1. Backhed F., Ley R.E., Sonnenburg J.L., Peterson D.A., Gordon J.I. Host-bacterial mutualism in the human intestine. Science. 2005;307:1915–1920. doi: 10.1126/science.1104816. [PubMed] [CrossRef] [Google Scholar]
2. Scanlan P.D., Shanahan F., Marchesi J.R. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol. 2008;8:79. doi: 10.1186/1471-2180-8-79. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
3. Huttenhower C., Gevers D., Knight R., Abubucker S., Badger J.H., Chinwalla A.T., Creasy H.H., Earl A.M., Fitzgerald M.G., Fulton R.S., et al. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207–214. [Google Scholar]
4. Huse S.M., Ye Y., Zhou Y., Fodor A.A. A core human microbiome as viewed through 16S rRNA sequence clusters. PLoS One. 2012;7:e34242. doi: 10.1371/journal.pone.0034242. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
5. Manichanh C., Rigottier-Gois L., Bonnaud E., Gloux K., Pelletier E., Frangeul L., Nalin R, Jarrin C., Chardon P., Marteau P., et al. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55:205–211. [PMC free article] [PubMed] [Google Scholar]
6. Bingham S.A., Day N.E., Luben R., Ferrari P., Slimani N., Norat T., Clavel-Chapelon F., Kesse E., Nieters A., Boeing H., et al. Dietary fibre in food and protection against colorectal cancer in the European Prospective Investigation into Cancer and Nutrition (EPIC): An observational study. Lancet. 2003;361:1496–1501. [PubMed] [Google Scholar]
7. Stephen A.M., Cummings J.H. Mechanism of action of dietary fiber in the human colon. Nature. 1980;284:283–284. doi: 10.1038/284283a0. [PubMed] [CrossRef] [Google Scholar]
8. Cummings J.H., Bingham S.A., Heaton K.W., Eastwood M.A. Fecal weight, colon cancer risk, and dietary-intake of nonstarch polysaccharides (dietary fiber) Gastroenterology. 1992;103:1783–1789. [PubMed] [Google Scholar]
9. Birkett A.M., Jones G.P., de Silva A.M., Young G.P., Muir J.G. Dietary intake and faecal excretion of carbohydrate by Australians: Importance of achieving stool weights greater than 150 g to improve faecal markers relevant to colon cancer risk. Eur. J. Clin. Nutr. 1997;51:625–632. doi: 10.1038/sj.ejcn.1600456. [PubMed] [CrossRef] [Google Scholar]
10. 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. doi: 10.1111/j.1462-2920.2009.01931.x. [PubMed] [CrossRef] [Google Scholar]
11. 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. doi: 10.1126/science.1223813. [PubMed] [CrossRef] [Google Scholar]
12. Cummings J.H., Macfarlane G.T. The control and consequences of bacterial fermentation in the human colon. J. Appl. Bacteriol. 1991;70:443–459. doi: 10.1111/j.1365-2672.1991.tb02739.x. [PubMed] [CrossRef] [Google Scholar]
13. Topping D.L., Clifton P.M. Short-chain fatty acids and human colonic function: Roles of resistant starch and nonstarch polysaccharides. Physiol. Rev. 2001;81:1031–1064. [PubMed] [Google Scholar]
14. Donohoe D.R., Garge N., Zhang X., Sun W., O’Connell T.M., Bunger M.K., Bultman S.J. The microbiome and butyrate regulate energy metabolism and autophagy in the mammalian colon. Cell. Metab. 2011;13:517–526. doi: 10.1016/j.cmet.2011.02.018. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
15. Trompette A., Gollwitzer E.S., Yadava K., Sichelstiel A.K., Sprenger N., Ngom-Bru C., Blanchard C., Junt T., Nicod L.P., Harries N.L., et al. Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis. Nat. Med. 2014;20:159–168. [PubMed] [Google Scholar]
16. Trent M.S., Stead C.M., Tran A.X., Hankins J.V. Diversity of endotoxin and its impact on pathogenesis. J. Endotoxin Res. 2006;12:205–223. doi: 10.1179/096805106X118825. [PubMed] [CrossRef] [Google Scholar]
17. Kamada N., Chen G., Nunez G. Harnessing pathogen-commensal relations. Nat. Med. 2012;18:1190–1191. doi: 10.1038/nm.2900. [PubMed] [CrossRef] [Google Scholar]
18. 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;469:543–547. [PubMed] [Google Scholar]
19. Cantarel B.L., Lombard V., Henrissat B. Complex carbohydrate utilization by the healthy human microbiome. PLoS One. 2012;7:e28742. doi: 10.1371/journal.pone.0028742. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
20. Xu J., Bjursell M.K., Himrod J., Deng S., Carmichael L.K., Chiang H.C., Hooper L.V., Gordon J.I. A genomic view of the human-Bacteroides thetaiotaomicron symbiosis. Science. 2003;299:2074–2076. doi: 10.1126/science.1080029. [PubMed] [CrossRef] [Google Scholar]
21. Sandberg A.S., Andlid T. Phytogenic and microbial phytases in human nutrition. Int. J. Food Sci. Technol. 2002;37:823–833. doi: 10.1046/j.1365-2621.2002.00641.x. [CrossRef] [Google Scholar]
22. Morvan B., Bonnemoy F., Fonty G., Gouet P. Quantitative determination of H2-utilizing acetogenic and sulfate-reducing bacteria and methanogenic archaea from digestive tract of different mammals. Curr. Microbiol. 1996;32:129–133. doi: 10.1007/s002849900023. [PubMed] [CrossRef] [Google Scholar]
23. Carbonero F., Benefiel A.C., Alizadeh-Ghamsari A.H., Gaskins H.R. Microbial pathways in colonic sulphur metabolism and links with health and disease. Front. Physiol. 2012;3:448. doi: 10.3389/fphys.2012.00448. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
24. Chatterjee S., Park S., Low K., Kong Y., Pimentel M. The degree of breath methane production in IBS correlates with the severity of constipation. Am. J. Gastroenterol. 2007;102:837–841. doi: 10.1111/j.1572-0241.2007.01072.x. [PubMed] [CrossRef] [Google Scholar]
25. 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. USA. 2008;105:16731–16736. [PMC free article] [PubMed] [Google Scholar]
26. Huurre A., Kalliomaki M., Rautava S., Rinne M., Salminen S., Isolauri E. Mode of delivery—Effects on gut microbiota and humoral immunity. Neonatology. 2008;93:236–240. doi: 10.1159/000111102. [PubMed] [CrossRef] [Google Scholar]
27. Kelly D., King T., Aminov R. Importance of microbial colonization of the gut in early life to the development of immunity. Mutat. Res. 2007;622:58–69. doi: 10.1016/j.mrfmmm.2007.03.011. [PubMed] [CrossRef] [Google Scholar]
28. Harmsen H.J., Wildeboer-Veloo A.C.M., 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. doi: 10.1097/00005176-200001000-00019. [PubMed] [CrossRef] [Google Scholar]
29. Coppa G.V., Zampini L., Galeazzi T., Gabrielli O. Prebiotics in human milk: A review. Dig. Liver Dis. 2006;38:S291–S294. doi: 10.1016/S1590-8658(07)60013-9. [PubMed] [CrossRef] [Google Scholar]
30. Arslanoglu S., Moro G.E., Schmitt J., Tandoi L., Rizzardi S., Boehm G. Early dietary intervention with a mixture of prebiotic oligosaccharides reduces the incidence of allergic manifestations and infections during the first two years of life. J. Nutr. 2008;138:1091–1095. [PubMed] [Google Scholar]
31. Barrett M.J., Donoghue V., Mooney E.E., Slevin M., Persaud T., Twomey E., Ryan S., Laffan E., Twomey A. Isolated acute non-cystic white matter injury in term infants presenting with neonatal encephalopathy. Arch. Dis. Child. Fetal Neonatal Ed. 2013;98:F158–F160. doi: 10.1136/archdischild-2011-301505. [PubMed] [CrossRef] [Google Scholar]
32. Sghir A., Gramet G., Suau A., Rochet V., Pochart P., Dore J. Quantification of bacterial groups within human fecal flora by oligonucleotide probe hybridization. Appl. Environ. Microbiol. 2000;66:2263–2266. doi: 10.1128/AEM.66.5.2263-2266.2000. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
33. Pokusaeva K., Fitzgerald G.F., van Sinderen D. Carbohydrate metabolism in Bifidobacteria. Genes Nutr. 2011;6:285–306. doi: 10.1007/s12263-010-0206-6. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
34. Yatsunenko T., Rey F.E., Manary M.J., Trehan I., Dominguez-Bello M.G., Contreras M., Magris M., Hidalgo G., Baldassano R.N., Anokhin A.P., et al. Human gut microbiome viewed across age and geography. Nature. 2012;486:222–227. [PMC free article] [PubMed] [Google Scholar]
35. Lakshminarayanan B., Harris H.M.B., Coakley M., O’Sullivan O., Stanton C., Pruteanu M., Shanahan F., O’Toole P.W., Ross R.P., Consortium E., et al. Prevalence and characterization of Clostridium perfringens from the faecal microbiota of elderly Irish subjects. J. Med. Microbiol. 2013;62:457–466. [PubMed] [Google Scholar]
36. Claesson M.J., Jeffery I.B., Conde S., Power S.E., O’Connor E.M., Cusack S., Harris H.M.B., Coakley M., Lakshminarayanan B., O’Sulliva O., et al. Gut microbiota composition correlates with diet and health in the elderly. Nature. 2012;488:178–184. [PubMed] [Google Scholar]
37. Huxley R.R., Ansary-Moghaddam A., Clifton P., Czernichow S., Parr C.L., Woodward M. The impact of dietary and lifestyle risk factors on risk of colorectal cancer: A quantitative overview of the epidemiological evidence. Int. J. Cancer. 2009;125:171–180. doi: 10.1002/ijc.24343. [PubMed] [CrossRef] [Google Scholar]
38. Benjamin J.L., Hedin C.R.H., Koutsoumpas A., Ng S.C., McCarthy N.E., Prescott N.J., Pessoa-Lopes P., Mathew C.G., Sanderson J., Hart A.L., et al. Smokers with active Crohn’s disease have a clinically relevant dysbiosis of the gastrointestinal microbiota. Inflamm. Bowel Dis. 2012;18:1092–1100. [PubMed] [Google Scholar]
39. Beamish L.A., Osornio-Vargas A.R., Wine E. Air pollution: An environmental factor contributing to intestinal disease. J. Crohns Colitis. 2011;5:279–286. doi: 10.1016/j.crohns.2011.02.017. [PubMed] [CrossRef] [Google Scholar]
40. Lutgendorff F., Akkermans L.M.A., Soderholm J.D. The role of microbiota and probiotics in stress-induced gastrointestinal damage. Curr. Mol. Med. 2008;8:282–298. doi: 10.2174/156652408784533779. [PubMed] [CrossRef] [Google Scholar]
41. Grenham S., Clarke G., Cryan J.F., Dinan T.G. Brain-gut-microbe communication in health and disease. Front. Physiol. 2011;2:94. doi: 10.3389/fphys.2011.00094. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
42. Clarke G., Grenham S., Scully P., Fitzgerald P., Moloney R.D., Shanahan F., Dinan T.G., Cryan J.F. The microbiome-gut-brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner. Mol. Psychiatry. 2013;18:666–673. doi: 10.1038/mp.2012.77. [PubMed] [CrossRef] [Google Scholar]
43. Finegold S.M., Dowd S.E., Gontcharova V., Liu C., Henley K.E., Wolcott R.D., Youn E., Summanen P.H., Granpeesheh D., Dixon D., et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe. 2010;16:444–453. [PubMed] [Google Scholar]
44. Parracho H., Bingham M.O., Gibson G.R., McCartney A.L. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J. Med. Microbiol. 2005;54:987–991. doi: 10.1099/jmm.0.46101-0. [PubMed] [CrossRef] [Google Scholar]
45. Wang L., Christophersen C.T., Sorich M.J., Gerber J.P., Angley M.T., Conlon M.A. Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism. Appl. Environ. Microbiol. 2011;77:6718–6721. doi: 10.1128/AEM.05212-11. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
46. Clarke S.F., Murphy E.F., O’Sullivan O., Lucy A.J., Humphreys M., Hogan A., Hayes P., O’Reilly M., Jeffery I.B., Wood-Martin R., et al. Exercise and associated dietary extremes impact on gut microbial diversity. Gut. 2014;63:1913–1920. [PubMed] [Google Scholar]
47. Ley R.E., Backhed F., Turnbaugh P., Lozupone C.A., Knight R.D., Gordon J.I. Obesity alters gut microbial ecology. Proc. Natl. Acad. Sci. USA. 2005;102:11070–11075. doi: 10.1073/pnas.0504978102. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
48. Ley R.E., Turnbaugh P.J., Klein S., Gordon J.I. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–1023. doi: 10.1038/4441022a. [PubMed] [CrossRef] [Google Scholar]
49. Turnbaugh P.J., Ley R.E., Mahowald M.A., Magrini V., Mardis E.R., Gordon J.I. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–1031. doi: 10.1038/nature05414. [PubMed] [CrossRef] [Google Scholar]
50. Delzenne N.M., Cani P.D. Interaction between obesity and the gut microbiota: Relevance in nutrition. Ann. Rev. Nutr. 2011;31:15–31. doi: 10.1146/annurev-nutr-072610-145146. [PubMed] [CrossRef] [Google Scholar]
51. 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., et al. Butyrate and propionate protect against diet-induced obesity and regulate gut hormones via free fatty acid receptor 3-independent mechanisms. PLoS One. 2012;7:e35240. doi: 10.1371/journal.pone.0035240.. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
52. Collado M.C., Isolauri E., Laitinen K., Salminen S. Distinct composition of gut microbiota during pregnancy in overweight and normal-weight women. Am. J. Clin. Nutr. 2008;88:894–899. [PubMed] [Google Scholar]
53. Kalliomaki M., Collado M.C., Salminen S., Isolauri E. Early differences in fecal microbiota composition in children may predict overweight. Am. J. Clin. Nutr. 2008;87:534–538. [PubMed] [Google Scholar]
54. Devkota S., Wang Y., Musch M.W., Leone V., Fehlner-Peach H., Nadimpalli A., Antonopoulos D.A., Jabri B., Chang E.B. Dietary-fat-induced taurocholic acid promotes pathobiont expansion and colitis in Il10−/− mice. Nature. 2012;487:104–108. [PMC free article] [PubMed] [Google Scholar]
55. 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. USA. 2010;107:14691–14696. doi: 10.1073/pnas.1005963107. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
56. Verdu E.F., Riddle M.S. Chronic gastrointestinal consequences of acute infectious diarrhea: Evolving concepts in epidemiology and pathogenesis. Am. J. Gastroenterol. 2012;107:981–989. doi: 10.1038/ajg.2012.65. [PubMed] [CrossRef] [Google Scholar]
57. Voigt R.M., Forsyth C.B., Green S.J., Mutlu E., Engen P., Vitaterna M.H., Turek F.W., Keshavarzian A. Circadian disorganization alters intestinal microbiota. PLoS One. 2014;9:e97500. doi: 10.1371/journal.pone.0097500. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
58. Hill M.J. Bacterial fermentation of complex carbohydrate in the human colon. Eur. J. Cancer Prev. 1995;4:353–358. doi: 10.1097/00008469-199510000-00004. [PubMed] [CrossRef] [Google Scholar]
59. Payne A.N., Chassard C., Lacroix C. Gut microbial adaptation to dietary consumption of fructose, artificial sweeteners and sugar alcohols: Implications for host-microbe interactions contributing to obesity. Obes. Rev. 2012;13:799–809. doi: 10.1111/j.1467-789X.2012.01009.x. [PubMed] [CrossRef] [Google Scholar]
60. Touvier M., Druesne-Pecollo N., Kesse-Guyot E., Andreeva V.A., Fezeu L., Galan P., Hercberg S., Latino-Martel P. Dual association between polyphenol intake and breast cancer risk according to alcohol consumption level: A prospective cohort study. Breast Cancer Res. Treat. 2013;137:225–236. doi: 10.1007/s10549-012-2323-y. [PubMed] [CrossRef] [Google Scholar]
61. Tuohy K.M., Conterno L., Gasperotti M., Viola R. Up-regulating the human intestinal microbiome using whole plant foods, polyphenols, and/or fiber. J. Agric. Food Chem. 2012;60:8776–8782. doi: 10.1021/jf2053959. [PubMed] [CrossRef] [Google Scholar]
62. 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. doi: 10.1016/j.resmic.2006.07.004. [PubMed] [CrossRef] [Google Scholar]
63. Tzounis X., Rodriguez-Mateos A., Vulevic J., Gibson G.R., Kwik-Uribe C., Spencer J.P.E. Prebiotic evaluation of cocoa-derived flavanols in healthy humans by using a randomized, controlled, double-blind, crossover intervention study. Am. J. Clin. Nutr. 2011;93:62–72. doi: 10.3945/ajcn.110.000075. [PubMed] [CrossRef] [Google Scholar]
64. Martin F.-P.J., Montoliu I., Nagy K., Moco S., Collino S., Guy P., Redeuil K., Scherer M., Rezzi S., Kochhar S., et al. Specific dietary preferences are linked to differing gut microbial metabolic activity in response to dark chocolate intake. J. Proteome Res. 2012;11:6252–6263. [PubMed] [Google Scholar]
65. Gill S.R., Pop M., DeBoy R.T., Eckburg P.B., Turnbaugh P.J., Samuel B.S., Gordon J.I., Relman D.A., Fraser-Liggett C.M., Nelson K.E., et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–1359. [PMC free article] [PubMed] [Google Scholar]
66. Baghurst P.A., Baghurst K.I., Record S.J. Dietary fibre, non-starch polysaccharides and resistant starch—A review. Food Aust. 1996;48:S3–S35. [Google Scholar]
67. Murphy N., Norat T., Ferrari P., Jenab M., Bueno-de-Mesquita B., Skeie G., Dahm C.C., Overvad K., Olsen A., Tjønneland A., et al. Dietary fibre intake and risks of cancers of the colon and rectum in the European Prospective Investigation into Cancer and Nutrition (EPIC) PLoS One. 2012;7:e39361. doi: 10.1371/journal.pone.0039361.. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
68. Aune D., Chan D.S.M., Lau R., Vieira R., Greenwood D.C., Kampman E., Norat T. Dietary fibre, whole grains, and risk of colorectal cancer: Systematic review and dose-response meta-analysis of prospective studies. BMJ. 2011;343:d6617. doi: 10.1136/bmj.d6617. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
69. Bodinham C.L., Smith L., Wright J., Frost G.S., Robertson M.D. Dietary fibre improves first-phase insulin secretion in overweight individuals. PloS One. 2012;7:e40834. doi: 10.1371/journal.pone.0040834. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
70. Hauner H., Bechthold A., Boeing H., Broenstrup A., Buyken A., Leschik-Bonnet E., Linseisen J., Schulze M., Strohm D., Wolfram G., et al. Evidence-based guideline of the German Nutrition Society: Carbohydrate Intake and prevention of nutrition-related diseases. Ann. Nutr. MeTab. 2012;60:1–58. [PubMed] [Google Scholar]
71. Sleeth M., Psichas A., Frost G. Weight gain and insulin sensitivity: A role for the glycaemic index and dietary fibre? Br. J. Nutr. 2013;109:1539–1541. doi: 10.1017/S0007114512005016. [PubMed] [CrossRef] [Google Scholar]
72. Windey K., de Preter V., Verbeke K. Relevance of protein fermentation to gut health. Mol. Nutr. Food Res. 2012;56:184–196. doi: 10.1002/mnfr.201100542. [PubMed] [CrossRef] [Google Scholar]
73. Mitchell B.L., Lawson M.J., Davies M., Grant A.K., Roediger W.E.W., Illman R.J., Topping D.L. Volatile fatty-acids in the human intestine—Studies in surgical patients. Nutr. Res. 1985;5:1089–1092. doi: 10.1016/S0271-5317(85)80140-8. [CrossRef] [Google Scholar]
74. Spiller G.A., Chernoff M.C., Hill R.A., Gates J.E., Nassar J.J., Shipley E.A. Effect of purified cellulose, pectin, and a low-residue diet on fecal volatile fatty-acids, transit-time, and fecal weight in humans. Am. J. Clin. Nutr. 1980;33:754–759. [PubMed] [Google Scholar]
75. Roediger W.E.W. Role of anaerobic-bacteria in the metabolic welfare of the colonic mucosa in man. Gut. 1980;21:793–798. doi: 10.1136/gut.21.9.793. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
76. 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. doi: 10.1017/S0007114512001948. [PubMed] [CrossRef] [Google Scholar]
77. Binder H.J. Role of colonic short-chain fatty acid transport in diarrhea. Ann. Rev. Physiol. 2010;72:297–313. doi: 10.1146/annurev-physiol-021909-135817. [PubMed] [CrossRef] [Google Scholar]
78. Wycherley T.P., Noakes M., Clifton P.M., Cleanthous X., Keogh J.B., Brinkworth G.D. A high-protein diet with resistance exercise training improves weight loss and body composition in overweight and obese patients with type 2 diabetes. Diabetes Care. 2010;33:969–976. doi: 10.2337/dc09-1974. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
79. Chao A., Thun M.J., Connell C.J., McCullough M.L., Jacobs E.J., Flanders W.D., Rodriguez C., Sinha R., Calle E.E. Meat consumption and risk of colorectal cancer. JAMA. 2005;97:906–916. [Google Scholar]
80. Norat T., Bingham S., Ferrari P., Slimani N., Jenab M., Mazuir M., Overvad K., Olsen A., Tjonneland A., Clavel F., et al. Meat, fish, and colorectal cancer risk: The European Prospective Investigation into Cancer and Nutrition. J. Natl. Cancer Inst. 2005;97:906–916. [PMC free article] [PubMed] [Google Scholar]
81. World Cancer Research Fund . Food, Nutrition, Physical Activity, and the Prevention of Colon Cancer: A Global Perspective. American Institute for Cancer Research; Washington, DC, USA: 2007. [Google Scholar]
82. World Cancer Research Fund . Food, Nutrition, Physical Activity, and the Prevention of Colorectal Cancer. American Institute for Cancer Research; Washington, DC, USA: 2011. Continuous Update Project Report. [Google Scholar]
83. Alexander D.D., Cushing C.A. Red meat and colorectal cancer: A critical summary of prospective epidemiological studies. Obes. Rev. 2011;12:e472–e493. doi: 10.1111/j.1467-789X.2010.00785.x. [PubMed] [CrossRef] [Google Scholar]
84. Oostindjer M., Alexander J., Vang G., Andersen G., Bryan N.S., Chen D., Corpet D.E., de Smet S., Dragsted L.O., Haug A., et al. The role of red and processed meat in colorectal cancer development: A perspective. Meat Sci. 2014;97:583–596. [PubMed] [Google Scholar]
85. Silvester K.R., Cummings J.H. Does digestibility of meat protein help explain large-bowel cancer risk. Nutr. Cancer. 1995;24:279–288. doi: 10.1080/01635589509514417. [PubMed] [CrossRef] [Google Scholar]
86. Macfarlane G.T., Macfarlane S. Bacteria, colonic fermentation, and gastrointestinal health. J. AOAC Int. 2012;95:50–60. doi: 10.5740/jaoacint.SGE_Macfarlane. [PubMed] [CrossRef] [Google Scholar]
87. Hughes R., Magee E.A., Bingham S. Protein degradation in the large intestine: Relevance to colorectal cancer. Curr. Issues Intest. Microbiol. 2000;1:51–58. [PubMed] [Google Scholar]
88. Toden S., Bird A.R., Topping D.L., Conlon M.A. Resistant starch attenuates colonic DNA damage induced by higher dietary protein in rats. Nutr. Cancer. 2005;51:45–51. doi: 10.1207/s15327914nc5101_7. [PubMed] [CrossRef] [Google Scholar]
89. Toden S., Bird A.R., Topping D.L., Conlon M.A. Differential effects of dietary whey, casein and soya on colonic DNA damage and large bowel SCFA in rats fed diets low and high in resistant starch. Br. J. Nutr. 2007;97:535–543. doi: 10.1017/S0007114507336817. [PubMed] [CrossRef] [Google Scholar]
90. Toden S., Bird A.R., Topping D.L., Conlon M.A. Dose-dependent reduction of dietary protein-induced colonocyte DNA damage by resistant starch in rats correlates more highly with caecal butyrate than with other short chain fatty acids. Cancer Biol. Ther. 2007;6:253–258. doi: 10.4161/cbt.6.2.3627. [PubMed] [CrossRef] [Google Scholar]
91. Toden S., Bird A.R., Topping D.L., Conlon M.A. High red meat diets induce greater numbers of colonic DNA double-strand breaks than white meat in rats: Attenuation by high-amylose maize starch. Carcinogenesis. 2007;28:2355–2362. doi: 10.1093/carcin/bgm216. [PubMed] [CrossRef] [Google Scholar]
92. Russell W.R., Gratz S.W., Duncan S.H., Holtrop G., Ince J., Scobbie L., Duncan G., Johnstone A.M., Lobley G.E., Wallace R.J., et al. High-protein, reduced-carbohydrate weight-loss diets promote metabolite profiles likely to be detrimental to colonic health. Am. J. Clin. Nutr. 2011;93:1062–1072. [PubMed] [Google Scholar]
93. Shaughnessy D.T., Gangarosa L.M., Schliebe B., Umbach D.M., Xu Z., MacIntosh B., Knize M.G., Matthews P.P., Swank A.E., Sandler R.S., et al. Inhibition of fried meat-induced colorectal DNA damage and altered systemic genotoxicity in humans by crucifera, chlorophyllin, and yogurt. PLoS One. 2011;6:e18707. doi: 10.1371/journal.pone.0018707.. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
94. Humphreys K.J., Conlon M.A., Young G.P., Topping D.L., Hu Y., Winter J.M., Bird A.R., Cobiac L., Kennedy N.A., Michael M.A., et al. Dietary manipulation of oncogenic microRNA expression in human rectal mucosa: A randomized trial. Cancer Prev. Res. 2014;7:786–795. [PubMed] [Google Scholar]
95. Brinkworth G.D., Noakes M., Clifton P.M., Bird A.R. Comparative effects of very low-carbohydrate, high-fat and high-carbohydrate, low-fat weight-loss diets on bowel habit and faecal short-chain fatty acids and bacterial populations. Br. J. Nutr. 2009;101:1493–1502. doi: 10.1017/S0007114508094658. [PubMed] [CrossRef] [Google Scholar]
96. Windey K., de Preter V., Iouat T., Schuit F., Herman J., Vansant G., Verbeke K. Modulation of protein fermentation does not affect fecal water toxicity: A randomized cross-over study in healthy subjects. PLoS One. 2012;7:e52387. doi: 10.1371/journal.pone.0052387. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
97. Lin H.C., Visek W.J. Colon mucosal cell damage by ammonia in rats. J. Nutr. 1991;121:887–893. [PubMed] [Google Scholar]
98. Kramer H. Dietary patterns, calories, and kidney disease. Adv. Chronic Kidney Dis. 2013;20:135–140. doi: 10.1053/j.ackd.2012.12.004. [PubMed] [CrossRef] [Google Scholar]
99. Koeth R.A., Wang Z., Levison B.S., Buffa J.A., Org E., Sheehy B.T., Britt E.B., Fu X., Wu Y., Li L., et al. Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat. Med. 2013;19:576–585. [PMC free article] [PubMed] [Google Scholar]
100. Moreira A.P.B., Texeira T.F.S., Ferreira A.B., Peluzio Mdo C., Alfenas Rde C. Influence of a high-fat diet on gut microbiota, intestinal permeability and metabolic endotoxaemia. Br. J. Nutr. 2012;108:801–809. doi: 10.1017/S0007114512001213. [PubMed] [CrossRef] [Google Scholar]
101. Ou J., de Lany J.P., Zhang M., Sharma S., O’Keefe S.J.D. Association between low colonic short-chain fatty acids and high bile acids in high colon cancer risk populations. Nutr. Cancer. 2012;64:34–40. doi: 10.1080/01635581.2012.630164. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
102. Ridlon J.M., Kang D.-J., Hylemon P.B. Bile salt biotransformations by human intestinal bacteria. J. Lipid Res. 2006;47:241–259. doi: 10.1194/jlr.R500013-JLR200. [PubMed] [CrossRef] [Google Scholar]
103. Soto-Vaca A., Gutierrez A., Losso J.N., Xu Z., Finley J.W. Evolution of phenolic compounds from color and flavor problems to health benefits. J. Agric. Food Chem. 2012;60:6658–6677. doi: 10.1021/jf300861c. [PubMed] [CrossRef] [Google Scholar]
104. Manach C., Williamson G., Morand C., Scalbert A., Remesy C. Bioavailability and bioefficacy of polyphenols in humans I. Review of 97 bioavailability studies. Am. J. Clin. Nutr. 2005;81:230S–242S. [PubMed] [Google Scholar]
105. Selma M.V., Espin J.C., Tomas-Barberan F.A. Interaction between phenolics and gut microbiota: Role in human health. J. Agric. Food Chem. 2009;57:6485–6501. doi: 10.1021/jf902107d. [PubMed] [CrossRef] [Google Scholar]
106. Forester S.C., Waterhouse A.L. Metabolites are key to understanding health effects of wine polyphenolics. J. Nutr. 2009;139:1824S–1831S. doi: 10.3945/jn.109.107664. [PubMed] [CrossRef] [Google Scholar]
107. Grün C.H., van Dorsten F.A., Jacobs D.M., le Belleguic M., van Velzen E.J.J., Bingham M.O., Janssen H.-G., van Duynhoven J.P.M. GC-MS methods for metabolic profiling of microbial fermentation products of dietary polyphenols in human and in vitro intervention studies. J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2008;871:212–219. doi: 10.1016/j.jchromb.2008.04.039. [PubMed] [CrossRef] [Google Scholar]
108. Lee C.Y. Challenges in providing credible scientific evidence of health benefits of dietary polyphenols. J. Funct. Foods. 2013;5:524–526. doi: 10.1016/j.jff.2012.10.018. [CrossRef] [Google Scholar]
109. Gross G., Jacobs D.M., Peters S., Possemiers S., van Duynhoven J., Vaughan E.E., van de Wiele T. In vitro bioconversion of polyphenols from black tea and red wine/grape juice by human intestinal microbiota displays strong interindividual variability. J. Agric. Food Chem. 2010;58:10236–10246. doi: 10.1021/jf101475m. [PubMed] [CrossRef] [Google Scholar]
110. Van Nuenen M., Venema K., van der Woude J.C.J., Kuipers E.J. The metabolic activity of fecal microbiota from healthy individuals and patients with inflammatory bowel disease. Dig. Dis. Sci. 2004;49:485–491. doi: 10.1023/B:DDAS.0000020508.64440.73. [PubMed] [CrossRef] [Google Scholar]
111. Cordain L., Eaton S.B., Sebastian A., Mann N., Lindeberg S., Watkins B.A., O’Keefe J.H., Brand-Miller J. Origins and evolution of the Western diet: Health implications for the 21st century. Am. J. Clin. Nutr. 2005;81:341–354. [PubMed] [Google Scholar]
112. Qin J., Li R., 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;464:59–65. [PMC free article] [PubMed] [Google Scholar]
113. Jeffery I.B., Claesson M.J., O’Toole P.W., Shanahan F. Categorization of the gut microbiota: Enterotypes or gradients? Nat. Rev. Microbiol. 2012;10:591–592. doi: 10.1038/nrmicro2859. [PubMed] [CrossRef] [Google Scholar]
114. 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. [PMC free article] [PubMed] [Google Scholar]
115. Lin A., Bik E.M., Costello E.K., Dethlefsen L., Haque R., Relman D.A., Singh U. Distinct distal gut microbiome diversity and composition in healthy children from Bangladesh and the United States. PLoS One. 2013;8:e53838. doi: 10.1371/journal.pone.0053838. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
116. Purushe J., Fouts D.E., Morrison M., White B.A., Mackie R.I., North American Consortium for Rumen Bacteria. Coutinho P.M., Henrissat B., Nelson K.E. Comparative genome analysis of Prevotella ruminicola and Prevotella bryantii: Insights into their environmental niche. Microb. Ecol. 2010;60:721–729. doi: 10.1007/s00248-010-9692-8. [PubMed] [CrossRef] [Google Scholar]
117. 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. Ann. Nutr. Metab. 2009;54:253–257. doi: 10.1159/000229505. [PubMed] [CrossRef] [Google Scholar]
118. 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. doi: 10.1017/S0007114511006362. [PubMed] [CrossRef] [Google Scholar]
119. Frank D.N., Amand A.L.S., Feldman R.A., Boedeker E.C., Harpaz N., Pace N.R. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc. Natl. Acad. Sci. USA. 2007;104:13780–13785. doi: 10.1073/pnas.0706625104. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
120. Gore C., Munro K., Lay C., Bibiloni R., Morris J., Woodcock A., Custovic A., Tannock G.W. Bifidobacterium pseudocatenulatum is associated with atopic eczema: A nested case-control study investigating the fecal microbiota of infants. J. Allergy Clin. Immunol. 2008;121:135–140. doi: 10.1016/j.jaci.2007.07.061. [PubMed] [CrossRef] [Google Scholar]
121. Schwiertz A., Taras D., Schaefer K., Beijer S., Bos N.A., Donus C., Hardt P.D. Microbiota and SCFA in lean and overweight healthy subjects. Obesity. 2010;18:190–195. doi: 10.1038/oby.2009.167. [PubMed] [CrossRef] [Google Scholar]
122. Lozupone C.A., Stombaugh J.I., Gordon J.I., Jansson J.K., Knight R. Diversity, stability and resilience of the human gut microbiota. Nature. 2012;489:220–230. doi: 10.1038/nature11550. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
123. Nava G.M., Carbonero F., Ou J., Benefiel A.C., O’Keefe S.J., Gaskins H.R. Hydrogenotrophic microbiota distinguish native Africans from African and European Americans. Environ. Microbiol. Rep. 2012;4:307–315. doi: 10.1111/j.1758-2229.2012.00334.x. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
124. Magee E.A., Richardson C.J., Hughes R., Cummings J.H. Contribution of dietary protein to sulfide production in the large intestine: An in vitro and a controlled feeding study in humans. Am. J. Clin. Nutr. 2000;72:1488–1494. [PubMed] [Google Scholar]
125. O’Keefe S.J.D., Kidd M., Espitalier-Noel G., Owira P. Rarity of colon cancer in Africans is associated with low animal product consumption, not fiber. Am. J. Gastroenterol. 1999;94:1373–1380. doi: 10.1111/j.1572-0241.1999.01089.x. [PubMed] [CrossRef] [Google Scholar]
126. Jumpertz R., Duc Son L., Turnbaugh P.J., Trinidad C., Bogardus C., Gordon J.I., Krakoff J. Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans. Am. J. Clin. Nutr. 2011;94:58–65. doi: 10.3945/ajcn.110.010132. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
127. 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., et al. High-fat diet determines the composition of the murine gut microbiome independently of obesity. Gastroenterology. 2009;137:1716–1724. [PMC free article] [PubMed] [Google Scholar]
128. Cani P.D., Neyrinck A.M., Fava F., Knauf C., Burcelin R.G., Tuohy K.M., Gibson G.R., Delzenne N.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. doi: 10.1007/s00125-007-0791-0. [PubMed] [CrossRef] [Google Scholar]
129. 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. [PubMed] [Google Scholar]
130. Neyrinck A.M., Possemiers S., Verstraete W., de Backer F., Cani P.D., Delzenne N.M. Dietary modulation of clostridial cluster XIVa gut bacteria (Roseburia spp.) by chitin-glucan fiber improves host metabolic alterations induced by high-fat diet in mice. J. Nutr. Biochem. 2012;23:51–59. [PubMed] [Google Scholar]
131. Deplancke B., Gaskins H.R. Microbial modulation of innate defense: Goblet cells and the intestinal mucus layer. Am. J. Clin. Nutr. 2001;73:1131S–1141S. [PubMed] [Google Scholar]
132. Kim Y.S., Ho S.B. Intestinal goblet cells and mucins in health and disease: Recent insights and progress. Curr. Gastroenterol. Rep. 2010;12:319–330. doi: 10.1007/s11894-010-0131-2. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
133. Hedemann M.S., Theil P.K., Knudsen K.E.B. The thickness of the intestinal mucous layer in the colon of rats fed various sources of non-digestible carbohydrates is positively correlated with the pool of SCFA but negatively correlated with the proportion of butyric acid in digesta. Br. J. Nutr. 2009;102:117–125. doi: 10.1017/S0007114508143549. [PubMed] [CrossRef] [Google Scholar]
134. Femia A.P., Giannini A., Fazi M., Tarquini E., Salvadori M., Roncucci L., Tonelli F., Dolara P., Caderni G. Identification of mucin depleted foci in the human colon. Cancer Prev. Res. 2008;1:562–567. doi: 10.1158/1940-6207.CAPR-08-0125. [PubMed] [CrossRef] [Google Scholar]
135. Femia A.P., Swidsinski A., Dolara P., Salvadori M., Amedei A., Caderni G. Mucin depleted foci, colonic preneoplastic lesions lacking Muc2, show up-regulation of Tlr2 but not bacterial infiltration. PLoS One. 2012;7:e29918. doi: 10.1371/journal.pone.0029918. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
136. Johansson M.E.V., Phillipson M., Petersson J., Velcich A., Holm L., Hansson G.C. The inner of the two Muc2 mucin-dependent mucus layers in colon is devoid of bacteria. Proc. Natl. Acad. Sci. USA. 2008;105:15064–15069. doi: 10.1073/pnas.0803124105. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
137. Png C.W., Linden S.K., Gilshenan K.S., Zoetendal E.G., McSweeney C.S., Sly L.I., McGuckin M.A., Florin T.H.J. Mucolytic bacteria with increased prevalence in IBD mucosa augment in vitro utilization of mucin by other bacteria. Am. J. Gastroenterol. 2010;105:2420–2428. doi: 10.1038/ajg.2010.281. [PubMed] [CrossRef] [Google Scholar]
138. Collado M.C., Derrien M., Isolauri E., de Vos W.M., Salminen S. Intestinal integrity and Akkermansia muciniphila, a mucin-degrading member of the intestinal microbiota present in infants, adults, and the elderly. Appl. Environ. Microbiol. 2007;73:7767–7770. doi: 10.1128/AEM.01477-07. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
139. Kerr C.A., Grice D.M., Tran C.D., Bauer D.C., Li D., Hendry P., Hannan G.N. Early life events influence whole-of-life metabolic health via gut microflora and gut permeability. Crit. Rev. Microbiol. 2014 in press. [PubMed] [Google Scholar]
140. Hooper L.V., Littman D.R., Macpherson A.J. Interactions between the microbiota and the immune system. Science. 2012;336:1268–1273. doi: 10.1126/science.1223490. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
141. Lebouvier T., Chaumette T., Paillusson S., Duyckaerts C., des Varannes S.B., Neunlist M., Derkinderen P. The second brain and Parkinson’s disease. Eur. J. Neurosci. 2009;30:735–741. doi: 10.1111/j.1460-9568.2009.06873.x. [PubMed] [CrossRef] [Google Scholar]
142. Awad R.A. Neurogenic bowel dysfunction in patients with spinal cord injury, myelomeningocele, multiple sclerosis and Parkinson’s disease. World J. Gastroenterol. 2011;17:5035–5048. doi: 10.3748/wjg.v17.i46.5035. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
143. Forsyth C.B., Shannon K.M., Kordower J.H., Voigt R.M., Shaikh M., Jaglin J.A., Estes J.D., Dodiya H.B., Keshavarzian A. Increased intestinal permeability correlates with sigmoid mucosa alpha-synuclein staining and endotoxin exposure markers in early Parkinson’s Disease. PLoS One. 2011;6:e28032. doi: 10.1371/journal.pone.0028032. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
144. Braak H., Rub U., Gai W.P., del Tredici K. Idiopathic Parkinson’s disease: Possible routes by which vulnerable neuronal types may be subject to neuroinvasion by an unknown pathogen. J. Neural Transm. 2003;110:517–536. doi: 10.1007/s00702-002-0808-2. [PubMed] [CrossRef] [Google Scholar]
145. Esteve E., Ricart W., Fernandez-Real J.-M. Gut microbiota interactions with obesity, insulin resistance and type 2 diabetes: Did gut microbiote co-evolve with insulin resistance? Curr. Opin. Clin. Nutr. Metab. Care. 2011;14:483–490. doi: 10.1097/MCO.0b013e328348c06d. [PubMed] [CrossRef] [Google Scholar]
146. Frazier T.H., DiBaise J.K., McClain C.J. Gut microbiota, intestinal permeability, obesity-induced inflammation, and liver injury. J. Parenter. Enter. Nutr. 2011;35:14S–20S. doi: 10.1177/0148607111413772. [PubMed] [CrossRef] [Google Scholar]
147. Cani P.D., Osto M., Geurts L., Everard A. Involvement of gut microbiota in the development of low-grade inflammation and type 2 diabetes associated with obesity. Gut Microbes. 2012;3:279–288. doi: 10.4161/gmic.19625. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
148. Anders H.-J., Andersen K., Stecher B. The intestinal microbiota, a leaky gut, and abnormal immunity in kidney disease. Kidney Int. 2013;83:1010–1016. doi: 10.1038/ki.2012.440. [PubMed] [CrossRef] [Google Scholar]
149. Piya M.K., Harte A.L., McTernan P.G. Metabolic endotoxaemia: Is it more than just a gut feeling? Curr. Opin. Lipidol. 2013;24:78–85. doi: 10.1097/MOL.0b013e32835b4431. [PubMed] [CrossRef] [Google Scholar]
150. Arumugam M., Raes J., Pelletier E., le Paslier D., Yamada T., Mende D.R., Fernandes G.R., Tap J., Bruls T., Batto J.M., et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174–180. [PMC free article] [PubMed] [Google Scholar]
151. McOrist A.L., Miller R.B., Bird A.R., Keogh J.B., Noakes M., Topping D.L., Conlon M.A. Fecal butyrate levels vary widely among individuals but are usually increased by a diet high in resistant starch. J. Nutr. 2011;141:883–889. doi: 10.3945/jn.110.128504. [PubMed] [CrossRef] [Google Scholar]
152. Abell G.C.J., Cooke C.M., Bennett C.N., Conlon M.A., McOrist A.L. Phylotypes related to Ruminococcus bromii are abundant in the large bowel of humans and increase in response to a diet high in resistant starch. FEMS Microbiol. Ecol. 2008;66:505–515. doi: 10.1111/j.1574-6941.2008.00527.x. [PubMed] [CrossRef] [Google Scholar]
153. Walker A.W., Ince J., Duncan S.H., Webster L.M., Holtrop G., Ze X., 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. [PMC free article] [PubMed] [Google Scholar]
154. Gibson G.R., Roberfroid M.B. Dietary modulation of the human colonic microbiota—Introducing the concept of prebiotics. J. Nutr. 1995;125:1401–1412. [PubMed] [Google Scholar]
155. Gibson G.R., Scott K.P., Rastall R.A., Tuohy K.M., Hotchkiss A., Dubert-Ferrandon A., Gareau M., Murphy E.F., Saulnier D., Loh G., et al. Dietary prebiotics: Current status and new definition. Food Sci. Technol. Bull. Funct. Foods. 2010;7:1–19. doi: 10.1616/1476-2137.15880. [CrossRef] [Google Scholar]
156. Bird A.R., Topping D.L. Resistant starch as a prebiotic. In: Versalovic J., Wilson M., editors. Therapeutic Microbiology: Probiotics and Related Strategies. ASM Press; Washington, DC, USA: 2008. pp. 159–173. [Google Scholar]
157. Clark M.J., Robien K., Slavin J.L. Effect of prebiotics on biomarkers of colorectal cancer in humans: A systematic review. Nutr. Rev. 2012;70:436–443. doi: 10.1111/j.1753-4887.2012.00495.x. [PubMed] [CrossRef] [Google Scholar]
158. Roberfroid M., Gibson G.R., Hoyles L., McCartney A.L., Rastall R., Rowland I., Wolvers D., Watzl B., Szajewska H., Stahl B., et al. Prebiotic effects: Metabolic and health benefits. Br. J. Nutr. 2010;104:S1–S63. [PubMed] [Google Scholar]
159. Brownawell A.M., Caers W., Gibson G.R., Kendall C.W.C., Lewis K.D., Ringel Y., Slavin J.L. Prebiotics and the health benefits of fiber: Current regulatory status, future research, and goals. J. Nutr. 2012;142:962–974. doi: 10.3945/jn.112.158147. [PubMed] [CrossRef] [Google Scholar]
160. Saad N., Delattre C., Urdaci M., Schmitter J.M., Bressollier P. An overview of the last advances in probiotic and prebiotic field. LWT Food Sci. Technol. 2013;50:1–16. doi: 10.1016/j.lwt.2012.05.014. [CrossRef] [Google Scholar]
161. Delzenne N.M., Neyrinck A.M., Backhed F., Cani P.D. Targeting gut microbiota in obesity: Effects of prebiotics and probiotics. Nat. Rev. Endocrinol. 2011;7:639–646. doi: 10.1038/nrendo.2011.126. [PubMed] [CrossRef] [Google Scholar]
162. Van Loo J., Coussement P., de Leenheer L., Hoebregs H., Smits G. On the presence of inulin and oligofructose as natural ingredients in the western diet. Crit. Rev. Food Sci. Nutr. 1995;35:525–552. doi: 10.1080/10408399509527714. [PubMed] [CrossRef] [Google Scholar]
163. Bird A.R., Conlon M.A., Christophersen C.T., Topping D.L. Resistant starch, large bowel fermentation and a broader perspective of prebiotics and probiotics. Benef. Microbes. 2010;1:423–431. doi: 10.3920/BM2010.0041. [PubMed] [CrossRef] [Google Scholar]
164. Conlon M.A., Bird A.R., Regina A., Morell M.K., Lockett T., Kang S., Molloy P., Kerr C.A., Shaw J., McSweeney C., et al. Resistant starches protect against colonic DNA damage and alter microbiota and gene expression in rats fed a western diet. J. Nutr. 2012;142:832–840. [PMC free article] [PubMed] [Google Scholar]
165. Roberfroid M. Prebiotics: The concept revisited. J. Nutr. 2007;137:830S–837S. [PubMed] [Google Scholar]
166. Bird A.R., Lopez-Rubio A., Shrestha A.K., Gidley M.J. Resistant starch in vitro and in vivo: Factors determining yield, structure, and physiological relevance. In: Kasapsis S., Norton I.T., Ubbink J.B., editors. Modern Biopolymer Science: Bridging the Divide between Fundamental Treatise and Industrial Application. Academic Press; Burlington, MA, USA: 2009. pp. 449–510. [Google Scholar]
167. Tremaroli V., Backhed F. Functional interactions between the gut microbiota and host metabolism. Nature. 2012;489:242–249. doi: 10.1038/nature11552. [PubMed] [CrossRef] [Google Scholar]
168. Crittenden R., Bird A.R., Gopal P., Henriksson A., Lee Y.K., Payne M.J. Probiotic research in Australia, New Zealand and the Asia-Pacific region. Curr. Pharm. Des. 2005;11:37–53. doi: 10.2174/1381612053382304. [PubMed] [CrossRef] [Google Scholar]
169. Floch M.H., Walker W.A., Madsen K., Sanders M.E., Macfarlane G.T., Flint H.J., Dieleman L.A., Ringel Y., Guandalini S., Kelley C.P., et al. Recommendations for probiotic use—2011 update. J. Clin. Gastroenterol. 2011;45:S168–S171. [PubMed] [Google Scholar]
170. Khani S., Hosseini H.M., Taheri M., Nourani M.R., Imani Fooladi A.A. Probiotics as an alternative strategy for prevention and treatment of human diseases: A review. Inflamm. Allergy Drug Targets. 2012;11:79–89. doi: 10.2174/187152812800392832. [PubMed] [CrossRef] [Google Scholar]
171. Mugambi M.N., Musekiwa A., Lombard M., Young T., Blaauw R. Probiotics, prebiotics infant formula use in preterm or low birth weight infants: A systematic review. Nutr. J. 2012;11:58. doi: 10.1186/1475-2891-11-58. [PMC free article] [PubMed] [CrossRef] [Google Scholar]
172. Johnston B.C., Ma S.S.Y., Goldenberg J.Z., Thorlund K., Vandvik P.O., Loeb M., Guyatt G.H. Probiotics for the prevention of Clostridium difficile-associated diarrhea: A systematic review and meta-analysis. Ann. Intern. Med. 2012;157:878–888. doi: 10.7326/0003-4819-157-12-201212180-00563. [PubMed] [CrossRef] [Google Scholar]
173. Hosseini A., Nikfar S., Abdollahi M. Probiotics use to treat irritable bowel syndrome. Expert Opin. Biol. Ther. 2012;12:1323–1334. doi: 10.1517/14712598.2012.707179. [PubMed] [CrossRef] [Google Scholar]
174. Augustin M.A., Sanguansri L., Lockett T. Nano- and micro-encapsulated systems for enhancing the delivery of resveratrol. Ann. N. Y. Acad. Sci. 2013;1290:107–112. doi: 10.1111/nyas.12130. [PubMed] [CrossRef] [Google Scholar]
175. Cook M.T., Tzortzis G., Charalampopoulos D., Khutoryanskiy V.V. Microencapsulation of probiotics for gastrointestinal delivery. J. Control. Release. 2012;162:56–67. doi: 10.1016/j.jconrel.2012.06.003. [PubMed] [CrossRef] [Google Scholar]