Impact of the gut microbiota, prebiotics, and probiotics on human health and disease

Biomedical Journal

Volumn 37, Issue 5, 2014, Pages 259-268

  Lin, Chuan Sheng ^a,b   Chang, Chih Jung ^a,b   Lu, Chia Chen ^c   Martel, Jan ^a   Ojcius, David M ^a,d   Ko, Yun Fei ^e,f   Young, John D ^a,e,f,g   Lai, Hsin Chih ^a,b  

^a CHANG GUNG UNIVERSITY   (Taiwan)

^b CHANG GUNG UNIVERSITY COLLEGE OF MEDICINE   (Taiwan)

^c FU JEN CATHOLIC UNIVERSITY   (Taiwan)

^d UNIVERSITY OF CALIFORNIA   (United States)

^e Chang Gung Medical Center   (Taiwan)

^f MING CHI UNIVERSITY OF TECHNOLOGY   (Taiwan)

^g ROCKEFELLER UNIVERSITY   (United States)

Author keywords

disease; gut microflora; immunity; prebiotics; probiotics

Indexed keywords

PREBIOTIC AGENT; PROBIOTIC AGENT;

CARBOHYDRATE METABOLISM; CHRONIC INFLAMMATION; CONSERVATIVE TREATMENT; DISEASE ASSOCIATION; DISEASES; DYSBIOSIS; FATTY LIVER; FECAL TRANSPLANTATION; FERMENTATION; HEALTH; HOMEOSTASIS; HOST; HUMAN; IMMUNOCOMPETENT CELL; IMMUNOPATHOLOGY; INTESTINE FLORA; LUNG FUNCTION; LUNG INFECTION; NONHUMAN; NUTRIENT; NUTRITIONAL HEALTH; OBESITY; PNEUMONIA; REVIEW; ANIMAL; GASTROINTESTINAL TRACT; IMMUNOLOGY; ISOLATION AND PURIFICATION; MICROBIOLOGY; MICROFLORA;

ANIMALS; GASTROINTESTINAL TRACT; HEALTH; HUMANS; MICROBIOTA; OBESITY; PREBIOTICS; PROBIOTICS;

EID: 84908650241     PISSN: 23194170     EISSN: None     Source Type: Journal    
DOI: 10.4103/2319-4170.138314     Document Type: Review

References (100)

1. Roberfroid M, Gibson GR, Hoyles L, McCartney AL, Rastall R, Rowland I, et al. Prebiotic effects: Metabolic and health benefits. Br J Nutr 2010;104 Suppl 2:S1-63
2. Reuter G. The Lactobacillus and Bifidobacterium microflora of the human intestine: Composition and succession. Curr Issues Intest Microbiol 2001;2:43-53
3. O'May GA, Reynolds N, Macfarlane GT. Effect of pH on an in vitro model of gastric microbiota in enteral nutrition patients. Appl Environ Microbiol 2005;71:4777-83
4. Booijink CC, El-Aidy S, Rajilic-Stojanovic M, Heilig HG, Troost FJ, Smidt H, et al. High temporal and inter-individual variation Detected in the human ileal microbiota. Environ Microbiol 2010;12:3213-27
5. Qin J, Li R, Raes J, Arumugam M, Burgdorf KS, Manichanh C, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010;464:59-65
6. Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science 2005;308:1635-8
7. Sommer F, Backhed F. The gut microbiota-masters of host development and physiology. Nat Rev Microbiol 2013;11:227-38
8. Blottiere HM, de Vos WM, Ehrlich SD, Dore J. Human intestinal metagenomics: State of the art and future. Curr Opin Microbiol 2013;16:232-9
9. Koboziev I, Reinoso Webb C, Furr KL, Grisham MB. Role of the enteric microbiota in intestinal homeostasis and inflammation. Free Radic Biol Med 2014;68C:122-33
10. Jin C, Flavell RA. Innate sensors of pathogen and stress: Linking inflammation to obesity. J Allergy Clin Immunol 2013;132:287-94
11. Ramakrishna BS, Roediger WE. Bacterial short chain fatty acids: Their role in gastrointestinal disease. Dig Dis 1990;8:337-45
12. Martens EC, Chiang HC, Gordon JI. Mucosal glycan foraging enhances fitness and transmission of a saccharolytic human gut bacterial symbiont. Cell Host Microbe 2008;4:447-57
13. Benjdia A, Martens EC, Gordon JI, Berteau O. Sulfatases and a radical S-Adenosyl-L-methionine (AdoMet) enzyme are key for mucosal foraging and fitness of the prominent human gut symbiont, Bacteroides thetaiotaomicron. J Biol Chem 2011;286:25973-82
14. Bruel L, Sulzenbacher G, Cervera Tison M, Pujol A, Nicoletti C, Perrier J, et al. Alpha-Galactosidase/sucrose kinase (AgaSK), a novel bifunctional enzyme from the human microbiome coupling galactosidase and kinase activities. J Biol Chem 2011;286:40814-23
15. Gloux K, Berteau O, El Oumami H, Beguet F, Leclerc M, Dore J. A metagenomic beta-glucuronidase uncovers a core adaptive function of the human intestinal microbiome. Proc Natl Acad Sci USA 2011;108 Suppl 1:4539-46
16. Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 2013;152:39-50
17. Asano Y, Hiramoto T, Nishino R, Aiba Y, Kimura T, Yoshihara K, et al. Critical role of gut microbiota in the production of biologically active, free catecholamines in the gut lumen of mice. Am J Physiol Gastrointest Liver Physiol 2012;303:G1288-95
18. Nafday SM, Chen W, Peng L, Babyatsky MW, Holzman IR, Lin J. Short-chain fatty acids induce colonic mucosal injury in rats with various postnatal ages. Pediatr Res 2005;57:201-4
19. Tremaroli V, Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature 2012;489:242-9
20. Sayin SI, Wahlstrom A, Felin J, Jantti S, Marschall HU, Bamberg K, et al. Gut microbiota regulates bile acid metabolism by reducing the levels of tauro-beta-muricholic acid, a naturally occurring FXR antagonist. Cell Metab 2013;17:225-35
21. Parracho HM, Bingham MO, Gibson GR, McCartney AL. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J Med Microbiol 2005;54:987-91
22. Benassi B, Leleu R, Bird T, Clifton P, Fenech M. Cytokinesis-block micronucleus cytome assays for the determination of genotoxicity and cytotoxicity of cecal water in rats and fecal water in humans. Cancer Epidemiol Biomarkers Prev 2007;16:2676-80
23. Blachier F, Davila AM, Mimoun S, Benetti PH, Atanasiu C, Andriamihaja M, et al. Luminal sulfide and large intestine mucosa: Friend or foe?. Amino Acids 2010;39:335-47
24. Mafra D, Barros AF, Fouque D. Dietary protein metabolism by gut microbiota and its consequences for chronic kidney disease patients. Future Microbiol 2013;8:1317-23
25. Ramakrishna BS. Role of the gut microbiota in human nutrition and metabolism. J Gastroenterol Hepatol 2013;28 Suppl 4:9-17
26. Shen W, Gaskins HR, McIntosh MK. Influence of dietary fat on intestinal microbes, inflammation, barrier function and metabolic outcomes. J Nutr Biochem 2014;25:270-80
27. Tang WH, Wang Z, Levison BS, Koeth RA, Britt EB, Fu X, et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. N Engl J Med 2013;368:1575-84
28. Ussher JR, Lopaschuk GD, Arduini A. Gut microbiota metabolism of L-carnitine and cardiovascular risk. Atherosclerosis 2013;231:456-61
29. Kim E, Coelho D, Blachier F. Review of the association between meat consumption and risk of colorectal cancer. Nutr Res 2013;33:983-94
30. Sun Y, O'Riordan MX. Regulation of bacterial pathogenesis by intestinal short-chain Fatty acids. Adv Appl Microbiol 2013;85:93-118
31. O'Connor EM. The role of gut microbiota in nutritional status. Curr Opin Clin Nutr Metab Care 2013;16:509-16
32. Dass NB, John AK, Bassil AK, Crumbley CW, Shehee WR, Maurio FP, et al. The relationship between the effects of short-chain fatty acids on intestinal motility in vitro and GPR43 receptor activation. Neurogastroenterol Motil 2007;19:66-74
33. Hong YH, Nishimura Y, Hishikawa D, Tsuzuki H, Miyahara H, Gotoh C, et al. Acetate and propionate short chain fatty acids stimulate adipogenesis via GPCR43. Endocrinology 2005;146:5092-9
34. Ge H, Li X, Weiszmann J, Wang P, Baribault H, Chen JL, et al. Activation of G protein-coupled receptor 43 in adipocytes leads to inhibition of lipolysis and suppression of plasma free fatty acids. Endocrinology 2008;149:4519-26
35. Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature 2013;504:446-50
36. Gao Z, Yin J, Zhang J, Ward RE, Martin RJ, Lefevre M, et al. Butyrate improves insulin sensitivity and increases energy expenditure in mice. Diabetes 2009;58:1509-17
37. Franchi L, Kamada N, Nakamura Y, Burberry A, Kuffa P, Suzuki S, et al. NLRC4-driven production of IL-1beta discriminates between pathogenic and commensal bacteria and promotes host intestinal defense. Nat Immunol 2012;13:449-56
38. Denning TL, Wang YC, Patel SR, Williams IR, Pulendran B. Lamina propria macrophages and dendritic cells differentially induce regulatory and interleukin 17-producing T cell responses. Nat Immunol 2007;8:1086-94
39. Kamada N, Hisamatsu T, Okamoto S, Sato T, Matsuoka K, Arai K, et al. 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;175:6900-8
40. Said-Sadier N, Ojcius DM. Alarmins, inflammasomes and immunity. Biomed J 2012;35:437-49
41. Prescott D, Lee J, Philpott DJ. An epithelial armamentarium to sense the microbiota. Semin Immunol 2013;25:323-33
42. Villena J, Kitazawa H. Modulation of Intestinal TLR4-Inflammatory Signaling Pathways by Probiotic Microorganisms: Lessons Learned from TL2937. Front Immunol 2014;4:512
43. Chen GY. Role of Nlrp6 and Nlrp12 in the maintenance of intestinal homeostasis. Eur J Immunol 2014;44:321-7
44. Ivanov, II, Atarashi K, Manel N, Brodie EL, Shima T, Karaoz U, et al. Induction of intestinal Th17 cells by segmented filamentous bacteria. Cell 2009;139:485-98
45. Ito T, Simons M. Probing asthenospheric density, temperature, and elastic moduli below the western United States. Science 2011;332:947-51
46. Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature 2008;453:620-5
47. O'Mahony C, Scully P, O'Mahony D, Murphy S, O'Brien F, Lyons A, et al. Commensal-induced regulatory T cells mediate protection against pathogen-stimulated NF-kappaB activation. PLoS Pathog 2008;4:e1000112
48. Lathrop SK, Bloom SM, Rao SM, Nutsch K, Lio CW, Santacruz N, et al. Peripheral education of the immune system by colonic commensal microbiota. Nature 2011;478:250-4
49. Hand TW, Dos Santos LM, Bouladoux N, Molloy MJ, Pagan AJ, Pepper M, et al. Acute gastrointestinal infection induces long-lived microbiota-specific T cell responses. Science 2012;337:1553-6
50. Chan YK, Estaki M, Gibson DL. Clinical consequences of diet-induced dysbiosis. Ann Nutr Metab 2013;63 Suppl 2:28-40
51. Butel MJ. Probiotics, gut microbiota and health. Med Mal Infect 2014;44:1-8
52. Backhed F, Ding H, Wang T, Hooper LV, Koh GY, Nagy A, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA 2004;101:15718-23
53. 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;444:1027-31
54. Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA 2005;102:11070-5
55. Amar J, Burcelin R, Ruidavets JB, Cani PD, Fauvel J, Alessi MC, et al. Energy intake is associated with endotoxemia in apparently healthy men. Am J Clin Nutr 2008;87:1219-23
56. Brun P, Castagliuolo I, Di Leo V, Buda A, Pinzani M, Palu G, et al. Increased intestinal permeability in obese mice: New evidence in the pathogenesis of nonalcoholic steatohepatitis. Am J Physiol Gastrointest Liver Physiol 2007;292:G518-25
57. Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM, et al. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes 2008;57:1470-81
58. Miyake Y, Yamamoto K. Role of gut microbiota in liver diseases. Hepatol Res 2013;43:139-46
59. Henao-Mejia J, Elinav E, Thaiss CA, Licona-Limon P, Flavell RA. Role of the intestinal microbiome in liver disease. J Autoimmun 2013;46:66-73
60. Henao-Mejia J, Elinav E, Thaiss CA, Flavell RA. The intestinal microbiota in chronic liver disease. Adv Immunol 2013;117:73-97
61. Sharma V, Garg S, Aggarwal S. Probiotics and liver disease. Perm J 2013;17:62-7
62. Compare D, Coccoli P, Rocco A, Nardone OM, De Maria S, Carteni M, et al. Gut-liver axis: The impact of gut microbiota on non alcoholic fatty liver disease. Nutr Metab Cardiovasc Dis 2012;22:471-6
63. Lade A, Noon LA, Friedman SL. Contributions of metabolic dysregulation and inflammation to nonalcoholic steatohepatitis, hepatic fibrosis, and cancer. Curr Opin Oncol 2014;26:100-7
64. Wiernsperger N. Hepatic function and the cardiometabolic syndrome. Diabetes Metab Syndr Obes 2013;6:379-88
65. Park JS, Seo JH, Youn HS. Gut Microbiota and Clinical Disease: Obesity and Nonalcoholic Fatty Liver Disease. Pediatr Gastroenterol Hepatol Nutr 2013;16:22-7
66. Orman ES, Odena G, Bataller R. Alcoholic liver disease: Pathogenesis, management, and novel targets for therapy. J Gastroenterol Hepatol 2013;28 Suppl 1:77-84
67. Trompette A, Gollwitzer ES, Yadava K, Sichelstiel AK, Sprenger N, Ngom-Bru C, et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat Med 2014;20:159-66
68. Willing BP, Russell SL, Finlay BB. Shifting the balance: Antibiotic effects on host-microbiota mutualism. Nat Rev Microbiol 2011;9:233-43
69. Jakobsson HE, Jernberg C, Andersson AF, Sjolund-Karlsson M, Jansson JK, Engstrand L. Short-Term antibiotic treatment has differing long-Term impacts on the human throat and gut microbiome. PLoS One 2010;5:e9836
70. Jernberg C, Lofmark S, Edlund C, Jansson JK. Long-Term ecological impacts of antibiotic administration on the human intestinal microbiota. ISME J 2007;1:56-66
71. Kim YG, Udayanga KG, Totsuka N, Weinberg JB, Nunez G, Shibuya A. Gut dysbiosis promotes M2 macrophage polarization and allergic airway inflammation via fungi-induced PGE (2). Cell Host Microbe 2014;15:95-102
72. Zelante T, Iannitti RG, Cunha C, De Luca A, Giovannini G, Pieraccini G, et al. Tryptophan catabolites from microbiota engage aryl hydrocarbon receptor and balance mucosal reactivity via interleukin-22. Immunity 2013;39:372-85
73. Slack E, Hapfelmeier S, Stecher B, Velykoredko Y, Stoel M, Lawson MA, et al. Innate and adaptive immunity cooperate flexibly to maintain host-microbiota mutualism. Science 2009;325:617-20
74. Gerritsen J, Smidt H, Rijkers GT, de Vos WM. Intestinal microbiota in human health and disease: The impact of probiotics. Genes Nutr 2011;6:209-40
75. Scher JU, Sczesnak A, Longman RS, Segata N, Ubeda C, Bielski C, et al. Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis. Elife 2013;2:e01202
76. Kamada N, Chen GY, Inohara N, Nunez G. Control of pathogens and pathobionts by the gut microbiota. Nat Immunol 2013;14:685-90
77. Chu H, Mazmanian SK. Innate immune recognition of the microbiota promotes host-microbial symbiosis. Nat Immunol 2013;14:668-75
78. Ichinohe T, Pang IK, Kumamoto Y, Peaper DR, Ho JH, Murray TS, et al. Microbiota regulates immune defense against respiratory tract influenza A virus infection. Proc Natl Acad Sci USA 2011;108:5354-9
79. Abt MC, Osborne LC, Monticelli LA, Doering TA, Alenghat T, Sonnenberg GF, et al. Commensal bacteria calibrate the activation threshold of innate antiviral immunity. Immunity 2012;37:158-70
80. Reid G, Jass J, Sebulsky MT, McCormick JK. Potential uses of probiotics in clinical practice. Clin Microbiol Rev 2003;16:658-72
81. Mileti E, Matteoli G, Iliev ID, Rescigno M. Comparison of the immunomodulatory properties of three probiotic strains of Lactobacilli using complex culture systems: Prediction for in vivo efficacy. PLoS One 2009;4:e7056
82. Wallace TC, Guarner F, Madsen K, Cabana MD, Gibson G, Hentges E, et al. Human gut microbiota and its relationship to health and disease. Nutr Rev 2011;69:392-403
83. Shida K, Nomoto K. Probiotics as efficient immunopotentiators: Translational role in cancer prevention. Indian J Med Res 2013;138:808-14
84. Duncan SH, Aminov RI, Scott KP, Louis P, Stanton TB, Flint HJ. Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces. Int J Syst Evol Microbiol 2006;56:2437-41
85. Everard A, Belzer C, Geurts L, Ouwerkerk JP, Druart C, Bindels LB, et al. Cross-Talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity. Proc Natl Acad Sci USA 2013;110:9066-71
86. Di Gioia D, Aloisio I, Mazzola G, Biavati B. Bifidobacteria: Their impact on gut microbiota composition and their applications as probiotics in infants. Appl Microbiol Biotechnol 2014;98:563-77
87. Vieira AT, Teixeira MM, Martins FS. The Role of Probiotics and Prebiotics in Inducing Gut Immunity. Front Immunol 2013;4:445
88. Delzenne NM, Neyrinck AM, Cani PD. Modulation of the gut microbiota by nutrients with prebiotic properties: Consequences for host health in the context of obesity and metabolic syndrome. Microb Cell Fact 2011;10 Suppl 1:S10
89. Rowland I, Capurso L, Collins K, Cummings J, Delzenne N, Goulet O, et al. Current level of consensus on probiotic science-report of an expert meeting-London, 23 November 2009. Gut Microbes 2010;1:436-9
90. De Filippo C, Cavalieri D, Di Paola M, Ramazzotti M, Poullet JB, Massart S, et al. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci USA 2010;107:14691-6
91. Martinez FD. The human microbiome. Early life determinant of health outcomes. Ann Am Thorac Soc 2014;11 Suppl 1:S7-12
92. Kaczmarczyk MM, Miller MJ, Freund GG. The health benefits of dietary fiber: Beyond the usual suspects of type 2 diabetes mellitus, cardiovascular disease and colon cancer. Metabolism 2012;61:1058-66
93. Shen Q, Zhao L, Tuohy KM. High-level dietary fibre up-regulates colonic fermentation and relative abundance of saccharolytic bacteria within the human faecal microbiota in vitro. Eur J Nutr 2012;51:693-705
94. Etxeberria U, Fernandez-Quintela A, Milagro FI, Aguirre L, Martinez JA, Portillo MP. Impact of polyphenols and polyphenol-rich dietary sources on gut microbiota composition. J Agric Food Chem 2013;61:9517-33
95. Borody TJ, Khoruts A. Fecal microbiota transplantation and emerging applications. Nat Rev Gastroenterol Hepatol 2012;9:88-96
96. van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med 2013;368:407-15
97. Petrof EO, Gloor GB, Vanner SJ, Weese SJ, Carter D, Daigneault MC, et al. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut. Microbiome 2013;1:3
98. Vrieze A, Van Nood E, Holleman F, Salojarvi J, Kootte RS, Bartelsman JF, et al. Transfer of intestinal microbiota from lean Donors increases insulin sensitivity in individuals with metabolic syndrome. Gastroenterology 2012;143:913-6.e7
99. Umu OC, Oostindjer M, Pope PB, Svihus B, Egelandsdal B, Nes IF, et al. Potential applications of gut microbiota to control human physiology. Antonie Van Leeuwenhoek 2013;104:609-18
100. Culligan EP, Sleator RD, Marchesi JR, Hill C. Metagenomics and novel gene discovery: Promise and potential for novel therapeutics. Virulence 2013;5:399-412