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ENGIHR supplement

Contribution of diet to the composition of the human gut microbiota

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Article: 26164 | Received 01 Nov 2015, Accepted 04 Feb 2016, Published online: 04 Feb 2015

References

  • Flint HJ, Scott KP, Louis P, Duncan SH. The role of the gut microbiota in nutrition and health. Nat Rev Gastroenterol Hepatol 2012; 9: 577–89.
  • 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.
  • El Kaoutari A, Armougom F, Gordon JI, Raoult D, Henrissat B. The abundance and variety of carbohydrate-active enzymes in the human gut microbiota. Nat Rev Microbiol 2013; 11: 497–504.
  • Reichardt N, Duncan SH, Young P, Belenguer A, McWilliam LC, Scott KP, et al. Phylogenetic distribution of three pathways for propionate production within the human gut microbiota. ISME J 2014; 8: 1323–35.
  • Louis P, Young P, Holtrop G, Flint HJ. Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA: acetate CoA-transferase gene. Environ Microbiol 2010; 12: 304–14.
  • Ze X, Duncan SH, Louis P, Flint HJ. Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 2012; 6: 1535–43.
  • Walker AW, Ince J, Duncan SH, Webster LM, Holtrop G, Ze X, et al. Dominant and diet-responsive groups of bacteria within the human colonic microbiota. ISME J 2011; 5: 220–30.
  • Lagier JC, Armougom F, Million M, Hugon P, Pagnier I, Robert C, et al. Microbial culturomics: paradigm shift in the human gut microbiome study. Clin Microbiol Infect 2012; 18: 1185–93.
  • Goodman AL, Kallstrom G, Faith JJ, Reyes A, Moore A, Dantas G, et al. Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice. Proc Natl Acad Sci USA 2011; 108: 6252–7.
  • Sullivan A, Edlund C, Nord CE. Effect of antimicrobial agents on the ecological balance of human microflora. Lancet Infect Dis 2001; 1: 101–14.
  • Kohanski MA, Dwyer DJ, Collins JJ. How antibiotics kill bacteria: from targets to networks. Nat Rev Microbiol 2010; 8: 423–35.
  • De La Cochetiere MF, Durand T, Lepage P, Bourreille A, Galmiche JP, Dore J. Resilience of the dominant human fecal microbiota upon short-course antibiotic challenge. J Clin Microbiol 2005; 43: 5588–92.
  • Dethlefsen L, Huse S, Sogin ML, Relman DA. The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. PLoS Biol 2008; 6: e280.
  • 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.
  • Tringe SG, Hugenholtz P. A renaissance for the pioneering 16S rRNA gene. Curr Opin Microbiol 2008; 11: 442–6.
  • Walker AW, Duncan SH, Louis P, Flint HJ. Phylogeny, culturing, and metagenomics of the human gut microbiota. Trends Microbiol 2014; 22: 267–74.
  • 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.
  • Arumugam M, Raes J, Pelletier E, Le Paslier D, Yamada T, Mende DR, et al. Enterotypes of the human gut microbiome. Nature 2011; 473: 174–80.
  • Wu GD, Chen J, Hoffmann C, Bittinger K, Chen YY, Keilbaugh SA, et al. Linking long-term dietary patterns with gut microbial enterotypes. Science 2011; 334: 105–8.
  • 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.
  • Le Chatelier E, Nielsen T, Qin J, Prifti E, Hildebrand F, Falony G, et al. Richness of human gut microbiome correlates with metabolic markers. Nature 2013; 500: 541–6.
  • Cotillard A, Kennedy SP, Kong LC, Prifti E, Pons N, Le Chatelier E, et al. Dietary intervention impact on gut microbial gene richness. Nature 2013; 500: 585–8.
  • Kabeerdoss J, Devi RS, Mary RR, Ramakrishna BS. Faecal microbiota composition in vegetarians: comparison with omnivores in a cohort of young women in southern India. Br J Nutr 2012; 108: 953–7.
  • Liszt K, Zwielehner J, Handschur M, Hippe B, Thaler R, Haslberger AG. Characterization of bacteria, clostridia and Bacteroides in faeces of vegetarians using qPCR and PCR-DGGE fingerprinting. Ann Nutr Metab 2009; 54: 253–7.
  • Matijasic BB, Obermajer T, Lipoglavsek L, Grabnar I, Avgustin G, Rogelj I. Association of dietary type with fecal microbiota in vegetarians and omnivores in Slovenia. Eur J Nutr 2014; 53: 1051–64.
  • Kim MS, Hwang SS, Park EJ, Bae JW. Strict vegetarian diet improves the risk factors associated with metabolic diseases by modulating gut microbiota and reducing intestinal inflammation. Environ Microbiol Rep 2013; 5: 765–75.
  • Zimmer J, Lange B, Frick JS, Sauer H, Zimmermann K, Schwiertz A, et al. A vegan or vegetarian diet substantially alters the human colonic faecal microbiota. Eur J Clin Nutr 2012; 66: 53–60.
  • Ou J, Carbonero F, Zoetendal EG, DeLany JP, Wang M, Newton K, et al. Diet, microbiota, and microbial metabolites in colon cancer risk in rural Africans and African Americans. Am J Clin Nutr 2013; 98: 111–20.
  • Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, et al. Human gut microbiome viewed across age and geography. Nature 2012; 486: 222–7.
  • Schnorr SL, Candela M, Rampelli S, Centanni M, Consolandi C, Basaglia G, et al. Gut microbiome of the Hadza hunter-gatherers. Nat Commun 2014; 5: 3654.
  • Grzeskowiak L, Collado MC, Mangani C, Maleta K, Laitinen K, Ashorn P, et al. Distinct gut microbiota in southeastern African and northern European infants. J Pediatr Gastroenterol Nutr 2012; 54: 812–16.
  • Carvalho-Wells AL, Helmolz K, Nodet C, Molzer C, Leonard C, McKevith B, et al. Determination of the in vivo prebiotic potential of a maize-based whole grain breakfast cereal: a human feeding study. Br J Nutr 2010; 104: 1353–6.
  • Costabile A, Klinder A, Fava F, Napolitano A, Fogliano V, Leonard C, et al. Whole-grain wheat breakfast cereal has a prebiotic effect on the human gut microbiota: a double-blind, placebo-controlled, crossover study. Br J Nutr 2008; 99: 110–20.
  • Martinez I, Lattimer JM, Hubach KL, Case JA, Yang J, Weber CG, et al. Gut microbiome composition is linked to whole grain-induced immunological improvements. ISME J 2013; 7: 269–80.
  • Lappi J, Salojarvi J, Kolehmainen M, Mykkanen H, Poutanen K, de Vos WM, et al. Intake of whole-grain and fiber-rich rye bread versus refined wheat bread does not differentiate intestinal microbiota composition in Finnish adults with metabolic syndrome. J Nutr 2013; 143: 648–55.
  • Vendrame S, Guglielmetti S, Riso P, Arioli S, Klimis-Zacas D, Porrini M. Six-week consumption of a wild blueberry powder drink increases bifidobacteria in the human gut. J Agric Food Chem 2011; 59: 12815–20.
  • Guglielmetti S, Fracassetti D, Taverniti V, Del Bo C, Vendrame S, Klimis-Zacas D, et al. Differential modulation of human intestinal bifidobacterium populations after consumption of a wild blueberry (Vaccinium angustifolium) drink. J Agric Food Chem 2013; 61: 8134–40.
  • Queipo-Ortuno MI, Boto-Ordonez M, Murri M, Gomez-Zumaquero JM, Clemente-Postigo M, Estruch R, et al. Influence of red wine polyphenols and ethanol on the gut microbiota ecology and biochemical biomarkers. Am J Clin Nutr 2012; 95: 1323–34.
  • Ukhanova M, Wang X, Baer DJ, Novotny JA, Fredborg M, Mai V. Effects of almond and pistachio consumption on gut microbiota composition in a randomised cross-over human feeding study. Br J Nutr 2014; 111: 2146–52.
  • Shinohara K, Ohashi Y, Kawasumi K, Terada A, Fujisawa T. Effect of apple intake on fecal microbiota and metabolites in humans. Anaerobe 2010; 16: 510–15.
  • Mitsou EK, Kougia E, Nomikos T, Yannakoulia M, Mountzouris KC, Kyriacou A. Effect of banana consumption on faecal microbiota: a randomised, controlled trial. Anaerobe 2011; 17: 384–7.
  • Liu Z, Lin X, Huang G, Zhang W, Rao P, Ni L. Prebiotic effects of almonds and almond skins on intestinal microbiota in healthy adult humans. Anaerobe 2014; 26: 1–6.
  • Fernando WM, Hill JE, Zello GA, Tyler RT, Dahl WJ, Van Kessel AG. Diets supplemented with chickpea or its main oligosaccharide component raffinose modify faecal microbial composition in healthy adults. Benef Microbes 2010; 1: 197–207.
  • Fernandez-Raudales D, Hoeflinger JL, Bringe NA, Cox SB, Dowd SE, Miller MJ, et al. Consumption of different soymilk formulations differentially affects the gut microbiomes of overweight and obese men. Gut Microbes 2012; 3: 490–500.
  • Jones JM. CODEX-aligned dietary fiber definitions help to bridge the ‘fiber gap’. Nutr J 2014; 13: 34.
  • Martinez I, Kim J, Duffy PR, Schlegel VL, 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: e15046.
  • Linetzky WD, Alves Pereira CC, Logullo L, Manzoni JT, Almeida D, Teixeira da Silva ML, et al. Microbiota benefits after inulin and partially hydrolized guar gum supplementation: a randomized clinical trial in constipated women. Nutr Hosp 2012; 27: 123–9.
  • Costabile A, Kolida S, Klinder A, Gietl E, Bauerlein M, Frohberg C, et al. A double-blind, placebo-controlled, cross-over study to establish the bifidogenic effect of a very-long-chain inulin extracted from globe artichoke (Cynara scolymus) in healthy human subjects. Br J Nutr 2010; 104: 1007–17.
  • Lecerf JM, Depeint F, Clerc E, Dugenet Y, Niamba CN, Rhazi L, et al. Xylo-oligosaccharide (XOS) in combination with inulin modulates both the intestinal environment and immune status in healthy subjects, while XOS alone only shows prebiotic properties. Br J Nutr 2012; 108: 1847–58.
  • Dewulf EM, Cani PD, Claus SP, Fuentes S, Puylaert PG, Neyrinck AM, et al. Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women. Gut 2013; 62: 1112–21.
  • Garcia-Peris P, Velasco C, Lozano MA, Moreno Y, Paron L, de la Cuerda C, et al. Effect of a mixture of inulin and fructo-oligosaccharide on Lactobacillus and Bifidobacterium intestinal microbiota of patients receiving radiotherapy: a randomised, double-blind, placebo-controlled trial. Nutr Hosp 2012; 27: 1908–15.
  • Benus RF, van der Werf TS, Welling GW, Judd PA, Taylor MA, Harmsen HJ, et al. Association between Faecalibacterium prausnitzii and dietary fibre in colonic fermentation in healthy human subjects. Br J Nutr 2010; 104: 693–700.
  • Vulevic J, Juric A, Tzortzis G, Gibson GR. A mixture of trans-galactooligosaccharides reduces markers of metabolic syndrome and modulates the fecal microbiota and immune function of overweight adults. J Nutr 2013; 143: 324–31.
  • Hooda S, Boler BM, Serao MC, Brulc JM, Staeger MA, Boileau TW, et al. 454 pyrosequencing reveals a shift in fecal microbiota of healthy adult men consuming polydextrose or soluble corn fiber. J Nutr 2012; 142: 1259–65.
  • Costabile A, Fava F, Roytio H, Forssten SD, Olli K, Klievink J, et al. Impact of polydextrose on the faecal microbiota: a double-blind, crossover, placebo-controlled feeding study in healthy human subjects. Br J Nutr 2012; 108: 471–81.
  • Baer DJ, Stote KS, Henderson T, Paul DR, Okuma K, Tagami H, et al. The metabolizable energy of dietary resistant maltodextrin is variable and alters fecal microbiota composition in adult men. J Nutr 2014; 144: 1023–9.
  • Walton GE, Lu C, Trogh I, Arnaut F, Gibson GR. A randomised, double-blind, placebo controlled cross-over study to determine the gastrointestinal effects of consumption of arabinoxylan-oligosaccharides enriched bread in healthy volunteers. Nutr J 2012; 11: 36.
  • Cloetens L, Broekaert WF, Delaedt Y, Ollevier F, Courtin CM, Delcour JA, et al. Tolerance of arabinoxylan-oligosaccharides and their prebiotic activity in healthy subjects: a randomised, placebo-controlled cross-over study. Br J Nutr 2010; 103: 703–13.
  • Rafter JJ, Child P, Anderson AM, Alder R, Eng V, Bruce WR. Cellular toxicity of fecal water depends on diet. Am J Clin Nutr 1987; 45: 559–63.
  • Islam SKBM, Fukiya S, Hagio M, Fujii N, Ishizuka S, Ooka T, et al. Bile acid is a host factor that regulates the composition of the cecal microbiota in rats. Gastroenterology 2011; 141: 1773–81.
  • David LA, Maurice CF, Carmody RN, Gootenberg DB, Button JE, Wolfe BE, et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 2014; 505: 559–63.
  • Russell WR, Gratz SW, Duncan SH, Holtrop G, Ince J, Scobbie L, 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: 1062–72.
  • Davenport ER, Mizrahi-Man O, Michelini K, Barreiro LB, Ober C, Gilad Y. Seasonal variation in human gut microbiome composition. PLoS One 2014; 9: e90731.
  • Vorholt JA. Microbial life in the phyllosphere. Nat Rev Microbiol 2012; 10: 828–40.
  • Leff JW, Fierer N. Bacterial communities associated with the surfaces of fresh fruits and vegetables. PLoS One 2013; 8: e59310.
  • Di Cagno R, Coda R, De Angelis M, Gobbetti M. Exploitation of vegetables and fruits through lactic acid fermentation. Food Microbiol 2013; 33: 1–10.