Impact of diet on the human intestinal microbiota

Current Opinion in Food Science

Volumn 2, Issue , 2015, Pages 71-77

  Tan, Huizi ^a,b   O'Toole, Paul W ^b,c  

^a JIANGNAN UNIVERSITY   (China)

^b UNIVERSITY COLLEGE CORK   (Ireland)

^c UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 84923383600     PISSN: 22147993     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cofs.2015.01.005     Document Type: Review

References (68)

1. Karlsson F., Tremaroli V., Nielsen J., Backhed F. Assessing the human gut microbiota in metabolic diseases. Diabetes 2013, 62:3341-3349.
2. Rosner J.L. Ten times more microbial cells than body cells in humans?. Microbe 2014, 9:47.
3. Qin J.J., Li R.Q., Raes J., Arumugam M., Burgdorf K.S., Manichanh C., Nielsen T., Pons N., Levenez F., Yamada T., et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature 2010, 464. 59-U70.
4. Biagi E., Candela M., Fairweather-Tait S., Franceschi C., Brigidi P. Ageing of the human metaorganism: the microbial counterpart. Age 2012, 34:247-267.
5. Mariat D., Firmesse O., Levenez F., Guimaraes V.D., Sokol H., Dore J., Corthier G., Furet J.P. The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age. Bmc Microbiol 2009, 9:6.
6. Zhang C.H., Zhang M.H., Wang S.Y., Han R.J., Cao Y.F., Hua W.Y., Mao Y.J., Zhang X.J., Pang X.Y., Wei C.C., et al. Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in mice. Isme J 2010, 4:232-241.
7. Hildebrandt M.A., Hoffmann C., Sherrill-Mix S.A., Keilbaugh S.A., Hamady M., Chen Y.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.
8. Turnbaugh P.J., Ridaura V.K., Faith J.J., Rey F.E., Knight R., Gordon J.I. The effect of diet on the human gut microbiome: a metagenomic analysis in humanized gnotobiotic mice. Sci Trans Med 2009, 1:10.
9. De Filippo C., Cavalieri D., Di Paola M., Ramazzotti M., Poullet J.B., Massart S., Collini S., Pieraccini G., Lionetti P. Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 2010, 107:14691-14696.
10. Moore W.E.C., Moore L.H. Intestinal floras of populations that have a high-risk of colon-cancer. Appl Environ Microbiol 1995, 61:3202-3207.
11. Kabeerdoss J., Devi R.S., Mary R.R., Ramakrishna B.S. Faecal microbiota composition in vegetarians: comparison with omnivores in a cohort of young women in southern India. Br J Nutr 2012, 108:953-957.
12. Liszt K., Zwielehner J., Handschur M., Hippe B., Thaler R., Haslberger A.G. Characterization of bacteria, clostridia and bacteroides in faeces of vegetarians using qPCR and PCR-DGGE fingerprinting. Annals Nutr Metab 2009, 54:253-257.
13. Zimmer J., Lange B., Frick J.S., Sauer H., Zimmermann K., Schwiertz A., Rusch K., Klosterhalfen S., Enck P. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. Eur J Clin Nutr 2012, 66:53-60.
14. 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.
15. Walker A.W., Ince J., Duncan S.H., Webster L.M., Holtrop G., Ze X.L., Brown D., Stares M.D., Scott P., Bergerat A., et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. Isme J 2011, 5:220-230.
16. Marques T.M., Wall R., Ross R.P., Fitzgerald G.F., Ryan C.A., Stanton C. Programming infant gut microbiota: influence of dietary and environmental factors. Curr Opin Biotechnol 2010, 21:149-156.
17. Thompson A.L. Developmental origins of obesity: early feeding environments, infant growth, and the intestinal microbiome. Am J Hum Biol 2012, 24:350-360.
18. Boehm G., Moro G. Structural and functional aspects of prebiotics used in infant nutrition. J Nutr 2008, 138:1818S-1828S.
19. Eswaran S., Muir J., Chey W.D. Fiber and functional gastrointestinal disorders. Am J Gastroenterol 2013, 108:718-727.
20. Martinez I., Kim J., Duffy P.R., Schlegel V.L., Walter J. Resistant starches types 2 and 4 have differential effects on the composition of the fecal microbiota in human subjects. Plos One 2010, 5:11.
21. Shinohara K., Ohashi Y., Kawasumi K., Terada A., Fujisawa T. Effect of apple intake on fecal microbiota and metabolites in humans. Anaerobe 2010, 16:510-515.
22. Sonnenburg E.D., Zheng H.J., Joglekar P., Higginbottom S.K., Firbank S.J., Bolam D.N., Sonnenburg J.L. Specificity of polysaccharide use in intestinal Bacteroides species determines diet-induced microbiota alterations. Cell 2010, 141. 1241-U1256.
23. Schwartz S., Friedberg I., Ivanov I.V., Davidson L.A., Goldsby J.S., Dahl D.B., Herman D., Wang M., Donovan S.M., Chapkin R.S. A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. Genome Biol 2012, 13:16.
24. Hehemann J.H., Correc G., Barbeyron T., Helbert W., Czjzek M., Michel G. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 2010, 464. 908-U123.
25. Souza B.W.S., Cerqueira M.A., Bourbon A.I., Pinheiro A.C., Martins J.T., Teixeira J.A., Coimbra M.A., Vicente A.A. Chemical characterization and antioxidant activity of sulfated polysaccharide from the red seaweed Gracilaria birdiae. Food Hydrocolloids 2012, 27:287-292.
26. Wichmann A., Allahyar A., Greiner T.U., Plovier H., Lunden G.O., Larsson T., Drucker D.J., Delzenne N.M., Cani P.D., Backhed F. Microbial modulation of energy availability in the colon regulates intestinal transit. Cell Host Microbe 2013, 14:582-590.
27. Flint H.J. Antibiotics and adiposity. Nature 2012, 488:601-602.
28. Vinolo M.A.R., Ferguson G.J., Kulkarni S., Damoulakis G., Anderson K., Bohlooly-Y M., Stephens L., Hawkins L., Curi P.T.R. SCFAs induce mouse neutrophil chemotaxis through the GPR43 receptor. Plos One 2011, 6:10.
29. Vinolo M.A.R., Rodrigues H.G., Nachbar R.T., Curi R. Regulation of inflammation by short chain fatty acids. Nutrients 2011, 3:858-876.
30. Goncalves P., Gregorio I., Catarino T.A., Martel F. The effect of oxidative stress upon the intestinal epithelial uptake of butyrate. Eur J Pharmacol 2013, 699:88-100.
31. Fung K.Y.C., Cosgrove L., Lockett T., Head R., Topping D.L. A review of the potential mechanisms for the lowering of colorectal oncogenesis by butyrate. Br J Nutr 2012, 108:820-831.
32. Maa M.C., Chang M.Y., Hsieh M.Y., Chen Y.J., Yang C.J., Chen Z.C., Li Y.K., Yen C.K., Wu R.R., Leu T.H. Butyrate reduced lipopolysaccharide-mediated macrophage migration by suppression of Src enhancement and focal adhesion kinase activity. J Nutr Biochem 2010, 21:1186-1192.
33. Park J.S., Lee E.J., Lee J.C., Kim W.K., Kim H.S. Anti-inflammatory effects of short chain fatty acids in IFN-gamma-stimulated RAW 264.7 murine macrophage cells: involvement of NF-kappa B and ERK signaling pathways. Int Immunopharmacol 2007, 7:70-77.
34. Hatayama H., Washita J., Kuwajima A., Abe T. The short chain fatty acid, butyrate, stimulates MUC2 mucin production in the human colon cancer cell line, LS174T. Biochem Biophys Res Commun 2007, 356:599-603.
35. Soret R., Chevalier J., De Coppet P., Poupeau G., Derkinderen P., Segain J.P., Neunlist M. Short-chain fatty acids regulate the enteric neurons and control gastrointestinal motility in rats. Gastroenterology 2010, 138. 1772-U1749.
36. Jeffery I.B., O'Toole P.W. Diet-microbiota interactions and their implications for healthy living. Nutrients 2013, 5:234-252.
37. Duncan S.H., Louis P., Thomson J.M., Flint H.J. The role of pH in determining the species composition of the human colonic microbiota. Environ Microbiol 2009, 11:2112-2122.
38. Fukuda S., Toh H., Hase K., Oshima K., Nakanishi Y., Yoshimura K., Tobe T., Clarke J.M., Topping D.L., Suzuki T., et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature 2011, 469:543-U791.
39. Hosseini E., Grootaert C., Verstraete W., Van de Wiele T. Propionate as a health-promoting microbial metabolite in the human gut. Nutr Rev 2011, 69:245-258.
40. Cruz-Bravo R.K., Guevara-Gonzalez R.G., Ramos-Gomez M., Oomah B.D., Wiersma P., Campos-Vega R., Loarca-Pina G. The fermented non-digestible fraction of common bean (Phaseolus vulgaris L.) triggers cell cycle arrest and apoptosis in human colon adenocarcinoma cells. Genes Nutr 2014, 9:12.
41. Boxma P.Y., van den Berg E., Geleijnse J.M., Laverman G.D., Schurgers L.J., Vermeer C., Kema I.P., Muskiet F.A., Navis G., Bakker S.J.L., et al. Vitamin K intake and plasma desphospho-uncarboxylated matrix Gla-protein levels in kidney transplant recipients. Plos One 2012, 7:8.
42. Fujita Y., Iki M., Tamaki J., Kouda K., Yura A., Kadowaki E., Sato Y., Moon J.S., Tomioka K., Okamoto N., et al. Association between vitamin K intake from fermented soybeans, natto, and bone mineral density in elderly Japanese men: the Fujiwara-kyo Osteoporosis Risk in Men (FORMEN) study. Osteoporosis Int 2012, 23:705-714.
43. 2 supplementation on functional vitamin K deficiency in hemodialysis patients: A randomized trial. Am J Kidney Dis 2012, 59:186-195.
44. Resta S.C. Effects of probiotics and commensals on intestinal epithelial physiology: implications for nutrient handling. J Physiol-London 2009, 587:4169-4174.
45. Pompei A., Cordisco L., Amaretti A., Zanoni S., Matteuzzi D., Rossi M. Folate production by bifidobacteria as a potential probiotic property. Appl Environ Microbiol 2007, 73:179-185.
46. Kim T.H., Yang J., Darling P.B., O'Connor D.L. A large pool of available folate exists in the large intestine of human infants and piglets. J Nutr 2004, 134:1389-1394.
47. Cotter P.D., Hill C., Ross R.P. Bacteriocins: developing innate immunity for food. Nat Rev Microbiol 2005, 3:777-788.
48. Birri D.J., Brede D.A., Nes I.F. Salivaricin D, a novel intrinsically trypsin-resistant lantibiotic from Streptococcus salivarius 5M6c isolated from a healthy infant. Appl Environ Microbiol 2012, 78:402-410.
49. Miyauchi E., O'Callaghan J., Butto L.F., Hurley G., Melgar S., Tanabe S., Shanahan F., Nally K., O'Toole P.W. Mechanism of protection of transepithelial barrier function by Lactobacillus salivarius: strain dependence and attenuation by bacteriocin production. Am J Physiol-Gastrointestinal Liver Physiol 2012, 303:G1029-G1041.
50. Shen Y., Torchia M.L.G., Lawson G.W., Karp C.L., Ashwell J.D., Mazmanian S.K. Outer membrane vesicles of a human commensal mediate immune regulation and disease protection. Cell Host Microbe 2012, 12:509-520.
51. Sokol H., Pigneur B., Watterlot L., Lakhdari O., Bermudez-Humaran L.G., Gratadoux J.J., Blugeon S., Bridonneau C., Furet J.P., Corthier G., et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci U S A 2008, 105:16731-16736.
52. Bhat R., Axtell R., Mitra A., Miranda M., Lock C., Tsien R.W., Steinman L. Inhibitory role for GABA in autoimmune inflammation. Proc Natl Acad Sci U S A 2010, 107:2580-2585.
53. Komatsuzaki N., Nakamura T., Kimura T., Shima J. Characterization of glutamate decarboxylase from a high gamma-aminobutyric acid (GABA)-producer, Lactobacillus paracasei. Biosci Biotechnol Biochem 2008, 72:278-285.
54. Barrett E., Ross R.P., O'Toole P.W., Fitzgerald G.F., Stanton C. gamma-Aminobutyric acid production by culturable bacteria from the human intestine. J Appl Microbiol 2012, 113:411-417.
55. Fetissov S.O., Sinno M.H., Coeffier M., Bole-Feysot C., Ducrotte P., Hokfelt T., Dehelotte P. Autoantibodies against appetite-regulating peptide hormones and neuropeptides: putative modulation by gut microflora. Nutrition 2008, 24:348-359.
56. Vila G., Grimm G., Resl M., Heinisch B., Einwallner E., Esterbauer H., Dieplinger B., Mueller T., Luger A., Clodi M. B-Type natriuretic peptide modulates ghrelin, hunger, and satiety in healthy men. Diabetes 2012, 61:2592-2596.
57. Nicholson J.K., Holmes E., Kinross J., Burcelin R., Gibson G., Jia W., Pettersson S. Host-gut microbiota metabolic interactions. Science 2012, 336:1262-1267.
58. Ott S.J., Musfeldt M., Wenderoth D.F., Hampe J., Brant O., Folsch U.R., Timmins K.N., Schreiber S. Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease. Gut 2004, 53:685-693.
59. Ley R.E., Turnbaugh P.J., Klein S., Gordon J.I. Microbial ecology: human gut microbes associated with obesity. Nature 2006, 444:1022-1023.
60. Cani P.D., Amar J., Iglesias M.A., Poggi M., Knauf C., Bastelica D., Neyrinck A.M., Fava F., Tuohy K.M., Chabo C., et al. Metabolic endotoxemia initiates obesity and insulin resistance. Diabetes 2007, 56:1761-1772.
61. Rees K. Primary prevention of cardiovascular disease with a mediterranean diet. N Engl J Med 2014, 370. 886-886.
62. Salas-Salvado J., Bullo M., Babio N., Martinez-Gonzalez M.A., Ibarrola-Jurado N., Basora J., Estruch R., Covas M.I., Corella D., Aros F., et al. Reduction in the incidence of type 2 diabetes with the mediterranean diet results of the PREDIMED-Reus nutrition intervention randomized trial. Diabetes Care 2011, 34:14-19.
63. Lopez-Legarrea P., Fuller N., Zulet M., Martinez J., Caterson I. The influence of Mediterranean, carbohydrate and high protein diets on gut microbiota composition in the treatment of obesity and associated inflammatory state. Asia Pac J Clin Nutr 2014, 23.
64. Smith M.I., Yatsunenko T., Manary M.J., Trehan I., Mkakosya R., Cheng J.Y., Kau A.L., Rich S.S., Concannon P., Mychaleckyj J.C., et al. Gut microbiomes of Malawian twin pairs discordant for Kwashiorkor. Science 2013, 339:548-554.
65. Gibson P.R., Shepherd S.J. Evidence-based dietary management of functional gastrointestinal symptoms: the FODMAP approach. J Gastroenterol Hepatol 2010, 25:252-258.
66. Jeffery I.B., O'Toole P.W., Ohman L., Claesson M.J., Deane J., Quigley E.M.M., Simren M. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut 2012, 61:997-1006.
67. Petrof E.O., Gloor G.B., Vanner S.J., Weese S.J., Carter D., Daigneault M.C., Brown E.M., Schroeter K., Allen-Vercoe E. Stool substitute transplant therapy for the eradication of Clostridium difficile infection: 'RePOOPulating' the gut. Microbiome 2013, 1:3.
68. Neef A., Sanz Y. Future for probiotic science in functional food and dietary supplement development. Curr Opin Clin Nutr Metab Care 2013, 16:679-687.