Dysbiosis in gastrointestinal disorders

Best Practice and Research: Clinical Gastroenterology

Volumn 30, Issue 1, 2016, Pages 3-15

  Chang, Christopher ^a   Lin, Henry ^a  

^a UNIVERSITY OF NEW MEXICO SCHOOL OF MEDICINE   (United States)

Author keywords

Dysbiosis; Inflammatory bowel disease; Irritable bowel syndrome; Metabolomics; Metagenomics; Microbiome; Microbiota; Nonalcoholic fatty liver disease; Obesity

Indexed keywords

ARTICLE; DYSBIOSIS; FATTY LIVER; GASTROINTESTINAL DISEASE; HUMAN; IMMUNE SYSTEM; INTESTINE FLORA; IRRITABLE COLON; METABOLOMICS; METAGENOMICS; MICROBIOME; MICROFLORA; NONALCOHOLIC FATTY LIVER; OBESITY; PATHOGENESIS; PATHOPHYSIOLOGY; REGULATORY MECHANISM; ANIMAL; DIET; MICROBIOLOGY; PHYSIOLOGY;

ANIMALS; DIET; DYSBIOSIS; GASTROINTESTINAL DISEASES; GASTROINTESTINAL MICROBIOME; HUMANS;

EID: 84959420804     PISSN: 15216918     EISSN: 15321916     Source Type: Journal    
DOI: 10.1016/j.bpg.2016.02.001     Document Type: Review

References (73)

1. I. Sekirov, S.L. Russell, L.C. Antunes, and B.B. Finlay Gut microbiota in health and disease Physiol Rev 90 3 2010 859 904
2. Human Microbiome Project C Structure, function and diversity of the healthy human microbiome Nature 486 7402 2012 207 214
3. E.B. Hollister, C. Gao, and J. Versalovic Compositional and functional features of the gastrointestinal microbiome and their effects on human health Gastroenterology 146 6 2014 1449 1458
4. Y. Wang, J.D. Hoenig, K.J. Malin, S. Qamar, E.O. Petrof, J. Sun, and et al. 16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis ISME J 3 8 2009 944 954
5. H. Bisgaard, N. Li, K. Bonnelykke, B.L. Chawes, T. Skov, G. Paludan-Muller, and et al. Reduced diversity of the intestinal microbiota during infancy is associated with increased risk of allergic disease at school age J Allergy Clin Immunol 128 3 2011 646 652 e1-5
6. C. Manichanh, L. Rigottier-Gois, E. Bonnaud, K. Gloux, E. Pelletier, L. Frangeul, and et al. Reduced diversity of faecal microbiota in Crohn's disease revealed by a metagenomic approach Gut 55 2 2006 205 211
7. J. Dicksved, J. Halfvarson, M. Rosenquist, G. Jarnerot, C. Tysk, J. Apajalahti, and et al. Molecular analysis of the gut microbiota of identical twins with Crohn's disease ISME J 2 7 2008 716 727
8. M.J. Claesson, I.B. Jeffery, S. Conde, S.E. Power, E.M. O'Connor, S. Cusack, and et al. Gut microbiota composition correlates with diet and health in the elderly Nature 488 7410 2012 178 184
9. E. Le Chatelier, T. Nielsen, J. Qin, E. Prifti, F. Hildebrand, G. Falony, and et al. Richness of human gut microbiome correlates with metabolic markers Nature 500 7464 2013 541 546
10. C. Palmer, E.M. Bik, D.B. DiGiulio, D.A. Relman, and P.O. Brown Development of the human infant intestinal microbiota PLoS Biol 5 7 2007 e177
11. J. Cheng, T. Ringel-Kulka, I. Heikamp-de Jong, Y. Ringel, I. Carroll, W.M. de Vos, and et al. Discordant temporal development of bacterial phyla and the emergence of core in the fecal microbiota of young children ISME J 2016 [in press]
12. T. Ringel-Kulka, J. Cheng, Y. Ringel, J. Salojarvi, I. Carroll, A. Palva, and et al. Intestinal microbiota in healthy U.S. young children and adults-a high throughput microarray analysis PLoS One 8 5 2013 e64315
13. E. Biagi, L. Nylund, M. Candela, R. Ostan, L. Bucci, E. Pini, and et al. Through ageing, and beyond: gut microbiota and inflammatory status in seniors and centenarians PLoS One 5 5 2010 e10667
14. L. Wrzosek, S. Miquel, M.L. Noordine, S. Bouet, M. Joncquel Chevalier-Curt, V. Robert, and et al. Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent BMC Biol 11 2013 61
15. J. Ye, Q. Pan, Y. Shang, X. Wei, Z. Peng, W. Chen, and et al. Core 2 mucin-type O-glycan inhibits EPEC or EHEC O157:H7 invasion into HT-29 epithelial cells Gut Pathog 7 2015 31
16. S. Vaishnava, C.L. Behrendt, A.S. Ismail, L. Eckmann, and L.V. Hooper Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface Proc Natl Acad Sci USA 105 52 2008 20858 20863
17. D.C. Savage, J.E. Siegel, J.E. Snellen, and D.D. Whitt Transit time of epithelial cells in the small intestines of germfree mice and ex-germfree mice associated with indigenous microorganisms Appl Environ Microbiol 42 6 1981 996 1001
18. B.S. Wostmann, C. Larkin, A. Moriarty, and E. Bruckner-Kardoss Dietary intake, energy metabolism, and excretory losses of adult male germfree Wistar rats Lab Anim Sci 33 1 1983 46 50
19. F. Guarner, and J.R. Malagelada Gut flora in health and disease Lancet 361 9356 2003 512 519
20. N. Kamada, and G. Nunez Regulation of the immune system by the resident intestinal bacteria Gastroenterology 146 6 2014 1477 1488
21. N. Arpaia, C. Campbell, X. Fan, S. Dikiy, J. van der Veeken, P. deRoos, and et al. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation Nature 504 7480 2013 451 455
22. K. Atarashi, T. Tanoue, K. Oshima, W. Suda, Y. Nagano, H. Nishikawa, and et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota Nature 500 7461 2013 232 236
23. Y. Furusawa, Y. Obata, S. Fukuda, T.A. Endo, G. Nakato, D. Takahashi, and et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells Nature 504 7480 2013 446 450
24. M. Bendiks, and M.V. Kopp The relationship between advances in understanding the microbiome and the maturing hygiene hypothesis Curr Allergy Asthma Rep 13 5 2013 487 494
25. G.A. Rook Regulation of the immune system by biodiversity from the natural environment: an ecosystem service essential to health Proc Natl Acad Sci USA 110 46 2013 18360 18367
26. S. Kitajima, M. Morimoto, E. Sagara, C. Shimizu, and Y. Ikeda Dextran sodium sulfate-induced colitis in germ-free IQI/Jic mice Exp Anim 50 5 2001 387 395
27. M. Nieuwdorp, P.W. Gilijamse, N. Pai, and L.M. Kaplan Role of the microbiome in energy regulation and metabolism Gastroenterology 146 6 2014 1525 1533
28. M. Membrez, F. Blancher, M. Jaquet, R. Bibiloni, P.D. Cani, R.G. Burcelin, and et al. Gut microbiota modulation with norfloxacin and ampicillin enhances glucose tolerance in mice FASEB J 22 7 2008 2416 2426
29. A. Vrieze, E. Van Nood, F. Holleman, J. Salojarvi, R.S. Kootte, J.F. Bartelsman, and et al. Transfer of intestinal microbiota from lean donors increases insulin sensitivity in individuals with metabolic syndrome Gastroenterology 143 4 2012 913 916 e7
30. R.E. Ley, F. Backhed, P. Turnbaugh, C.A. Lozupone, R.D. Knight, and J.I. Gordon Obesity alters gut microbial ecology Proc Natl Acad Sci USA 102 31 2005 11070 11075
31. R.E. Ley, P.J. Turnbaugh, S. Klein, and J.I. Gordon Microbial ecology: human gut microbes associated with obesity Nature 444 7122 2006 1022 1023
32. F. Backhed, J.K. Manchester, C.F. Semenkovich, and J.I. Gordon Mechanisms underlying the resistance to diet-induced obesity in germ-free mice Proc Natl Acad Sci USA 104 3 2007 979 984
33. F. Backhed, H. Ding, T. Wang, L.V. Hooper, G.Y. Koh, A. Nagy, and et al. The gut microbiota as an environmental factor that regulates fat storage Proc Natl Acad Sci USA 101 44 2004 15718 15723
34. P.J. Turnbaugh, R.E. Ley, M.A. Mahowald, V. Magrini, E.R. Mardis, and J.I. Gordon An obesity-associated gut microbiome with increased capacity for energy harvest Nature 444 7122 2006 1027 1031
35. V.K. Ridaura, J.J. Faith, F.E. Rey, J. Cheng, A.E. Duncan, A.L. Kau, and et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice Science 341 6150 2013 1241214
36. B. Schnabl, and D.A. Brenner Interactions between the intestinal microbiome and liver diseases Gastroenterology 146 6 2014 1513 1524
37. M. Mouzaki, E.M. Comelli, B.M. Arendt, J. Bonengel, S.K. Fung, S.E. Fischer, and et al. Intestinal microbiota in patients with nonalcoholic fatty liver disease Hepatology 58 1 2013 120 127
38. M. Raman, I. Ahmed, P.M. Gillevet, C.S. Probert, N.M. Ratcliffe, S. Smith, and et al. Fecal microbiome and volatile organic compound metabolome in obese humans with nonalcoholic fatty liver disease Clin Gastroenterol Hepatol 11 7 2013 868 875 e1-3
39. L. Zhu, S.S. Baker, C. Gill, W. Liu, R. Alkhouri, R.D. Baker, and et al. Characterization of gut microbiomes in nonalcoholic steatohepatitis (NASH) patients: a connection between endogenous alcohol and NASH Hepatology 57 2 2013 601 609
40. M.E. Dumas, R.H. Barton, A. Toye, O. Cloarec, C. Blancher, A. Rothwell, and et al. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice Proc Natl Acad Sci USA 103 33 2006 12511 12516
41. J. Henao-Mejia, E. Elinav, C. Jin, L. Hao, W.Z. Mehal, T. Strowig, and et al. Inflammasome-mediated dysbiosis regulates progression of NAFLD and obesity Nature 482 7384 2012 179 185
42. T. Le Roy, M. Llopis, P. Lepage, A. Bruneau, S. Rabot, C. Bevilacqua, and et al. Intestinal microbiota determines development of non-alcoholic fatty liver disease in mice Gut 62 12 2013 1787 1794
43. E. Bellaguarda, and E.B. Chang IBD and the gut microbiota-from bench to personalized medicine Curr Gastroenterol Rep 17 4 2015 15
44. A.D. Kostic, R.J. Xavier, and D. Gevers The microbiome in inflammatory bowel disease: current status and the future ahead Gastroenterology 146 6 2014 1489 1499
45. Y. Ogura, D.K. Bonen, N. Inohara, D.L. Nicolae, F.F. Chen, R. Ramos, and et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease Nature 411 6837 2001 603 606
46. D.N. Frank, A.L. St Amand, R.A. Feldman, E.C. Boedeker, N. Harpaz, and N.R. Pace Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases Proc Natl Acad Sci USA 104 34 2007 13780 13785
47. P. Lepage, R. Hasler, M.E. Spehlmann, A. Rehman, A. Zvirbliene, A. Begun, and et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis Gastroenterology 141 1 2011 227 236
48. S. Sepehri, R. Kotlowski, C.N. Bernstein, and D.O. Krause Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease Inflamm Bowel Dis 13 6 2007 675 683
49. D. Gevers, S. Kugathasan, L.A. Denson, Y. Vazquez-Baeza, W. Van Treuren, B. Ren, and et al. The treatment-naive microbiome in new-onset Crohn's disease Cell Host Microbe 15 3 2014 382 392
50. M. Martinez-Medina, X. Aldeguer, M. Lopez-Siles, F. Gonzalez-Huix, C. Lopez-Oliu, G. Dahbi, and et al. Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohn's disease Inflamm Bowel Dis 15 6 2009 872 882
51. P. Ryan, R.G. Kelly, G. Lee, J.K. Collins, G.C. O'Sullivan, J. O'Connell, and et al. Bacterial DNA within granulomas of patients with Crohn's disease-detection by laser capture microdissection and PCR Am J Gastroenterol 99 8 2004 1539 1543
52. S. Schippa, V. Iebba, V. Totino, F. Santangelo, M. Lepanto, C. Alessandri, and et al. A potential role of Escherichia coli pathobionts in the pathogenesis of pediatric inflammatory bowel disease Can J Microbiol 58 4 2012 426 432
53. H. Sokol, B. Pigneur, L. Watterlot, O. Lakhdari, L.G. Bermudez-Humaran, J.J. Gratadoux, and et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients Proc Natl Acad Sci USA 105 43 2008 16731 16736
54. X.C. Morgan, T.L. Tickle, H. Sokol, D. Gevers, K.L. Devaney, D.V. Ward, and et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment Genome Biol 13 9 2012 R79
55. J.M. Norman, S.A. Handley, M.T. Baldridge, L. Droit, C.Y. Liu, B.C. Keller, and et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease Cell 160 3 2015 447 460
56. R.S. Choung, and G.R. Locke 3rd Epidemiology of IBS Gastroenterol Clin North Am 40 1 2011 1 10
57. E.A. Mayer, T. Savidge, and R.J. Shulman Brain-gut microbiome interactions and functional bowel disorders Gastroenterology 146 6 2014 1500 1512
58. G.D. Abrams, and J.E. Bishop Effect of the normal microbial flora on gastrointestinal motility Proc Soc Exp Biol Med Soc Exp Biol Med 126 1 1967 301 304
59. E. Husebye, P.M. Hellstrom, F. Sundler, J. Chen, and T. Midtvedt Influence of microbial species on small intestinal myoelectric activity and transit in germ-free rats Am J Physiol Gastrointest Liver Physiol 280 3 2001 G368 G380
60. M. Pimentel, and C. Chang Inflammation and microflora Gastroenterol Clin North Am 40 1 2011 69 85
61. M. Simren, G. Barbara, H.J. Flint, B.M. Spiegel, R.C. Spiller, S. Vanner, and et al. Intestinal microbiota in functional bowel disorders: a Rome foundation report Gut 62 1 2013 159 176
62. E. Giamarellos-Bourboulis, J. Tang, E. Pyleris, A. Pistiki, C. Barbatzas, J. Brown, and et al. Molecular assessment of differences in the duodenal microbiome in subjects with irritable bowel syndrome Scand J Gastroenterol 50 9 2015 1076 1087
63. M. Rajilic-Stojanovic, E. Biagi, H.G. Heilig, K. Kajander, R.A. Kekkonen, S. Tims, and et al. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome Gastroenterology 141 5 2011 1792 1801
64. K. Gecse, R. Roka, L. Ferrier, M. Leveque, H. Eutamene, C. Cartier, and et al. Increased faecal serine protease activity in diarrhoeic IBS patients: a colonic lumenal factor impairing colonic permeability and sensitivity Gut 57 5 2008 591 599
65. A.C. Ford, B.M. Spiegel, N.J. Talley, and P. Moayyedi Small intestinal bacterial overgrowth in irritable bowel syndrome: systematic review and meta-analysis Clin Gastroenterol Hepatol 7 12 2009 1279 1286
66. E.D. Shah, R.J. Basseri, K. Chong, and M. Pimentel Abnormal breath testing in IBS: a meta-analysis Dig Dis Sci 55 9 2010 2441 2449
67. E. Pyleris, E.J. Giamarellos-Bourboulis, D. Tzivras, V. Koussoulas, C. Barbatzas, and M. Pimentel The prevalence of overgrowth by aerobic bacteria in the small intestine by small bowel culture: relationship with irritable bowel syndrome Dig Dis Sci 57 5 2012 1321 1329
68. M. Pimentel, A. Lembo, W.D. Chey, S. Zakko, Y. Ringel, J. Yu, and et al. Rifaximin therapy for patients with irritable bowel syndrome without constipation N Engl J Med 364 1 2011 22 32
69. M. Pimentel, S. Park, J. Mirocha, S.V. Kane, and Y. Kong The effect of a nonabsorbed oral antibiotic (rifaximin) on the symptoms of the irritable bowel syndrome: a randomized trial Ann Intern Med 145 8 2006 557 563
70. D. Kunkel, R.J. Basseri, M.D. Makhani, K. Chong, C. Chang, and M. Pimentel Methane on breath testing is associated with constipation: a systematic review and meta-analysis Dig Dis Sci 56 6 2011 1612 1618
71. M. Pimentel, H.C. Lin, P. Enayati, B. van den Burg, H.R. Lee, J.H. Chen, and et al. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity Am J Physiol Gastrointest Liver Physiol 290 6 2006 G1089 G1095
72. G. Kim, F. Deepinder, W. Morales, L. Hwang, S. Weitsman, C. Chang, and et al. Methanobrevibacter smithii is the predominant methanogen in patients with constipation-predominant IBS and methane on breath Dig Dis Sci 57 12 2012 3213 3218
73. M. Pimentel, C. Chang, K.S. Chua, J. Mirocha, J. DiBaise, S. Rao, and et al. Antibiotic treatment of constipation-predominant irritable bowel syndrome Dig Dis Sci 59 6 2014 1278 1285