4,277
Views
7
CrossRef citations to date
0
Altmetric
Engihr Supplement

Manipulating the gut microbiota to maintain health and treat disease

, , &
Article: 25877 | Published online: 02 Feb 2015

References

  • de Vos WM, de Vos EA. Role of the intestinal microbiome in health and disease: from correlation to causation. Nutr Rev 2012; 70(Suppl 1): S45–56.
  • 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.
  • 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.
  • Vrieze A, Holleman F, Zoetendal EG, de Vos WM, Hoekstra JB, Nieuwdorp M. The environment within: how gut micro-biota may influence metabolism and body composition. Diabetologia 2010; 53: 606–13.
  • 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.
  • Scaldaferri F, Gerardi V, Lopetuso LR, Del Zompo F, Mangiola F, Boskoski I et al. Gut microbial flora, prebiotics, and probiotics in IBD: their current usage and utility. Biomed Res Int 2013; 2013: 435268.
  • Midtvedt T, Zabarovsky E, Norin E, Bark J, Gizatullin R, Kashuba V et al. Increase of faecal tryptic activity relates to changes in the intestinal microbiome: analysis of Crohn's disease with a multidisciplinary platform. PLoS One 2013; 8: e66074.
  • Hungin AP, Mulligan C, Pot B, Whorwell P, Agreus L, Fracasso P et al. Systematic review: probiotics in the management of lower gastrointestinal symptoms in clinical practice - an evidence-based international guide. Aliment Pharmacol Ther 2013; 38: 864–86.
  • Sanders ME, Guarner F, Guerrant R, Holt PR, Quigley EM, Sartor RB et al. An update on the use and investigation of probiotics in health and disease. Gut 2013; 62: 787–96.
  • Gibson GR, Roberfroid MB. Dietary modulation of the human colonic microbiota: introducing the concept of prebiotics. J Nutr 1995; 125: 1401–12.
  • Gibson GR, Scott KP, Rastall RA, Tuohy KM, Hotchkiss A, Dubert-Ferrandon A et al. Dietary prebiotics: current status and new definition. Food Sci Technol Bull Funct Foods 2010; 7: 1–19.
  • Roberfroid M. Prebiotics : the concept revisited. J Nutr 2007; 137: 830S–7S.
  • Macfarlane G, Steed H, Macfarlane S. Bacterial metabolism and health-related effects of galacto-oligosaccharides and other prebiotics. J Appl Microbiol 2008; 104: 305–44.
  • Roberfroid MB. Inulin-type fructans: functional food ingredients. J Nutr 2007; 137: 2493S–502S.
  • Falony G, De Vuyst L. Ecological interactions of bacteria in the human gut. In: Charlampopoulos D, Rastall RA, eds. Prebiotics, and probiotics Science and Technology. New York, USA: Springer; 2009, p. 641–82.
  • Duncan SH, Louis P, Flint HJ. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol 2004; 70: 5810–7.
  • Falony G, Vlachou A, Verbrugghe K, De Vuyst L. Cross-feeding between Bifidobacterium longum BB536 and acetate-converting, butyrate-producing colon bacteria during growth on oligofructose. Appl Environ Microbiol 2006; 72: 7835–41.
  • Belenguer A, Duncan SH, Calder AG, Holtrop G, Louis P, Lobley GE et al. Two routes of metabolic cross-feeding between Bifidobacterium adolescentis and butyrate-producing anaerobes from the human gut. Appl Environ Microbiol 2006; 72: 3593–9.
  • Chassard C, Bernalier-Donadille A. H2 and acetate transfers during xylan fermentation between a butyrate-producing xylanolytic species and hydrogenotrophic microorganisms from the human gut. FEMS Microbiol Lett 2006; 254: 116–22.
  • Falony G, Calmeyn T, Leroy F, De Vuyst L. Coculture fermentations of Bifidobacterium species and Bacteroides thetaiotaomicron reveal a mechanistic insight into the pre-biotic effect of inulin-type fructans. Appl Environ Microbiol 2009; 75: 2312–9.
  • Scott KP, Martin JC, Duncan SH, Flint HJ. Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria, in vitro. Fems Microbiol Ecol 2014; 87: 30–40.
  • Cecchini DA, Laville E, Laguerre S, Robe P, Leclerc M, Doré J et al. Functional metagenomics reveals novel pathways of prebiotic breakdown by human gut bacteria. PLoS One 2013; 8: e72766.
  • Falony G, Lazidou K, Verschaeren A, Weckx S, Maes D, De Vuyst L. In vitro kinetic analysis of fermentation of pre-biotic inulin-type fructans by Bifidobacterium species reveals four different phenotypes. Appl Environ Microbiol 2009; 75: 454–61.
  • Rivière A, Moens F, Selak M, Maes D, Weckx S, De Vuyst L. The ability of bifidobacteria to degrade arabinoxylan oligo-saccharide constituents and derived oligosaccharides is strain dependent. Appl Environ Microbiol 2014; 80: 204–17.
  • Sierra C, Bernal M-J, Blasco J, Martinez R, Dalmau J, Ortufio I et al. Prebiotic effect during the first year of life in healthy infants fed formula containing GOS as the only prebiotic: a multicentre, randomised, double-blind and placebo-controlled trial. Eur J Nutr 2014. (in press).
  • Klaassens ES, Boesten RJ, Haarman M, Knol J, Schuren FH, Vaughan EE et al. Mixed-species genomic microarray analysis of fecal samples reveals differential transcriptional responses of bifidobacteria in breast-and formula-fed infants. Appl Environ Microbiol 2009; 75: 2668–76.
  • Scott KP, Martin JC, Campbell G, Mayer C-D, Flint HJ. Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium “Roseburia inulinivorans”. J Bacteriol 2006; 188: 4340–9.
  • Aminov RI, Walker AW, Duncan SH, Harmsen HJ, Welling GW, Flint HJ. Molecular diversity, cultivation, and improved detection by fluorescent in situ hybridization of a dominant group of human gut bacteria related to Roseburia spp. or Eubacterium rectale. Appl Environ Microbiol 2006; 72: 6371–6.
  • 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.
  • 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.
  • Rajilie-Stojanovie M, Heilig HG, Tims S, Zoetendal EG, Vos WM. Long-term monitoring of the human intestinal micro-biota composition. Environ Microbiol 2013; 15: 1146–59.
  • Marietta EV, Gomez AM, Yeoman C, Tilahun AY, Clark CR, Luckey DH et al. Low incidence of spontaneous type 1 diabetes in non-obese diabetic mice raised on gluten-free diets is associated with changes in the intestinal microbiome. PLoS One 2013; 8: e78687.
  • Weir TL, Manter DK, Sheflin AM, Barnett BA, Heuberger AL, Ryan ER Stool microbiome and metabolome differences between colorectal cancer patients and healthy adults. PLoS One 2013; 8: e70803.
  • Ze X, Duncan SH, Louis P, Flint HJ. Rum inococcus bromii is a keystone species for the degradation of resistant starch in the human colon. ISME J 2012; 6: 1535–43.
  • Abell GC, Cooke CM, Bennett CN, Conlon MA, McOrist AL. 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: 505–15.
  • Kovatcheva-Datchary P, Egert M, Maathuis A, Rajilié-Stojanovié M, De Graaf AA, Smidt H et al. Linking phylogenetic identities of bacteria to starch fermentation in an in vitro model of the large intestine by RNA-based stable isotope probing. Environ Microbiol 2009; 11: 914–26.
  • 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.
  • Duncan SH, Belenguer A, Holtrop G, Johnstone AM, Flint HJ, Lobley GE. Reduced dietary intake of carbohydrates by obese subjects results in decreased concentrations of butyrate and butyrate-producing bacteria in feces. Appl Environ Microbiol 2007; 73: 1073–8.
  • McIntyre A, Gibson P, Young G. Butyrate production from dietary fibre and protection against large bowel cancer in a rat model. Gut 1993; 34: 386–91.
  • Scheppach W Effects of short chain fatty acids on gut morphology and function. Gut 1994; 35: S35–8.
  • Wang T, Cai G, Qiu Y, Fei N, Zhang M, Pang X et al. Structural segregation of gut microbiota between colorectal cancer patients and healthy volunteers. ISME J 2011; 6: 320–9.
  • Louis P, Flint HJ. Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine. FEMS Microbiol Lett 2009; 294: 1–8.
  • Ramirez-Farias C, Slezak K, Fuller Z, Duncan A, Holtrop G, Louis P. Effect of inulin on the human gut microbiota: stimulation of Bifidobacterium adolescentis and Faecalibacterium prausnitzii. Br J Nutr 2009; 101: 541–50.
  • Sokol H, Seksik P, Furet J, Firmesse O, Nion-Larmurier I, Beaugerie L et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflam Bowel Dis 2009; 15: 1183–9.
  • Lopez-Siles M, Khan TM, Duncan SH, Harmsen HJ, Garcia-Gil LJ, Flint HJ. Cultured representatives of two major phylogroups of human colonic Faecalibacterium prausnitzii can utilize pectin, uronic acids, and host-derived substrates for growth. Appl Environ Microbiol 2012; 78: 420–8.
  • Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermüdez-Humarán LG, Gratadoux J-J et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci 2008; 105: 16731–6.
  • Stewart CS, Duncan SH, Cave DR. Oxalobacter formigenes and its role in oxalate metabolism in the human gut. FEMS Microbiol Lett 2004; 230: 1–7.
  • Hoppe B. An update on primary hyperoxaluria. Nat Rev Nephrol 2012; 8: 467–75.
  • Siener R, Bangen U, Sidhu H, Hönow R, von Unruh G, Hesse A. The role of Oxalobacter formigenes colonization in calcium oxalate stone disease. Kidney Int 2013; 83: 1144–9.
  • Lange JN, Wood KD, Wong H, Otto R, Mufarrij PW, Knight J et al. Sensitivity of human strains of Oxalobacter formigenes to commonly prescribed antibiotics. Urology 2012; 79: 1286–9.
  • Siva S, Barrack ER, Reddy G, Thamilselvan V, Thamilselvan S, Menon M et al. A critical analysis of the role of gut Oxalobacter formigenes in oxalate stone disease. BJU Int 2009; 103: 18–21.
  • Hoppe B, von Unruh G, Laube N, Hesse A, Sidhu H. Oxalate degrading bacteria: new treatment option for patients with primary and secondary hyperoxaluria? Urol Res 2005; 33: 372–5.
  • Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 2011; 141: 1782–91.
  • Tilg H, Moschen AR. Microbiota and diabetes: an evolving relationship. Gut 2014; 63: 1513–21. doi: 10.1136/gugn1-2014-306928.
  • Deeth H, Tamime A. Yogurt: nutritive and therapeutic aspects. J Food Protect 1981; 44: 78–86.
  • Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ, Pot B et al. Expert consensus document: The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nat Rev Gastroenterol Hepatol 2014; 11: 506–14.
  • FAO/WHO Working Group (2001). Report of a joint FAO/ WHO expert consultation on evaluation of health and nutritional properties of probiotics in food including powder milk with live lactic acid bacteria. Córdoba, Argentina: FAO/WHO; 2001.
  • Sanders ME. Probiotics: considerations for human health. Nutr Rev 2003; 61: 91–9.
  • Savaiano DA, Abou El, Anouar A, Smith DE, Levitt MD. Lactose malabsorption from yogurt, pasteurized yogurt, sweet acidophilus milk, and cultured milk in lactase-deficient individuals. Am J Clin Nutr 1984; 40: 1219–23.
  • Rabot S, Rafter J, Rijkers GT, Watzl B, Antoine J-M. Guidance for substantiating the evidence for beneficial effects of probiotics: impact of probiotics on digestive system metabolism. J Nutr 2010; 140: 677S – 89S.
  • Savaiano DA, Levitt MD. Milk intolerance and microbe-containing dairy foods. J Dairy Sci 1987; 70: 397–406.
  • Okombo J, Liebman M. Probiotic-induced reduction of gastrointestinal oxalate absorption in healthy subjects. Urol Res 2010; 38: 169–78.
  • Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell 2013; 155: 1451–63.
  • Midtvedt T. The gut: a triggering place for autism-possibilities and challenges. Microb Ecol Health Dis 2012; 23. doi: 10.3402/mehd.v23i0.18982.
  • MacFabe DF. Short-chain fatty acid fermentation products of the gut microbiome: implications in autism spectrum disorders. Microb Ecol Health Dis 2012; 23. doi: 10.3402/mehd.v23i0.19260.
  • Dinan TG, Stanton C, Cryan JF. Psychobiotics: a novel class of psychotropic. Biol Psychiatry 2013; 74: 720–6.
  • Shenderov BA, Midtvedt T. Epigenomic programing: a future way to health? Microb Ecol Health Dis 2014; 25.
  • Alfaleh K, Anabrees J, Bassler D, Al-Kharfi T. Probiotics for prevention of necrotizing enterocolitis in preterm infants. Cochrane Database Syst Rev 2011: CD005496.
  • Hempel S, Newberry SJ, Maher AR, Wang Z, Miles JN, Shanman R et al. Probiotics for the prevention and treatment of antibiotic-associated diarrhea: a systematic review and meta-analysis. JAMA 2012; 307: 1959–69.
  • Goldenberg JZ, Ma SS, Saxton JD, Martzen MR, Vandvik PO, Thorlund K et al. Probiotics for the prevention of Clostridium difficde-associated diarrhea in adults and children. Cochrane Database Syst Rev 2013: CD006095.
  • Hell M, Bernhofer C, Stalzer P, Kern JM, Claassen E. Probiotics in Clostridium difficile infection: reviewing the need for a multistrain probiotic. Benef Microbes 2013; 4: 39–51.
  • Greenwood C, Morrow AL, Lagomarcino AJ, Altaye M, Taft DH, Yu Z et al. Early empiric antibiotic use in preterm infants is associated with lower bacterial diversity and higher relative abundance of enterobacter. J Pediatr 2014; 165: 23–9.
  • Blaser M. Antibiotic overuse: stop the killing of beneficial bacteria. Nature 2011; 476: 393–4.
  • Koning CJ, Jonkers DM, Stobberingh EE, Mulder L, Rombouts FM, Stockbrugger RW. The effect of a multi-species probiotic on the intestinal microbiota and bowel movements in healthy volunteers taking the antibiotic amoxycillin. Am J Gastroenterol 2008; 103: 178–89.
  • Engelbrektson A, Korzenik JR, Pittler A, Sanders ME, Klaenhammer TR, Leyer G et al. Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy. J Med Microbiol 2009; 58: 663–70.
  • Rehman A, Heinsen FA, Koenen ME, Venema K, Knecht H, Hellmig S et al. Effects of probiotics and antibiotics on the intestinal homeostasis in a computer controlled model of the large intestine. BMC Microbiol 2012; 12: 47.
  • Tillisch K, Labus J, Kilpatrick L, Jiang Z, Stains J, Ebrat B et al. Consumption of fermented milk product with probiotic modulates brain activity. Gastroenterology 2013; 144: 1394–401, 401e1–4.
  • Bäckhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307: 1915–20.
  • Putaala H, Salusjärvi T, Nordstrom M, Saarinen M, Ouwehand AC, Bech Hansen E et al. Effect of four probiotic strains and Escherichia coli 0157: H7 on tight junction integrity and cyclo-oxygenase expression. Res Microbiol 2008; 159: 692–8.
  • Van Hemert S, Verwer J, Schuetz B. Clinical studies evaluat-ing effects of probiotics on parameters of intestinal barrier function. Adv Microbiol 2013; 3: 212–21.
  • Sang L-X, Chang B, Zhang W-L, Wu X-M, Li X-H, Jiang M. Remission induction and maintenance effect of probiotics on ulcerative colitis: a meta-analysis. World J Gastroenterol 2010; 16: 1908.
  • Klaenhammer TR, Kleerebezem M, Kopp MV, Rescigno M. The impact of probiotics and prebiotics on the immune system. Nat Rev Immunol 2012; 12: 728–34.
  • Guerin-Danan C, Chabanet C, Pedone C, Popot F, Vaissade P, Bouley C et al. Milk fermented with yogurt cultures and Lactobacillus casei compared with yogurt and gelled milk: influence on intestinal microflora in healthy infants. Am J Clin Nutr 1998; 67: 111–7.
  • Bernbom N, Licht TR, Brogren CH, Jelle B, Johansen AH, Badiola I et al. Effects of Lactococcus lactis on composition of intestinal microbiota: role of nisin. Appl Environ Microbiol 2006; 72: 239–44.
  • Gerritsen J, Timmerman HM, Fuentes S, van Minnen LP, Panneman H, Konstantinov SR et al. Correlation between protection against sepsis by probiotic therapy and stimulation of a novel bacterial phylotype. Appl Environ Microbiol 2011; 77: 7749–56.
  • Ouwehand AC, Lagstrom H, Suomalainen T, Salminen S. Effect of probiotics on constipation, fecal azoreductase activity and fecal mucin content in the elderly. Ann Nutr Metab 2002; 46: 159–62.
  • McNulty NP, Yatsunenko T, Hsiao A, Faith JJ, Muegge BD, Goodman AL et al. The impact of a consortium of fermented milk strains on the gut microbiome of gnotobiotic mice and monozygotic twins. Sci Transl Med 2011; 3: 106ra06.
  • Zhang F, Luo W, Shi Y, Fan Z, Ji G. Should we standardize the 1,700-year-old fecal microbiota transplantation? Am J Gastroenterol 2012; 107: 1755; author reply p. 55–6.
  • Merde LA. Excursions in scientific, cultural, and socio-cultural coprology. New York: Randon House; 1999.
  • Bakken JS. Fecal bacteriotherapy for recurrent Clostridium difficile infection. Anaerobe 2009; 15: 285–9.
  • Swaminath A. The power of poop: patients getting ahead of their doctors using self-administered fecal transplants. Am J Gastroenterol 2014; 109: 777–8.
  • Brandt LJ, Reddy SS. Fecal microbiota transplantation for recurrent Clostridium difficile infection. J Clin Gastroenterol 2011; 45(Suppl): S159–67.
  • 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.
  • Midtvedt T, Norin E, Benno P, Dahlgren A-L. Response to Surawicz et al. Am J Gastroenterol 2013; 108: 1931–2.
  • Bakken JS, Borody T, Brandt LJ, Brill JV, Demarco DC, Franzos MA et al. Treating Clostridium difficile infection with fecal microbiota transplantation. Clin Gastroenterol Hepatol 2011; 9: 1044–9.
  • Surawicz CM, Brandt LJ, Binion DG, Ananthakrishnan AN, Curry SR, Gilligan PH et al. Guidelines for diagnosis, treatment, and prevention of Clostridium difficile infections. Am J Gastroenterol 2013; 108: 478–98; quiz 99.
  • Debast SB, Bauer MP, Kuijper EJ. European Society of Clinical Microbiology and Infectious Diseases: update of the treatment guidance document for Clostridium difficile infection. Clin Microbiol Infect 2014; 20\(Suppl 2): 1–26.
  • Smits LP, Bouter KE, de Vos WM, Borody TJ, Nieuwdorp M. Therapeutic potential of fecal microbiota transplantation. Gastroenterology 2013; 145: 946–53.
  • Morken MH, Valeur J, Norin E, Midtvedt T, Nysaeter G, Berstad A. Antibiotic or bacterial therapy in post-giardiasis irritable bowel syndrome. Scand J Gastroenterol 2009; 44: 1296–303.
  • Anderson JL, Edney RJ, Whelan K. Systematic review: faecal microbiota transplantation in the management of inflammatory bowel disease. Aliment Pharmacol Ther 2012; 36: 503–16.
  • Allegretti JR, Hamilton M.I. Restoring the gut microbiome for the treatment of inflammatory bowel diseases. World J Gastroenterol 2014; 20: 3468–74.
  • Kunde S, Pham A, Bonczyk S, Crumb T, Duba M, Conrad H, Jr., et al. Safety, tolerability, and clinical response after fecal transplantation in children and young adults with ulcerative colitis. J Pediatr Gastroenterol Nutr 2013; 56: 597–601.
  • 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: 913–16-e7.
  • Aroniadis OC, Brandt U. Fecal microbiota transplantation: past, present and future. Curr Opin Gastroenterol 2013; 29: 79–84.
  • Gustafsson A, Berstad A, Lund-Tonnesen S, Midtvedt T, Norin E. The effect of faecal enema on five microflora-associated characteristics in patients with antibiotic-associated diarrhoea. Scand J Gastroenterol 1999; 34: 580–6.
  • Brandt LJ, Aroniadis OC. An overview of fecal microbiota transplantation: techniques, indications, and outcomes. Gastrointest Endosc 2013; 78: 240–9.
  • Smith MB, Kelly C, Alm EJ. Policy: how to regulate faecal transplants. Nature 2014; 506: 290–1.