Dysbiosis of the gut microbiota in disease

References

• Savage DC. Microbial ecology of the gastrointestinal tract. Ann Rev Microbiol 1977; 31: 107–33.
   Google Scholar
• Reyes A, Haynes M, Hanson N, Angly FE, Heath AC, Rohwer F et al,. Viruses in the faecal microbiota of monozygotic twins and their mothers. Nature 2010; 466: 334–8.
   Google Scholar
• Kamada N, Seo SU, Chen GY, Nunez G. Role of the gut microbiota in immunity and inflammatory disease. Nat Rev Immunol 2013; 13: 321–35.
   Google Scholar
• Tanoue T, Umesaki Y, Honda K. Immune responses to gut microbiota-commensals and pathogens. Gut Microbes 2010; 1: 224–33.
   Google Scholar
• Wen L, Ley RE, Volchkov PY, Stranges PB, Avanesyan L, Stonebraker AC et al. Innate immunity and intestinal microbiota in the development of Type 1 diabetes. Nature 2008; 455: 1109–13.
   Google Scholar
• Zoetendal EG, Akkermans AD, De Vos WM. Temperature gradient gel electrophoresis analysis of 16S rRNA from human fecal samples reveals stable and host-specific communities of active bacteria. Appl Environ Microbiol 1998; 64: 3854–9.
   Google Scholar
• Turnbaugh PJ, Hamady M, Yatsunenko T, Cantarel BL, Duncan A, Ley RE et al. A core gut microbiome in obese and lean twins. Nature 2009; 457: 480–4.
   Google Scholar
• Rajilic-Stojanovic M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007; 9: 2125–36.
   Google Scholar
• Zoetendal EG, Rajilic-Stojanovic M, de Vos WM. High-throughput diversity and functionality analysis of the gastro-intestinal tract microbiota. Gut 2008; 57: 1605–15.
   Google Scholar
• 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.
   Google Scholar
• Nicholson JK, Holmes E, Kinross J, Burcelin R, Gibson G, Jia W et al. Host-gut microbiota metabolic interactions. Science 2012; 336: 1262–7.
   Google Scholar
• Blaut M, Clavel T. Metabolic diversity of the intestinal microbiota: implications for health and disease. J Nutr 2007; 137: 751S–5S.
   Google Scholar
• Marchesi J, Shanahan F. The normal intestinal microbiota. Curr Opin Infect Dis 2007; 20: 508–13.
   Google Scholar
• Roediger WEW. Utilization of nutrients by isolated epithelial-cells of the rat colon. Gastroenterology 1982; 83: 424–9.
   Google Scholar
• Bergman EN. Energy contributions of volatile fatty-acids from the gastrointestinal-tract in various species. Physiol Rev 1990; 70: 567–90.
   Google Scholar
• den Besten G, van Eunen K, Groen AK, Venema K, Reijngoud DJ, Bakker BM. The role of short-chain fatty acids in the interplay between diet, gut microbiota, and host energy metabolism. J Lipid Res 2013; 54: 2325–40.
   Google Scholar
• Brown AJ, Goldsworthy SM, Barnes AA, Eilert MM, Tcheang L, Daniels D et al. The orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids. J Biol Chem 2003; 278: 11312–9.
   Google Scholar
• Layden BT, Angueira AR, Brodsky M, Durai V, Lowe WL. Short chain fatty acids and their receptors: new metabolic targets. Transl Res 2013; 161: 131–40.
   Google Scholar
• Schilderink R, Verseijden C, de Jonge WJ. Dietary inhibitors of histone deacetylases in intestinal immunity and homeostasis. Front Immunol 2013; 4: 226. doi: 10.3389/fimmu.2013.00226.
   Google Scholar
• Selma MV, Espin JC, Tomas-Barberan FA. Interaction between phenolics and gut microbiota: role in human health. J Agric Food Chem 2009; 57: 6485–501.
   Google Scholar
• Cardona F, Andrés-Lacueva C, Tulipani S, Tinahones FJ, Queipo-Ortufio MI. Benefits of polyphenols on gut microbiota and implications in human health. J Nutr Biochem 2013; 24: 1415–22.
   Google Scholar
• 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.
   Google Scholar
• Aron-Wisnewsky J, Gaborit B, Dutour A, Clement K. Gut microbiota and non-alcoholic fatty liver disease: new insights. Clin Microbiol Infect 2013; 19: 338–48.
   Google Scholar
• Drenick EJ, Fisler J, Johnson D. Hepatic steatosis after intestinal bypass - prevention and reversal by metronidazole, irrespective of protein-calorie malnutrition. Gastroenterology 1982; 82: 535–48.
   Google Scholar
• Dumas ME, Barton RH, Toye A, Cloarec O, Blancher C, Rothwell A et al. Metabolic profiling reveals a contribution of gut microbiota to fatty liver phenotype in insulin-resistant mice. Proc Natl Acad Sci USA 2006; 103: 12511–6.
   Google Scholar
• Corbin KD, Zeisel SH. Choline metabolism provides novel insights into nonalcoholic fatty liver disease and its progression. Curr Opin Gastroenterol 2012; 28: 159–65.
   Google Scholar
• Wang Z, Klipfell E, Bennett BJ, Koeth R, Levison BS, Dugar B et al. Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease. Nature 2011; 472: 57–63.
   Google Scholar
• Koeth RA, Wang Z, Levison BS, Buffa JA, Org E, Sheehy BT et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nat Med 2013; 19: 576–85.
   Google Scholar
• Baumgart DC, Carding SR. Inflammatory bowel disease: cause and immunobiology. Lancet 2007; 369: 1627–40.
   Google Scholar
• Hansen J, Gulati A, Sartor RB. The role of mucosal immunity and host genetics in defining intestinal commensal bacteria. Curr Opin Gastroenterol 2010; 26: 564–71.
   Google Scholar
• Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA 2007; 104: 13780–5.
   Google Scholar
• Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran LG, Gratadoux JJ et al. Faecalibacterium praus-nitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients. Proc Natl Acad Sci USA 2008; 105: 16731–6.
   Google Scholar
• Joossens M, Huys G, Cnockaert M, De Preter V, Verbeke K, Rutgeerts P et al. Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives. Gut 2011; 60: 631–7.
   Google Scholar
• Miguel S, Martin R, Rossi O, Bermudez-Humaran LG, Chatel JM, Sokol H et al. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol 2013; 16: 255–61.
   Google Scholar
• Darfeuille-Michaud A, Boudeau J, Bulois P, Neut C, Glasser AL, Barnich N et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology 2004; 127: 412–21.
   Google Scholar
• Rosenfeld G, Bressler B. Mycobacterium avium paratuberculosis and the etiology of Crohn’s disease: a review of the controversy from the clinician’s perspective. Can J Gastroenterol 2010; 24: 619–24.
   Google Scholar
• Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 2014; 15: 382–92.
   Google Scholar
• Carroll IM, Chang YH, Park J, Sartor RB, Ringel Y Luminal and mucosal-associated intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Gut Pathog 2010; 2: 19.
   Google Scholar
• Krogius-Kurikka L, Lyra A, Malinen E, Aarnikunnas J, Tuimala J, Paulin L et al. Microbial community analysis reveals high level phylogenetic alterations in the overall gastrointestinal microbiota of diarrhoea-predominant irritable bowel syndrome sufferers. BMC Gastroenterol 2009; 9: 95.
   Google Scholar
• Salonen A, de Vos WM, Palva A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology 2010; 156: 3205–15.
   Google Scholar
• De Palma G, Nadal I, Medina M, Donat E, Ribes-Koninckx C, Calabuig M et al. Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol 2010; 10: 63.
   Google Scholar
• Shen XJ, Rawls JF, Randall T, Burcal L, Mpande CN, Jenkins N et al. Molecular characterization of mucosal adherent bacteria and associations with colorectal adenomas. Gut Microbes 2010; 1: 138–47.
   Google Scholar
• Olivares M, Neef A, Castillejo G, Palma GD, Varea V, Capilla A et al. The HLA-DQ2 genotype selects for early intestinal microbiota composition in infants at high risk of developing coeliac disease. Gut 2014. doi: 10.1136/gutjn1-2014-306931.
   Google Scholar
• 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.
   Google Scholar
• Ley RE, Tumbaugh PJ, Klein S, Gordon JI. Microbial ecology: human gut microbes associated with obesity. Nature 2006; 444: 1022–3.
   Google Scholar
• Collado MC, 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: 894–9.
   Google Scholar
• Duncan SH, Lobley GE, Holtrop G, Ince J, Johnstone AM, Louis P et al. Human colonic microbiota associated with diet, obesity and weight loss. Int J Obes 2008; 32: 1720–4.
   Google Scholar
• Kalliomaki M, Collado MC, Salminen S, Isolauri E. Early differences in fecal microbiota composition in children may predict overweight. Am J Clin Nutr 2008; 87: 534–8.
   Google Scholar
• Nadal I, Santacruz A, Marcos A, Wamberg J, Garagorri JM, Moreno LA et al. Shifts in clostridia, bacteroides and immunoglobulin-coating fecal bacteria associated with weight loss in obese adolescents. Int J Obes 2009; 33: 758–67.
   Google Scholar
• Santacruz A, Marcos A, Wamberg J, Marti A, Martin-Matillas M, Campoy C et al. Interplay between weight loss and gut microbiota composition in overweight adolescents. Obesity 2009; 17: 1906–15.
   Google Scholar
• Schwiertz A, Taras D, Schafer K, Beijer S, Bos NA, Donus C et al. Microbiota and SCFA in lean and overweight healthy subjects. Obesity 2010; 18: 190–5.
   Google Scholar
• Zhang H, DiBaise JK, Zuccolo A, Kudrna D, Braidotti M, Yu Y et al. Human gut microbiota in obesity and after gastric bypass. Proc Natl Acad Sci USA 2009; 106: 2365–70.
   Google Scholar
• Cani PD, Bibiloni R, Knauf C, Waget A, Neyrinck AM, Delzenne NM et al. Changes in gut microbiota control metabolic endotoxemia-induced inflammation in high-fat diet-induced obesity and diabetes in mice. Diabetes 2008; 57: 1470–81.
   Google Scholar
• Tumbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 2006; 444: 1027–31.
   Google Scholar
• Backhed F, Manchester JK, Semenkovich CF, Gordon JI. Mechanisms underlying the resistance to diet-induced obesity in germ-free mice. Proc Natl Acad Sci USA 2007; 104: 979–84.
   Google Scholar
• Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science 2013; 341: 1241214.
   Google Scholar
• Larsen N, Vogensen FK, van den Berg FW, Nielsen DS, Andreasen AS, Pedersen BK et al. Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One 2010; 5: e9085.
   Google Scholar
• Qin J, Li Y, Cai Z, Li S, Zhu J, Zhang F et al. A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature 2012; 490: 55–60.
   Google Scholar
• Karlsson FH, Tremaroli V, Nookaew I, Bergstrom G, Behre CJ, Fagerberg B et al. Gut metagenome in European women with normal, impaired and diabetic glucose control. Nature 2013; 498: 99–103.
   Google Scholar
• 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.
   Google Scholar
• 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.
   Google Scholar
• Kong LC, Tap J, Aron-Wisnewsky J, Pelloux V, Basdevant A, Bouillot JL et al. Gut microbiota after gastric bypass in human obesity: increased richness and associations of bacterial genera with adipose tissue genes. Am J Clin Nutr 2013; 98: 16–24.
   Google Scholar
• Li JV, Ashrafian H, Bueter M, Kinross J, Sands C, le Roux CW et al. Metabolic surgery profoundly influences gut microbial-host metabolic cross-talk. Gut 2011; 60: 1214–23.
   Google Scholar
• Li JV, Reshat R, Wu Q, Ashrafian H, Bueter M, le Roux CW et al. Experimental bariatric surgery in rats generates a cytotoxic chemical environment in the gut contents. Front Microbiol 2011; 2: 183.
   Google Scholar
• Windey K, De Preter V, Louat T, Schuit F, Herman J, Vansant G et al. 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.
   Google Scholar
• Evenepoel P, Meijers BKI, Bammens BRM, Verbeke K. Uremic toxins originating from colonic microbial metabolism. Kidney Int Suppl 2009; 76: S12–S9.
   Google Scholar
• Sirich TL, Meyer TW, Gondouin B, Brunet P, Niwa T. Protein-bound molecules: a large family with a bad character. Semin Nephrol 2014; 34: 106–17.
   Google Scholar
• Poesen R, Meijers B, Evenepoel P. The colon: an overlooked site for therapeutics in dialysis patients. Semin Dial 2013; 26: 323–32.
   Google Scholar
• Neufeld K, Kang N, Bienenstock J, Foster J. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol Motil 2011; 23: 255–64, el19.
   Google Scholar
• Gaykema R, Goehler LE, Lyte M. Brain response to cecal infection with Campylobacter jejuni: analysis with Fos immunohistochemistry. Brain Behav Immun 2004; 18: 238–45.
   Google Scholar
• Goehler LE, Gaykema R, Opitz N, Reddaway R, Badr N, Lyte M. Activation in vagal afferents and central autonomic path-ways: early responses to intestinal infection with Campylobacter jejuni. Brain Behav Immun 2005; 19: 334–44.
   Google Scholar
• Goehler LE, Park SM, Opitz N, Lyte M, Gaykema R. Campylobacter jejuni infection increases anxiety-like behavior in the holeboard: possible anatomical substrates for viscer-osensory modulation of exploratory behavior. Brain Behav Immun 2008; 22: 354–66.
   Google Scholar
• Lyte M, Li W, Opitz N, Gaykema R, Goehler LE. Induction of anxiety-like behavior in mice during the initial stages of infection with the agent of murine colonic hyperplasia Citrobacter rodentium. Physiol Behav 2006; 89: 350–7.
   Google Scholar
• Li H, Cao Y Lactic acid bacterial cell factories for gamma-aminobutyric acid. Amino Acids 2010; 39: 1107–16.
   Google Scholar
• Lyte M. Probiotics function mechanistically as delivery vehicles for neuroactive compounds: microbial endocrinology in the design and use of probiotics. Bioessays 2011; 33: 574–81.
   Google Scholar
• Bravo JA, Forsythe P, Chew MV, Escaravage E, Savignac HM, Dinan TG et al. Ingestion of Lactobacillus strain regulates emotional behavior and central GABA receptor expression in a mouse via the vagus nerve. Proc Natl Acad Sci USA 2011; 108: 16050–5.
   Google Scholar
• Collins J, Borojevic R, Verdu EF, Huizinga JD, Ratcliffe EM. Intestinal microbiota influence the early postnatal development of the enteric nervous system. Neurogastroenterol Motil 2014; 26: 98–107.
   Google Scholar
• Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu XN et al. Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice. J Physiol 2004; 558: 263–75.
   Google Scholar
• Diaz Heijtz R, Wang S, Anuar F, Qian Y, Bjorkholm B, Samuelsson A et al. Normal gut microbiota modulates brain development and behavior. Proc Natl Acad Sci USA 2011; 108: 3047–52.
   Google Scholar
• 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.
   Google Scholar
• Cámara RJ, Ziegler R, Begré S, Schoepfer AM, von Känel R. The role of psychological stress in inflammatory bowel disease: quality assessment of methods of 18 prospective studies and suggestions for future research. Digestion 2009; 80: 129–39.
   Google Scholar
• Mawdsley J, Rampton D. Psychological stress in IBD: new insights into pathogenic and therapeutic implications. Gut 2005; 54: 1481–91.
   Google Scholar
• Maes M, Kubera M, Leunis J-C, Berk M. Increased IgA and IgM responses against gut commensals in chronic depression: further evidence for increased bacterial translocation or leaky gut. J Affect Disord 2012; 141: 55–62.
   Google Scholar
• O’Mahony L, McCarthy J, Kelly P, Hurley G, Luo F, Chen K et al. Lactobacillus and bifidobacterium in irritable bowel syndrome: symptom responses and relationship to cytokine profiles. Gastroenterology 2005; 128: 541–51.
   Google Scholar
• Desbonnet L, Garrett L, Clarke G, Kiely B, Cryan J, Dinan T. Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. Neuroscience 2010; 170: 1179–88.
   Google Scholar
• Myint A-M, Kim YK, Verkerk R, Scharpé S, Steinbusch H, Leonard B. Kynurenine pathway in major depression: evidence of impaired neuroprotection. J Affect Disord 2007; 98: 143–51.
   Google Scholar
• Song C, Wang H. Cytokines mediated inflammation and decreased neurogenesis in animal models of depression. Prog Neuropsychopharmacol Biol Psychiatry 2011; 35: 760–8.
   Google Scholar
• Benton D, Williams C, Brown A. Impact of consuming a milk drink containing a probiotic on mood and cognition. Eur J Clin Nutr 2006; 61: 355–61.
   Google Scholar
• Messaoudi M, Lalonde R, Violle N, Javelot H, Desor D, Nejdi A et al. Assessment of psychotropic-like properties of a probiotic formulation (Lactobacillus helveticus R0052 and Bifidobacterium longum R0175) in rats and human subjects. Br J Nutr 2011; 105: 755–64.
   Google Scholar
• 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.
   Google Scholar
• Dapoigny M, Piche T, Ducrotte P, Lunaud B, Cardot J-M, Bernalier-Donadille A. Efficacy and safety profile of LCR35 complete freeze-dried culture in irritable bowel syndrome: a randomized, double-blind study. World J Gastroenterol 2012; 18: 2067.
   Google Scholar
• Whorwell PJ, Altringer L, Morel J, Bond Y, Charbonneau D, O’Mahony L et al. Efficacy of an encapsulated probiotic Bifidobacterium infantis 35624 in women with irritable bowel syndrome. Am J Gastroenterol 2006; 101: 1581–90.
   Google Scholar
• Dickerson FB, Stallings C, Origoni A, Katsafanas E, Savage CL, Schweinfurth LA et al. Effect of probiotic supplementation on schizophrenia symptoms and association with gastro-intestinal functioning: a randomized, placebo-controlled trial. Prim Care Companion CNS Disord 2014; 16: pii: PCC. 13m01579.
   Google Scholar
• Vaghef-Mehrabany E, Alipour B, Homayouni-Rad A, Sharif S-K, Asghari-Jafarabadi M, Zavvari S. Probiotic supplementation improves inflammatory status in patients with rheumatoid arthritis. Nutrition 2014; 30: 430–5.
   Google Scholar
• Gismondo MR, Drago L, Lombardi A. Review of probiotics available to modify gastrointestinal flora. Int J Antimicrob Agents 1999; 12: 287–92.
   Google Scholar
• Wilhelm SM, Brubaker CM, Varcak EA, Kale-Pradhan PB. Effectiveness of probiotics in the treatment of irritable bowel syndrome. Pharmacotherapy 2008; 28: 496–505.
   Google Scholar
• Brandt LJ, Aroniadis OC. An overview of fecal microbiota transplantation: techniques, indications, and outcomes. Gastrointest Endosc 2013; 78: 240–9.
   Google Scholar