson JK, Holmes E. Species variation in the fecal metabolome gives insight into differential gastrointestinal function. J Proteome Res 2008, 7:352-360. 10.1021/pr070340k, 18052033.
61. Martin FP, Wang Y, Yap IK, Sprenger N, Lindon JC, Rezzi S, Kochhar S, Holmes E, Nicholson JK. Topographical variation in murine intestinal metabolic profiles in relation to microbiome speciation and functional ecological activity. J Proteome Res 2009, 8:3464-3474. 10.1021/pr900099x, 19492798.
62. Martin FP, Dumas ME, Wang Y, Legido-Quigley C, Yap IK, Tang H, Zirah S, Murphy GM, Cloarec O, Lindon JC, Sprenger N, Fay LB, Kochhar S, van Bladeren P, Holmes E, Nicholson JK. A top-down systems biology view of microbiome-mammalian metabolic interactions in a mouse model. Mol Syst Biol 2007, 3:112. 10.1038/msb4100153, 2673711, 17515922.
63. Sousa T, Paterson R, Moore V, Carlsson A, Abrahamsson B, Basit AW. The gastrointestinal microbiota as a site for the biotransformation of drugs. Int J Pharm 2008, 363:1-25. 10.1016/j.ijpharm.2008.07.009, 18682282.
64. Aura AM, Mattila I, Hyotylainen T, Gopalacharyulu P, Bounsaythip C, Oresic M, Oksman-Caldentey KM. Drug metabolome of the Simvastatin formed by human intestinal microbiota in vitro. Mol Biosyst 2011, 7:437-446. 10.1039/c0mb00023j, 21060933.
65. Scanlan PD, Shanahan F, Clune Y, Collins JK, O'Sullivan GC, O'Riordan M, Holmes E, Wang Y, Marchesi JR. Culture-independent analysis of the gut microbiota in colorectal cancer and polyposis. Environ Microbiol 2008, 10:789-798. 10.1111/j.1462-2920.2007.01503.x, 18237311.
66. Lakhdari O, Cultrone A, Tap J, Gloux K, Bernard F, Ehrlich SD, Lefevre F, Dore J, Blottiere HM. Functional metagenomics: a high throughput screening method to decipher microbiota-driven NF-kappaB modulation in the human gut. PLoS One 2010, 5:e13092. 10.1371/journal.pone.0013092, 2948039, 20927194.
67. Singhal S, Dian D, Keshavarzian A, Fogg L, Fields JZ, Farhadi A. The role of oral hygiene in inflammatory bowel disease. Dig Dis Sci 2010, 56:170-175. 10.1007/s10620-010-1263-9, 20458622.
68. Rehman A, Lepage P, Nolte A, Hellmig S, Schreiber S, Ott SJ. Transcriptional activity of the dominant gut mucosal microbiota in chronic inflammatory bowel disease patients. J Med Microbiol 2010, 59:1114-1122. 10.1099/jmm.0.021170-0, 20522625.
69. Wagner J, Short K, Catto-Smith AG, Cameron DJ, Bishop RF, Kirkwood CD. Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease. PLoS One 2008, 3:e3578. 10.1371/journal.pone.0003578, 2572839, 18974839.
70. Fukata M, Abreu MT. TLR4 signalling in the intestine in health and disease. Biochem Soc Trans 2007, 35:1473-1478. 10.1042/BST0351473, 18031248.
71. Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, Schilter HC, Rolph MS, Mackay F, Artis D, Xavier RJ, Teixeira MM, Mackay CR. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature 2009, 461:1282-1286. 10.1038/nature08530, 19865172.
72. Bjorksten B. Effects of intestinal microflora and the environment on the development of asthma and allergy. Springer Semin Immunopathol 2004, 25:257-270. 10.1007/s00281-003-0142-2, 15007630.
73. Vael C, Desager K. The importance of the development of the intestinal microbiota in infancy. Curr Opin Pediatr 2009, 21:794-800. 10.1097/MOP.0b013e328332351b, 19770768.
74. O'Mahony SM, Marchesi JR, Scully P, Codling C, Ceolho AM, Quigley EM, Cryan JF, Dinan TG. Early life stress alters behavior, immunity, and microbiota in rats: implications for irritable bowel syndrome and psychiatric illnesses. Biol Psychiatry 2009, 65:263-267.
75. Girard SA, Bah TM, Kaloustian S, Lada-Moldovan L, Rondeau I, Tompkins TA, Godbout R, Rousseau G. Lactobacillus helveticus and Bifidobacterium longum taken in combination reduce the apoptosis propensity in the limbic system after myocardial infarction in a rat model. Br J Nutr 2009, 102:1420-1425. 10.1017/S0007114509990766, 19563693.
76. Rao AV, Bested AC, Beaulne TM, Katzman MA, Iorio C, Berardi JM, Logan AC. A randomized, double-blind, placebo-controlled pilot study of a probiotic in emotional symptoms of chronic fatigue syndrome. Gut Pathog 2009, 1:6. 10.1186/1757-4749-1-6, 2664325, 19338686.
77. Song Y, Liu C, Finegold SM. Real-time PCR quantitation of clostridia in feces of autistic children. Appl Environ Microbiol 2004, 70:6459-6465. 10.1128/AEM.70.11.6459-6465.2004, 525120, 15528506.
78. Hambly RJ, Rumney CJ, Cunninghame M, Fletcher JM, Rijken PJ, Rowland IR. Influence of diets containing high and low risk factors for colon cancer on early stages of carcinogenesis in human flora-associated (HFA) rats. Carcinogenesis 1997, 18:1535-1539. 10.1093/carcin/18.8.1535, 9276627.
79. Alpert C, Sczesny S, Gruhl B, Blaut M. Long-term stability of the human gut microbiota in two different rat strains. Curr Issues Mol Biol 2008, 10:17-24.
80. Gerard P, Beguet F, Lepercq P, Rigottier-Gois L, Rochet V, Andrieux C, Juste C. Gnotobiotic rats harboring human intestinal microbiota as a model for studying cholesterol-to-coprostanol conversion. FEMS Microbiol Ecol 2004, 47:337-343. 10.1016/S0168-6496(03)00285-X, 19712322.
81. Manichanh C, Reeder J, Gibert P, Varela E, Llopis M, Antolin M, Guigo R, Knight R, Guarner F. Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res 2010, 20:1411-1419. 10.1101/gr.107987.110, 20736229.
82. Yap IK, Li JV, Saric J, Martin FP, Davies H, Wang Y, Wilson ID, Nicholson JK, Utzinger J, Marchesi JR, Holmes E. Metabonomic and microbiological analysis of the dynamic effect of vancomycin-induced gut microbiota modification in the mouse. J Proteome Res 2008, 7:3718-3728. 10.1021/pr700864x, 18698804.
83. Borody TJ, Warren EF, Leis SM, Surace R, Ashman O, Siarakas S. Bacteriotherapy using fecal flora: toying with human motions. J Clin Gastroenterol 2004, 38:475-483. 10.1097/01.mcg.0000128988.13808.dc, 15220681.
84. Bengmark S. Bioecologic control of the gastrointestinal tract: the role of flora and supplemented probiotics and synbiotics. Gastroenterol Clin North Am 2005, 34:413-436. viii, 10.1016/j.gtc.2005.05.002, 16084305.
85. Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 1995, 125:1401-1412.
86. Borody TJ. 'Flora Power' - fecal bacteria cure chronic C. difficile diarrhea. Am J Gastroenterol 2000, 95:3028-3029.
87. You DM, Franzos MA, Holman RP. Successful treatment of fulminant Clostridium difficile infection with fecal bacteriotherapy. Ann Intern Med 2008, 148:632-633.
88. Khoruts A, Dicksved J, Jansson JK, Sadowsky MJ. Changes in the composition of the human fecal microbiome after bacteriotherapy for recurrent Clostridium difficile-associated diarrhea. J Clin Gastroenterol 2010, 44:354-360.
89. Martin FP, Wang Y, Sprenger N, Yap IK, Lundstedt T, Lek P, Rezzi S, Ramadan Z, van Bladeren P, Fay LB, Kochhar S, Lindon JC, Holmes E, Nicholson JK. Probiotic modulation of symbiotic gut microbial-host metabolic interactions in a humanized microbiome mouse model. Mol Syst Biol 2008, 4:157. 2238715, 18197175.
90. Guarner F. Prebiotics, probiotics and helminths: the 'natural' solution?. Dig Dis 2009, 27:412-417. 10.1159/000228582, 19786773.
91. Desbonnet L, Garrett L, Clarke G, Kiely B, Cryan JF, Dinan TG. Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. Neuroscience 2010, 170:1179-1188. 10.1016/j.neuroscience.2010.08.005, 20696216.
92. Wallace BD, Wang H, Lane KT, Scott JE, Orans J, Koo JS, Venkatesh M, Jobin C, Yeh LA, Mani S, Redinbo MR. Alleviating cancer drug toxicity by inhibiting a bacterial enzyme. Science 2010, 330:831-835. 10.1126/science.1191175, 21051639.
93. Shanahan F. Therapeutic implications of manipulating and mining the microbiota. J Physiol 2009, 587:4175-4179. 10.1113/jphysiol.2009.174649, 2754358, 19505978.
94. Hamady ZZ, Scott N, Farrar MD, Lodge JP, Holland KT, Whitehead T, Carding SR. Xylan-regulated delivery of human keratinocyte growth factor-2 to the inflamed colon by the human anaerobic commensal bacterium Bacteroides ovatus. Gut 2010, 59:461-469. 10.1136/gut.2008.176131, 19736360.
95. Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y, Parameswaran P, Crowell MD, Wing R, Rittmann BE, Krajmalnik-Brown R. Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA 2009, 106:2365-2370. 10.1073/pnas.0812600106, 2629490, 19164560.
96. Rubino F. Is type 2 diabetes an operable intestinal disease? A provocative yet reasonable hypothesis. Diabetes Care 2008, 31(Suppl 2):S290-296. 10.2337/dc08-s271, 18227499.
97. Vijay-Kumar M, Aitken JD, Carvalho FA, Cullender TC, Mwangi S, Srinivasan S, Sitaraman SV, Knight R, Ley RE, Gewirtz AT. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science 2010, 328:228-231. 10.1126/science.1179721, 20203013.
98. Turnbaugh PJ, Ridaura VK, Faith JJ, Rey FE, Knight R, Gordon JI. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Transl Med 2009, 1:6ra14. 2894525, 20368178.
99. Waldram A, Holmes E, Wang Y, Rantalainen M, Wilson ID, Tuohy KM, McCartney AL, Gibson GR, Nicholson JK. Top-down systems biology modeling of host metabotype-microbiome associations in obese rodents. J Proteome Res 2009, 8:2361-2375. 10.1021/pr8009885, 19275195.
100. Turnbaugh PJ, Gordon JI. The core gut microbiome, energy balance and obesity. J Physiol 2009, 587:4153-4158. 10.1113/jphysiol.2009.174136, 2754355, 19491241.
101. Koenig JE, Spor A, Scalfone N, Fricker AD, Stombaugh J, Knight R, Angenent LT, Ley RE. Microbes and Health Sackler Colloquium: succession of microbial consortia in the developing infant gut microbiome. Proc Natl Acad Sci USA