Impacts of gut bacteria on human health and diseases

International Journal of Molecular Sciences

Volumn 16, Issue 4, 2015, Pages 7493-7519

  Zhang, Yu Jie ^a   Li, Sha ^b   Gan, Ren You ^c   Zhou, Tong ^a   Xu, Dong Ping ^a   Li, Hua Bin ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b THE UNIVERSITY OF HONG KONG   (Hong Kong)

^c UNIVERSITY OF HONG KONG   (Hong Kong)

Author keywords

Cancer; Gut bacteria; Human health; Obesity

Indexed keywords

ACTINOBACTERIA; AUTISM; BACTEROIDETES; CLOSTRIDIA; CONSTIPATION; CROHN DISEASE; DIGESTIVE SYSTEM CANCER; DISEASES; EUBACTERIUM; FIRMICUTES; FUSOBACTERIA; HEALTH; HEART DISEASE; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; HYPERCHOLESTEROLEMIA; IMMUNE SYSTEM; INSULIN DEPENDENT DIABETES MELLITUS; INTESTINE FLORA; KIDNEY DISEASE; LACTIC ACID BACTERIUM; NON INSULIN DEPENDENT DIABETES MELLITUS; NONALCOHOLIC FATTY LIVER; NONHUMAN; OBESITY; PROTEOBACTERIA; REVIEW; RHEUMATOID ARTHRITIS; SLEEP; ULCERATIVE COLITIS; VERRUCOMICROBIA; ANIMAL; BACTERIUM; DISEASE; ECOSYSTEM; GASTROINTESTINAL TRACT; MICROBIOLOGY; MICROFLORA; PATHOGENICITY; PHYSIOLOGY;

PROBIOTIC AGENT;

ANIMALS; BACTERIA; DISEASE; ECOSYSTEM; GASTROINTESTINAL TRACT; HUMANS; MICROBIOTA; PROBIOTICS;

EID: 84927641279     PISSN: 16616596     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms16047493     Document Type: Review

References (130)

1. Clark, J.A.; Coopersmith, C.M. Intestinal crosstalk: A new paradigm for understanding the gut as the "motor" of critical illness. Shock 2007, 28, 384-393.
2. Honda, K.; Takeda, K. Regulatory mechanisms of immune responses to intestinal bacteria. Mucosal Immunol. 2009, 2, 187-196.
3. Bischoff, S.C.; Kramer, S. Human mast cells, bacteria, and intestinal immunity. Immunol. Rev. 2007, 217, 329-337.
4. Palmer, C.; Bik, E.M.; DiGiulio, D.B.; Relman, D.A.; Brown, P.O. Development of the human infant intestinal microbiota. PLoS. Biol. 2007, 5, 1556-1573.
5. Gerritsen, J.; Smidt, H.; Rijkers, G.T.; de Vos, W.M. Intestinal microbiota in human health and disease: The impact of probiotics. Genes Nutr. 2011, 6, 209-240.
6. Woodmansey, E.J. Intestinal bacteria and ageing. J. Appl. Microbiol. 2007, 102, 1178-1186.
7. Hill, D.A.; Artis, D. Intestinal bacteria and the regulation of immune cell homeostasis. Annu. Rev. Immunol. 2010, 28, 623-667.
8. Mueller, C.; Macpherson, A.J. Layers of mutualism with commensal bacteria protect us from intestinal inflammation. Gut 2006, 55, 276-284.
9. Guarner, F.; Malagelada J.R. Gut flora in health and disease. Lancet 2003, 361, 512-519.
10. Tsuji, M.; Suzuki, K.; Kinoshita, K.; Fagarasan, S. Dynamic interactions between bacteria and immune cells leading to intestinal IgA synthesis. Semin. Immunol. 2008, 20, 59-66.
11. Tuohy, K.M.; Hinton, D.J.; Davies, S.J.; Crabbe, M.J.; Gibson, G.R.; Ames, J.M. Metabolism of Maillard reaction products by the human gut microbiota-implications for health. Mol. Nutr. Food Res. 2006, 50, 847-857.
12. Ulluwishewa, D.; Anderson, R.C.; McNabb, W.C.; Moughan, P.J.; Wells, J.M.; Roy, N.C. Regulation of tight junction permeability by intestinal bacteria and dietary components. J. Nutr. 2011, 141, 769-776.
13. Macfarlane, G.T.; Cummings, J.H. Probiotics and prebiotics: Can regulating the activities of intestinal bacteria benefit health? BMJ 1999, 318, 999-1003.
14. Akaza, H. Prostate cancer chemoprevention by soy isoflavones: Role of intestinal bacteria as the "second human genome". Cancer Sci. 2012, 103, 969-975.
15. Hermann-Bank, M.L.; Skovgaard, K.; Stockmarr, A.; Larsen, N.; Molbak, L. The gut microbiotassay: A high-throughput qPCR approach combinable with next generation sequencing to study gut microbial diversity. BMC Genomics 2013, 14, doi:10.1186/1471-2164-14-788.
16. Vaughan, E.E.; Heilig, H.; Ben-Amor, K.; de Vos, W.M. Diversity, vitality and activities of intestinal lactic acid bacteria and bifidobacteria assessed by molecular approaches. FEMS Microbiol. Rev. 2005, 29, 477-490.
17. Stecher, B.; Hardt W. The role of microbiota in infectious disease. Trends Microbiol. 2008, 16, 107-114.
18. Beaud, D.; Tailliez P.; Anba-Mondoloni J. Genetic characterization of the β-glucuronidase enzyme from a human intestinal bacterium, Ruminococcus gnavus. Microbiology 2005, 151, 2323-2330.
19. Fung, Q.M.; Szilagyi, A. Carbohydrate elimination or adaptation diet for symptoms of intestinal discomfort in IBD: Rationales for "Gibsons' Conundrum". Int. J. Inflamm. 2012, 2012, doi:10.1155/2012/493717.
20. Lanning, D.K.; Rhee, K.J.; Knight, K.L. Intestinal bacteria and development of the β-lymphocyte repertoire. Trends Immunol. 2005, 26, 419-425.
21. Compare, D.; Coccoli, P.; Rocco, A.; Nardone, O.M.; De Maria, S.; Carteni, M.; Nardone, G. Gut-liver axis: The impact of gut microbiota on non alcoholic fatty liver disease. Nutr. Metab. Cardiovasc. Dis. 2012, 22, 471-476.
22. Strauch, U.G.; Obermeier, F.; Grunwald, N.; Gurster, S.; Dunger, N.; Schultz, M.; Griese, D.P.; Mahler, M.; Scholmerich, J.; Rath, H.C. Influence of intestinal bacteria on induction of regulatory T cells: Lessons from a transfer model of colitis. Gut 2005, 54, 1546-1552.
23. Arpaia, N.; Campbell, C.; Fan, X.Y.; Dikiy, S.; van der Veeken, J.; DeRoos, P.; Liu, H.; Cross, J.R.; Pfeffer, K.; Coffer, P.J.; Rudensky, A.Y. Metabolites produced by commensal bacteria promote peripheral regulatory T-cell generation. Nature 2013, 504, 451-455.
24. Macfarlane, S.; Steed, H.; Macfarlane, G.T. Intestinal bacteria and inflammatory bowel disease. Crit. Rev. Clin. Lab. Sci. 2009, 46, 25-54.
25. Jalanka-Tuovinen, J.; Salonen, A.; Nikkila, J.; Immonen, O.; Kekkonen, R.; Lahti, L, Palva, A.; de Vos, W.M. Intestinal microbiota in healthy adults: Temporal analysis reveals individual and common core and relation to intestinal symptoms. PLoS ONE 2011, 6, e23035.
26. Landete, J.M. Plant and mammalian lignans: A review of source, intake, metabolism, intestinal bacteria and health. Food Res. Int. 2012, 46, 410-424.
27. Fuentealba, C.; Figuerola, F.; Estevez, A.M.; Bastias, J.M.; Munoz, O. Bioaccessibility of lignans from flaxseed (Linum usitatissimum L.) determined by Single Batch in vitro simulation of the digestive Pprocess. J. Sci. Food. Agric. 2014, 94, 1729-1738.
28. Clavel, T.; Henderson, G.; Alpert, C.A.; Philippe, C.; Rigottier-Gois, L.; Dore, J.; Blaut, M. Intestinal bacterial communities that produce active estrogen-like compounds enterodiol and enterolactone in humans. Appl. Environ. Microbiol. 2005, 71, 6077-6085.
29. Atkinson, C.; Frankenfeld, C.L.; Lampe, J.W. Gut bacterial metabolism of the soy isoflavone daidzein: Exploring the relevance to human health. Exp. Biol. Med. 2005, 230, 155-170.
30. Brown, K.; DeCoffe, D.; Molcan, E.; Gibson, D.L. Diet-induced dysbiosis of the intestinal microbiota and the effects on immunity and disease. Nutrients 2012, 4, 1095-1119.
31. Harmsen, H.; Wildeboer-Veloo, A.; Raangs, G.C.; Wagendorp, A.A.; Klijn, N.; Bindels, J.G.; Welling, G.W. Analysis of intestinal flora development in breast-fed and formula-fed infants by using molecular identification and detection methods. J. Pediatr. Gastroenterol. Nutr. 2000, 30, 61-67.
32. Fallani, M.; Young, D.; Scott, J.; Norin, E.; Amarri, S.; Adam, R.; Aguilera, M.; Khanna, S.; Gil, A.; Edwards, C.A.; Dore, J. Intestinal microbiota of 6-week-old infants across Europe: Geographic influence beyond delivery mode, breast-feeding, and antibiotics. J. Pediatr. Gastroenterol. Nutr. 2010, 51, 77-84.
33. Tachon, S.; Lee, B.; Marco, M.L. Diet alters probiotic Lactobacillus persistence and function in the intestine. Environ. Microbiol. 2014, 16, 2915-2926.
34. Wu, G.D.; Chen, J.; Hoffmann, C.; Bittinger, K.; Chen, Y.Y.; Keilbaugh, S.A.; Bewtra, M.; Knights, D.; Walters, W.A.; Knight, R.; et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011, 334, 105-108.
35. David, L.A.; Maurice, C.F.; Carmody, R.N.; Gootenberg, D.B.; Button, J.E.; Wolfe, B.E.; Ling, A.V.; Devlin, A.S.; Varma, Y.; Fischbach, M.A.; et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014, 505, 559-560.
36. Lee, H.C.; Jenner, A.M.; Low, C.S.; Lee, Y.K. Effect of tea phenolics and their aromatic fecal bacterial metabolites on intestinal microbiota. Res. Microbiol. 2006, 157, 876-884.
37. Parkar, S.G.; Trower, T.M.; Stevenson, D.E. Fecal microbial metabolism of polyphenols and its effects on human gut microbiota. Anaerobe 2013, 23, 12-19.
38. Koecher, K.J.; Thomas, W.; Slavin, J.L. Healthy subjects experience bowel changes on enteral diets; addition of a fiber blend attenuates stool weight and gut bacteria decreases without changes in gas. J. Parenter. Enter. Nutr. 2013, 25, 132-138.
39. Sofi, M.H.; Gudi, R.; Karumuthil-Melethil, S.; Perez, N.; Johnson, B.M.; Vasu, C. pH of drinking water influences the composition of gut microbiome and type 1 diabetes incidence. Diabetes 2014, 63, 632-644.
40. Kato, I.; Boleij, A.; Kortman, G.; Roelofs, R.; Djuric, Z.; Severson, R.K.; Tjalsma, H. Partial associations of dietary iron, smoking and intestinal bacteria with colorectal cancer risk. Nutr. Cancer 2013, 65, 169-177.
41. Wang, J.; Zhao, H.; Kong, W.; Jin, C.; Zhao, Y.; Qu, Y.; Xiao, X. Microcalorimetric assay on the antimicrobial property of five hydroxyanthraquinone derivatives in rhubarb (Rheum palmatum L.) to Bifidobacterium adolescentis. Phytomedicine 2010, 17, 684-689.
42. Gibson, G.R.; Roberfroid, M.B. Dietary modulation of the human colonic microbiota: Introducing the concept of prebiotics. J. Nutr. 1995, 125, 1401-1412.
43. Gibson, G.R.; Probert, H.M.; Loo, J.V.; Rastall, R.A.; Roberfroid, M.B. Dietary modulation of the human colonic microbiota: Updating the concept of prebiotics. Nutr. Res. Rev. 2004, 17, 259-275.
44. Macfarlane, G.T.; Steed, H.; Macfarlane, S. Bacterial metabolism and health-related effects of galacto-oligosaccharides and other prebiotics. J. Appl. Microbiol. 2008, 104, 305-344.
45. Ljungh, A.; Wadstrom, T. Lactic acid bacteria as probiotics. Curr. Issues Intest. Microbiol. 2006, 7, 73-89.
46. Bongaerts, G.; Severijnen, R.; Timmerman, H. Effect of antibiotics, prebiotics and probiotics in treatment for hepatic encephalopathy. Med. Hypotheses 2005, 64, 64-68.
47. Kruis, W. Review article: Antibiotics and probiotics in inflammatory bowel disease. Aliment. Pharmacol. Ther. 2004, 20, 75-78.
48. Lye, H.S.; Kuan, C.Y.; Ewe, J.A.; Fung, W.Y.; Liong, M.T. The improvement of hypertension by probiotics: Effects on cholesterol, diabetes, renin, and phytoestrogens. Int. J. Mol. Sci. 2009, 10, 3755-3775.
49. Kumar, M.; Kumar, A.; Nagpal, R.; Mohania, D.; Behare, P.; Verma, V.; Kumar, P.; Poddar, D.; Aggarwal, P.K.; Henry, C.J.; et al. Cancer-preventing attributes of probiotics: An update. Int. J. Food Sci. Nutr. 2010, 61, 473-496.
50. Meneghin, F.; Fabiano, V.; Mameli, C.; Zuccotti, G.V. Probiotics and atopic dermatitis in children. Pharmaceuticals 2012, 5, 727-744.
51. Wilcox, M.H. Clostridium difficile infection and pseudomembranous colitis. Best Pract. Res. Clin. Gastroenterol. 2003, 17, 475-492.
52. Hoentjen, F.; Welling, G.W.; Harmsen, H.J.; Zhang, X.; Snart, J.; Tannock, G.W. Lien, K.; Churchill, T.A.; Lupicki, M.; Dieleman, L.A. Reduction of colitis by prebiotics in HLA-B27 transgenic rats is associated with microflora changes and immunomodulation. Inflamm. Bowel Dis. 2005, 11, 977-985.
53. Jostins, L.; Ripke, S.; Weersma, R.K.; Duerr, R.H.; McGovern, D.P.; Hui, K.Y.; Lee, J.C.; Schumm, L.P.; Sharma, Y.; Anderson, C.A.; et al. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012, 491, 119-124.
54. Cummings, J.H.; Macfarlane, G.T.; Macfarlane, S. Intestinal bacteria and ulcerative colitis. Curr. Issues Intest. Microbiol. 2003, 4, 9-20.
55. Bullock, N.R.; Booth, J.C.L.; Gibson, G.R. Comparative composition of bacteria in the human intestinal microflora during remission and active ulcerative colitis. Curr. Issues Intest. Microbiol. 2004, 5, 59-64.
56. Heimesaat, M.M.; Fischer, A.; Siegmund, B.; Batra, A.; Loddenkemper, C.; Liesenfeld, O.; Blaut, M.; Gobel, U.B.; Schumann, R.R.; Bereswill, S. Shifts towards pro-inflammatory intestinal bacteria aggravate acute murine colitis and ileitis via toll-like-receptor signaling. Int. J. Med. Microbiol. 2007, 29743, 81-82.
57. Kamada, N.; Hisamatsu, T.; Okamoto, S.; Sato, T.; Matsuoka, K.; Arai, K.; Nakai, T.; Hasegawa, A.; Inoue, N.; Watanabe, N.; Akagawa, K.S.; Hibi, T. Abnormally differentiated subsets of intestinal macrophage play a key role in Th1-dominant chronic colitis through excess production of IL-12 and IL-23 in response to bacteria. J. Immunol. 2005, 175, 6900-6908.
58. Machiels, K.; Joossens, M.; Sabino, J.; de Preter, V.; Arijs, I.; Eeckhaut, V.; Ballet, V.; Claes, K.; van Immerseel, F.; Verbeke, K.; et al. A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis. Gut 2014, 63, 1275-1283.
59. Lepage, P.; Haesler, R.; Spehlmann, M.E.; Rehman, A.; Zvirbliene, A.; Begun, A.; Ott, S.; Kupcinskas, L.; Dore, J.; Raedler, A.; Schreiber, S. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology 2011, 141, 227-236.
60. Bhattacharjee, A. Oral micro-particulate colon targeted drug delivery system for the treatment of Crohn's disease: A review. Int. J. Life Sci. Pharm. Res. 2012, 1, 31-39.
61. Seksik, P.; Rigottier-Gois, L.; Gramet, G.; Sutren, M.; Pochart, P.; Marteau, P.; Jian, R.; Dore, J. Alterations of the dominant faecal bacterial groups in patients with Crohn's disease of the colon. Gut 2003, 52, 237-242.
62. Joossens, M.; Huys, G.; Cnockaert, M.; de Preter, V.; Verbeke, K.; Rutgeerts, P.; Vandamme, P.; Vermeire, S. Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 2011, 60, 631-637.
63. Gevers, D.; Kugathasan, S.; Denson, L.A.; Vazquez-Baeza, Y.; van Treuren, W.; Ren, B.; Schwager, E.; Knights, D.; Song, S.J.; Yassour, M.; et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 2014, 15, 382-392.
64. Leach, S.T.; Mitchell, H.M.; Eng, W.R.; Zhang, L.; Day, A.S. Sustained modulation of intestinal bacteria by exclusive enteral nutrition used to treat children with Crohn's disease. Aliment. Pharm. Ther. 2008, 28, 724-733.
65. Tighe, M.P.; Cummings, J.; Afzal, N.A. Nutrition and inflammatory bowel disease: Primary or adjuvant therapy. Curr. Opin. Clin. Nutr. Metab. Care 2011, 14, 491-496.
66. Ding, S.L.; Chi, M.M.; Scull, B.P.; Rigby, R.; Schwerbrock, N.; Magness, S.; Jobin, C.; Lund, P.K. High-fat diet: Bacteria interactions promote intestinal inflammation which precedes and correlates with obesity and insulin resistance in mouse. PLoS ONE 2010, 5, e12191.
67. Hildebrandt, M.A.; Hoffmann, C.; Sherrill-Mix, S.A.; Keilbaugh, S.A.; Hamady, M.; Chen, Y.; Knight, R.; Ahima, R.S.; Bushman, F.; Wu, G.D. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology 2009, 137, 1716-1724.
68. Armougom, F.; Henry, M.; Vialettes, B.; Raccah, D.; Raoult, D. Monitoring bacterial community of human gut microbiota reveals an increase in Lactobacillus in obese patients and Methanogens in anorexic patients. PLoS ONE 2009, 4, e7125.
69. Cluny, N.L.; Reimer, R.A.; Sharkey, K.A. Cannabinoid signalling regulates inflammation and energy balance: The importance of the brain-gut axis. Brain Behav. Immun. 2012, 26, 691-698.
70. Leung, J.; Burke, B.; Ford, D.; Garvin, G.; Korn, C.; Sulis, C.; Bhadelia, N. Possible association between obesity and Clostridium difficile infection. Emerg. Infect. Dis. 2013, 19, 1791-1798.
71. Lin, H.V.; Frassetto, A.; Kowalik, E.J., Jr.; Nawrocki, A.R.; Lu, M.M.; Kosinski, J.R.; Hubert, J.A.; Szeto, D.; Yao, X.; Forrest, G.; Marsh, D.J. Butyrate and propionate protect against diet-Induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms. PLoS ONE 2012, 7, e352404.
72. Moran, C.P.; Shanahan, F. Gut microbiota and obesity: Role in aetiology and potential therapeutic target. Best Pract. Res. Clin. Gastroenterol. 2014, 28, 585-597.
73. Gorissen, L.; Raes, K.; Weckx, S.; Dannenberger, D.; Leroy, F.; de Vuyst, L.; de Smet, S. Production of conjugated linoleic acid and conjugated linolenic acid isomers by Bifidobacterium species. Appl. Microbiol. Biotechnol. 2010, 87, 2257-2266.
74. Lee, H.Y.; Park, J.H.; Seok, S.H.; Baek, M.W.; Kim, D.J.; Lee, K.E.; Paek, K.S.; Lee, Y.; Park, J H. Human originated bacteria, Lactobacillus rhamnosus PL60, produce conjugated linoleic acid and show anti-obesity effects in diet-induced obese mice. Biochem. Biophys. Acta 2006, 1761, 736-744.
75. Poutahidis, T.; Kleinewietfeld, M.; Smillie, C.; Levkovich, T.; Perrotta, A.; Bhela, S.; Varian, B.J.; Ibrahim, Y.M.; Lakritz, J.R.; Kearney, S.M.; et al. Microbial reprogramming inhibits western diet-associated obesity. PLoS ONE 2013, 8, e685967.
76. Mozaffarian, D.; Hao, T.; Rimm, E.B.; Willett, W.C.; Hu, F.B. Changes in diet and lifestyle and long-term weight gain in women and men. N. Engl. J. Med. 2011, 364, 2392-2404.
77. De los Reyes-Gavilan, C.G.; Delzenne, N.M.; Gonzalez, S.; Gueimonde, M.; Salazar, N. Development of functional foods to fight against obesity Opportunities for probiotics and prebiotics. Agro Food Ind. Hi Tech 2014, 25, 35-39.
78. Kelishadi, R.; Farajian, S.; Safavi, M.; Mirlohi, M.; Hashemipour, M. A randomized triple-masked controlled trial on the effects of synbiotics on inflammation markers in overweight children. J. Pediatr. 2014, 90, 161-168.
79. Ridaura, V.K.; Faith, J.J.; Rey, F.E.; Cheng, J.; Duncan, A.E.; Kau, A.L.; Griffin, N.W.; Lombard, V.; Henrissat, B.; Bain, J.R.; et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013, 341, doi:10.1126/science.1241214.
80. Walker, A.W.; Parkhill, J. Fighting obesity with bacteria. Science 2013, 341, 1069-1070.
81. Davies, S.S.; Chen, Z.Y.; Guo, L.L.; Zhang, Y.Q.; Stien, X.; Coulon, D. Incorporation of therapeutically modified bacteria into gut microbiota prevents obesity. Free Radic. Biol. Med. 2012, 532, doi:10.1016/j.freeradbiomed.2012.10.250.
82. Burcelin, R.; Serino, M.; Chabo, C.; Blasco-Baque, V.; Amar, J. Gut microbiota and diabetes: From pathogenesis to therapeutic perspective. Acta Diabetol. 2011, 48, 257-273.
83. Cani, P.D.; Neyrinck, A.M.; Fava, F.; Knauf, C.; Burcelin, R.G.; Tuohy, K.M. Selective increases of bifidobacteria in gut microflora improve high-fat diet induced diabetes in mice through a mechanism associated with endotoxaemia. Diabetologia 2007, 50, 2374-2383.
84. Musso, G.; Gambino, R.; Cassader, M. Interactions between gut microbiota and host metabolism predisposing to obesity and diabetes. Annu. Rev. Med. 2011, 62, 361-380.
85. Nara, N.; Alkanani, A.K.; Ir, D.; Robertson, C.E.; Wagner, B.D.; Frank, D.N.; Zipris, D. The role of the intestinal microbiota in type 1 diabetes. Clin. Immunol. 2013, 146, 112-119.
86. Brown, C.T.; Davis-Richardson, A.G.; Giongo, A.; Gano, K.A.; Crabb, D.B.; Mukherjee, N.; Casella, G.; Drew, J.C.; Ilonen, J.; Knip, M.; et al. Gut microbiome metagenomics analysis suggests a functional model for the development of autoimmunity for type 1 diabetes. PLoS ONE 2011, 6, e25792.
87. Murri, M.; Leiva, I.; Gomez-Zumaquero, J.M.; Tinahones, F.J.; Cardona, F.; Soriguer, F.; Queipo-Ortuno, M.I. Gut microbiota in children with type 1 diabetes differs from that in healthy children: A case-control study. BMC Med. 2013, 11, doi:10.1186/1741-7015-11-46.
88. Larsen, N.; Vogensen, F.K.; van den Berg, F.; Nielsen, D.S.; Andreasen, A.S.; Pedersen, B.K.; Abu Al-Soud, W.; Sorensen, S.J.; Hansen, L.H.; Jakobsen, M. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS ONE 2010, 5, e90852.
89. Amar, J.; Chabo, C.; Waget, A.; Klopp, P.; Vachoux, C.; Bermudez-Humaran, L.G.; Smirnova, N.; Berge, M.; Sulpice, T.; Lahtinen, S.; et al. Intestinal mucosal adherence and translocation of commensal bacteria at the early onset of type 2 diabetes: Molecular mechanisms and probiotic treatment. EMBO Mol. Med. 2011, 3, 559-572.
90. Brugman, S.; Klatter, F.A.; Visser, J.; Wildeboer-Veloo, A.; Harmsen, H.; Rozing, J.; Bos, N.A. Antibiotic treatment partially protects against type 1 diabetes in the Bio-Breeding diabetes-prone rat. Is the gut flora involved in the development of type 1 diabetes? Diabetologia 2006, 49, 2105-2108.
91. Morowitz, M.J.; Carlisle, E.M.; Alverdy, J.C. Contributions of intestinal bacteria to nutrition and metabolism in the critically ill. Surg. Clin. N. Am. 2011, 91, 771-785.
92. Wu, W.C.; Zhao, W.; Li, S. Small intestinal bacteria overgrowth decreases small intestinal motility in the NASH rats. World J. Gastroenterol. 2008, 14, 313-317.
93. Kajiya, M.; Sato, K.; Silva, M.; Ouhara, K.; Do, P.M.; Shanmugam, K.T.; Kawai, T. Hydrogen from intestinal bacteria is protective for Concanavalin A-induced hepatitis. Biochem. Biophys. Res. Commun. 2009, 386, 316-321.
94. Mutlu, E.; Keshavarzian, A.; Engen, P.; Forsyth, C.B.; Sikaroodi, M.; Gillevet, P. Intestinal dysbiosis: A possible mechanism of alcohol-induced endotoxemia and alcoholic steatohepatitis in rats. Alcohol. Clin. Exp. Res. 2009, 33, 1836-1846.
95. Llovet, J.M.; Bartoli, R.; March, F.; Planas, R.; Vinado, B.; Cabre, E.; Arnal, J.C.; Pere, A.; Vicenc, G.; Miquel, A. Translocated intestinal bacteria cause spontaneous bacterial peritonitis in cirrhotic rats: Molecular epidemiologic evidence. J. Hepatol. 1998, 28, 307-313.
96. De Gottardi, A.; McCoy, K.D. Evaluation of the gut barrier to intestinal bacteria in non-alcoholic fatty liver disease. J. Hepatol. 2011, 55, 1181-1183.
97. Sandek, A.; Bauditz, J.; Swidsinski, A.; Buhner, S.; Weber-Eibel, J.; von Haehling, S.; Schroedl, W.; Karhausen, T.; Doehner, W.; Rauchhaus, M.; et al. Altered intestinal function in patients with chronic heart failure. J. Am. Coll. Cardiol. 2007, 50, 1561-1569.
98. Sandek, A.; Anker, S.D.; von Haehling, S. The gut and intestinal bacteria in chronic heart failure. Curr. Drug. Metab. 2009, 10, 22-28.
99. Krack, A.; Sharma, R.; Figulla, H.R.; Anker, S.D. The importance of the gastrointestinal system in the pathogenesis of heart failure. Eur. Heart J. 2005, 26, 2368-2374.
100. Bosch, M.; Fuentes, M.C.; Audivert, S.; Bonachera, M.A.; Peiro, S.; Cune, J. Lactobacillus plantarum CECT 7527, 7528 and 7529: Probiotic candidates to reduce cholesterol levels. J. Sci. Food Agric. 2014, 94, 803-809.
101. Lam, V.; Su, J.D.; Koprowski, S.; Hsu, A.N.; Tweddell, J.S.; Rafiee, P.; Gross, G.J.; Salzman, N.H.; Baker, J.E. Intestinal microbiota determine severity of myocardial infarction in rats. FASEB J. 2012, 26, 1727-1735.
102. Kang, M.J.; Ko, G.S.; Oh, D.G.; Kim, J.S.; Noh, K.; Kang, W.; Yoon, W.K.; Kim, H.C.; Jeong, H.G.; Jeong, T.C. Role of metabolism by intestinal microbiota in pharmacokinetics of oral baicalin. Arch. Pharm. Res. 2014, 37, 371-378.
103. Chu, F.F.; Esworthy, S.; Chu, P.G.; Huycke, M.; Doroshow, J. Bacteria-induced intestinal cancer in mice with disrupted Gpx1 and Gpx2 genes. Free Radic. Biol. Med. 2003, 351, 165-166.
104. Weir, T.L.; Manter, D.K.; Sheflin, A.M.; Barnett, B.A.; Heuberger, A.L.; Ryan, E.P. Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS ONE 2013, 8, e70803.
105. Boleij, A.; Tjalsma, H. Gut bacteria in health and disease: A survey on the interface between intestinal microbiology and colorectal cancer. Biol. Rev. 2012, 87, 701-730.
106. Singh, J.; Rivenson, A.; Tomita, M.; Shimamura, S.; Ishibashi, N.; Reddy, B.S. Bifidobacterium longum, a lactic acid-producing intestinal bacterium inhibits colon cancer and modulates the intermediate biomarkers of colon carcinogenesis. Carcinogenesis 1997, 18, 833-841.
107. Viaud, S.; Saccheri, F.; Mignot, G.; Yamazaki, T.; Daillere, R.; Hannani, D.; Enot, D.P.; Pfirschke, C.; Engblom, C.; Pittet, M.J.; et al. The intestinal microbiota modulates the anticancer immune effects of cyclophosphamide. Science 2013, 342, 971-976.
108. Poutahidis, T.; Cappelle, K.; Levkovich, T.; Lee, C.W.; Doulberis, M.; Ge, Z.M.; Fox, J.G.; Horwitz, B.H.; Erdman, S.E. Pathogenic intestinal bacteria enhance prostate cancer development via systemic activation of immune cells in mice. PLoS ONE 2013, 8, e739338.
109. Sugiyama, Y.; Masumori, N.; Fukuta, F.; Yoneta, A.; Hida, T.; Yamashita, T.; Minatoya, M.; Nagata, Y.; Mori, M.; Tsuji, H.; et al. Influence of isoflavone intake and equol-producing intestinal flora on prostate cancer risk. Asian Pacific. J. Cancer Prev. 2013, 14, 1-4.
110. Gori, A.; Rizzardini, G.; Van'T Land, B.; Amor, K.B.; van Schaik, J.; Torti, C.; Bandera, A.; Knol, J.; Benlhassan-Chahour, K.; Trabattoni, D.; et al. Specific prebiotics modulate gut microbiota and immune activation in HAART-naive HIV-infected adults: Results of the "COPA" pilot randomized trial. Mucosal Immunol. 2011, 4, 554-563.
111. Zajac, V, Stevurkova, V.; Matelova, L.; Ujhazy, E. Detection of HIV-1 sequences in intestinal bacteria of HIV/AIDS patients. Neuroendocrinol. Lett. 2007, 28, 591-595.
112. Vujkovic-Cvijin, I.; Dunham, R.M.; Iwai, S.; Maher, M.C.; Albright, R.G.; Broadhurst, M.J.; Hernandez, R.D.; Lederman, M.M.; Huang, Y.; Somsouk, M.; et al. Dysbiosis of the gut microbiota is associated with HIV disease progression and tryptophan aatabolism. Sci. Transl. Med. 2013, 5, doi:10.1126/scitranslmed.3006438.
113. Gori, A.; Tincati, C.; Rizzardini, G.; Torti, C.; Quirino, T.; Haarman, M.; Ben Amor, K.; van Schaik, J.; Vriesema, A.; Knol, J.; et al. Early impairment of gut function and gut flora supporting a role for alteration of gastrointestinal mucosa in human immunodeficiency virus pathogenesis. J. Clin. Microbiol. 2008, 46, 757-758.
114. Wolf, B.W.; Wheeler, K.B.; Ataya, D.G.; Garleb, K.A. Safety and tolerance of Lactobacillus reuteri supplementation to a population infected with the human immunodeficiency virus. Food Chem. Toxicol. 1998, 36, 1085-1094.
115. Hemsworth, J.; Hekmat, S.; Reid, G. The development of micronutrient supplemented probiotic yogurt for people living with HIV: Laboratory testing and sensory evaluation. Innov. Food Sci. Emerg. Technol. 2011, 12, 79-84.
116. Adams, J.B., Johansen, L.J.; Powell, L.D.; Quig, D.; Rubin, R.A. Gastrointestinal flora and gastrointestinal status in children with autism-comparisons to typical children and correlation with autism severity. BMC Gastroenterol. 2011, 11, doi:10.1186/1471-230X-11-22.
117. Cryan, J.F.; Dinan, T.G. Mind-altering microorganisms: The impact of the gut microbiota on brain and behaviour. Nat. Rev. Neurosci. 2012, 13, 701-712.
118. Heberling, C.A.; Dhurjati, P.S.; Sasser, M. Hypothesis for a systems connectivity model of autism spectrum disorder pathogenesis: Links to gut bacteria, oxidative stress, and intestinal permeability. Med. Hypotheses 2013, 80, 264-270.
119. Song, Y.L.; Liu, C.X.; Finegold, S.A. Real-time PCR quantitation of clostridia in feces of autistic children. Appl. Environ. Microb. 2004, 70, 6459-6465.
120. Finegold, S.M. State of the art; microbiology in health and disease. Intestinal bacterial flora in autism. Anaerobe 2011, 17, 367-368.
121. Finegold, S.M.; Molitoris, D.; Song, Y.L.; Liu, C.X.; Vaisanen, M.L.; Bolte, E.; McTeague, M.; Sandler, R.; Wexler, H.; Marlowe, E.M.; et al. Gastrointestinal microflora studies in late-onset autism. Clin. Infect. Dis. 2002, 351, 6-16.
122. Finegold, S.M. Desulfovibrio species are potentially important in regressive autism. Med. Hypotheses 2011, 77, 270-274.
123. De Angelis, M.; Piccolo, M.; Vannini, L.; Siragusa, S.; de Giacomo, A.; Serrazzanetti, D.I.; Cristofori, F.; Guerzoni, M.E.; Gobbetti, M.; Francavilla, R. Fecal microbiota and metabolome of children with autism and Pervasive Developmental Disorder Not Otherwise Specified. PLoS ONE 2013, 8, e76993.
124. Ono, S.; Komada, Y.; Kamiya, T.; Shirakawa, S. A pilot study of the relationship between bowel habits and sleep health by actigraphy measurement and fecal flora analysis. J. Physiol. Anthropol. 2008, 27, 145-151.
125. Taurog, J.D.; Richardson, J.A.; Croft, J.T.; Simmons, W.A.; Zhou, M.; Fernandez-Sueiro, J.L.; Balish, E.; Hammer, R.E. The germfree state prevents development of gut and joint inflammatory disease in HLA-B27 transgenic rats. J. Exp. Med. 1994, 180, 2359-2364.
126. Rehakova, Z.; Capkova, J.; Stepankova, R.; Sinkora, J.; Louzecka, A.; Ivanyi, P.; Weinreich, S. Germ-free mice do not develop ankylosing enthesopathy, a spontaneous joint disease. Hum. Immunol. 2000, 61, 555-558.
127. Yeoh, N.; Burton, J.P.; Suppiah, P.; Reid, G.; Stebbings, S. The role of the microbiome in rheumatic diseases. Curr. Rheumatol. Rep. 2013, 15, doi:10.1007/s11926-012-0314-y.
128. Kotanko, P.; Carter, M.; Levin, N.W. Intestinal bacterial microflora-a potential source of chronic inflammation in patients with chronic kidney disease. Nephrol. Dial. Transpl. 2006, 21, 2057-2060.
129. Smith, E.A.; Macfarlane, G.T. Enumeration of human colonic bacteria producing phenolic and indolic compounds: Effects of pH, carbohydrate availability and retention time on dissimilatory aromatic amino acid metabolism. J. Appl. Bacteriol. 1996, 81, 288-302.
130. Shiba, T.; Kawakami, K.; Sasaki, T.; Makino, I.; Kato, I.; Kobayashi, T.; Uchida, K.; Kaneko, K. Effects of intestinal bacteria-derived p-cresyl sulfate on Th1-type immune response in vivo and in vitro. Toxicol. Appl. Pharm. 2014, 274, 191-199.