Abstract
The human gut harbors more than 1014 microorganisms, with bacteria being the main population. Gut microbial composition and diversity participates in vital physiologic and immunologic processes maintaining host homeostasis. The disruption of the healthy microbial structure has been associated with various gastrointestinal disorders including inflammatory bowel disease, celiac disease, irritable bowel syndrome and others.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Aas J, Gessert CE, Bakken JS. Recurrent Clostridium difficile colitis: case series involving 18 patients treated with donor stool administered via a nasogastric tube. Clin Infect Dis. 2003;36(5):580–5.
Agrawal A, Houghton LA, Morris J, Reilly B, Guyonnet D, Goupil Feuillerat N, et al. Clinical trial: the effects of a fermented milk product containing Bifidobacterium lactis DN-173 010 on abdominal distension and gastrointestinal transit in irritable bowel syndrome with constipation. Aliment Pharmacol Ther. 2009;29(1):104–14.
Ahmed I, Roy B, Khan S, Septer S, Umar S. Microbiome, metabolome and inflammatory bowel disease. Microorganisms. 2016;4(2):20.
Allen SJ, Martinez EG, Gregorio GV, Dans LF. Probiotics for treating acute infectious diarrhoea. Cochrane Database Syst Rev. 2010. https://doi.org/10.1002/14651858.CD003048.pub3. Accessed 1 Jul 2020. Cochrane Infectious Diseases Group, editor.
Alvarez-Curto E, Milligan G. Metabolism meets immunity: the role of free fatty acid receptors in the immune system. Biochem Pharmacol. 2016;114:3–13.
An D, Oh SF, Olszak T, Neves JF, Avci FY, Erturk-Hasdemir D, et al. Sphingolipids from a symbiotic microbe regulate homeostasis of host intestinal natural killer T cells. Cell. 2014;156(1–2):123–33.
Angelakis E, Merhej V, Raoult D. Related actions of probiotics and antibiotics on gut microbiota and weight modification. Lancet Infect Dis. 2013;13(10):889–99.
Anitha M, Vijay-Kumar M, Sitaraman SV, Gewirtz AT, Srinivasan S. Gut microbial products regulate murine gastrointestinal motility via toll-like receptor 4 signaling. Gastroenterology. 2012;143(4):1006–1016.e4.
Atarashi K, Tanoue T, Oshima K, Suda W, Nagano Y, Nishikawa H, et al. Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota. Nature. 2013;500(7461):232–6.
Austin M, Mellow M, Tierney WM. Fecal microbiota transplantation in the treatment of Clostridium difficile infections. Am J Med. 2014;127(6):479–83.
Baer F, Von Koschitzky H, Roblick U, Bruch HP, Schulze L, Sonnenborn U, et al. Cell-free supernatants of Escherichia coli Nissle 1917 modulate human colonic motility: evidence from an in vitro organ bath study. Neurogastroenterol Motil. 2009;21(5):559–e17.
Balsari A, Ceccarelli A, Dubini F, Fesce E, Poli G. The fecal microbial population in the irritable bowel syndrome. Microbiologica. 1982;5(3):185–94.
Bamba T, Kanauchi O, Andoh A, Fujiyama Y. A new prebiotic from germinated barley for nutraceutical treatment of ulcerative colitis. J Gastroenterol Hepatol. 2002;17(8):818–24.
Barko PC, McMichael MA, Swanson KS, Williams DA. The gastrointestinal microbiome: a review. J Vet Intern Med. 2018;32(1):9–25.
Bascuñán KA, Araya M, Roncoroni L, Doneda L, Elli L. Dietary gluten as a conditioning factor of the gut microbiota in celiac disease. Adv Nutr. 2019;11:160–74.
Basso PJ, Câmara NOS, Sales-Campos H. Microbial-based therapies in the treatment of inflammatory bowel disease—an overview of human studies. Front Pharmacol. 2019;9:1571.
Bassotti G, Villanacci V, Antonelli E, Morelli A, Salerni B. Enteric glial cells: new players in gastrointestinal motility? Lab Investig. 2007;87(7):628–32.
Baumgart M, Dogan B, Rishniw M, Weitzman G, Bosworth B, Yantiss R, et al. Culture independent analysis of ileal mucosa reveals a selective increase in invasive Escherichia coli of novel phylogeny relative to depletion of Clostridiales in Crohn’s disease involving the ileum. ISME J. 2007;1(5):403–18.
Bellini M, Gambaccini D, Stasi C, Urbano MT, Marchi S, Usai-Satta P. Irritable bowel syndrome: a disease still searching for pathogenesis, diagnosis and therapy. World J Gastroenterol. 2014;20(27):8807–20.
Benjamin JL, Hedin CRH, Koutsoumpas A, Ng SC, McCarthy NE, Hart AL, et al. Randomised, double-blind, placebo-controlled trial of fructo-oligosaccharides in active Crohn’s disease. Gut. 2011;60(7):923–9.
Bennet SMP, Ohman L, Simren M. Gut microbiota as potential orchestrators of irritable bowel syndrome. Gut Liver. 2015;9(3):318–31. http://www.gutnliver.org/journal/view.html?doi=10.5009/gnl14344. Accessed 22 Jun 2020.
Bercik P, Denou E, Collins J, Jackson W, Lu J, Jury J, et al. The Intestinal microbiota affect central levels of brain-derived neurotropic factor and behavior in mice. Gastroenterology. 2011a;141(2):599–609.e3.
Bercik P, Park AJ, Sinclair D, Khoshdel A, Lu J, Huang X, et al. The anxiolytic effect of Bifidobacterium longum NCC3001 involves vagal pathways for gut-brain communication. Neurogastroenterol Motil. 2011b;23(12):1132–9.
Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, et al. Comparison of small gut and whole gut microbiota of first-degree relatives with adult celiac disease patients and controls. Front Microbiol. 2019;10:164.
Bonder MJ, Tigchelaar EF, Cai X, Trynka G, Cenit MC, Hrdlickova B, et al. The influence of a short-term gluten-free diet on the human gut microbiome. Genome Med. 2016;8(1):45.
Borody TJ, George L, Andrews P, Brandl S, Noonan S, Cole P, et al. Bowel-flora alteration: a potential cure for inflammatory bowel disease and irritable bowel syndrome? Med J Aust. 1989;150(10):604.
Borody TJ, Leis S, McGrath K, et al. Treatment of chronic constipation and colitis using human probiotic infusions. Probiotics, prebiotics and new foods conference; 2001 Sep 2; Rome, Italy.
Borody TJ, Warren EF, Leis S, Surace R, Ashman O. Treatment of ulcerative colitis using fecal bacteriotherapy. J Clin Gastroenterol. 2003;37(1):42–7.
Botschuijver S, Roeselers G, Levin E, Jonkers DM, Welting O, Heinsbroek SEM, et al. Intestinal fungal dysbiosis is associated with visceral hypersensitivity in patients with irritable bowel syndrome and rats. Gastroenterology. 2017;153(4):1026–39.
Botschuijver S, Welting O, Levin E, Maria-Ferreira D, Koch E, Montijn RC, et al. Reversal of visceral hypersensitivity in rat by Menthacarin ® , a proprietary combination of essential oils from peppermint and caraway, coincides with mycobiome modulation. Neurogastroenterol Motil. 2018;30(6):e13299.
Brint EK, MacSharry J, Fanning A, Shanahan F, Quigley EMM. Differential expression of toll-like receptors in patients with irritable bowel syndrome. Am J Gastroenterol. 2011;106(2):329–36.
Brun P, Castagliuolo I, Leo VD, Buda A, Pinzani M, Palù G, et al. Increased intestinal permeability in obese mice: new evidence in the pathogenesis of nonalcoholic steatohepatitis. Am J Physiol Gastrointest Liver Physiol. 2007;292(2):G518–25.
Buhner S, Li Q, Vignali S, Barbara G, De Giorgio R, Stanghellini V, et al. Activation of human enteric neurons by supernatants of colonic biopsy specimens from patients with irritable bowel syndrome. Gastroenterology. 2009;137(4):1425–34.
Bures J. Small intestinal bacterial overgrowth syndrome. World J Gastroenterol. 2010;16(24):2978.
Camilleri M, Gorman H. Intestinal permeability and irritable bowel syndrome. Neurogastroenterol Motil. 2007;19(7):545–52.
Caminero A, McCarville JL, Galipeau HJ, Deraison C, Bernier SP, Constante M, et al. Duodenal bacterial proteolytic activity determines sensitivity to dietary antigen through protease-activated receptor-2. Nat Commun. 2019;10(1):1198.
Cammarota G, Ianiro G, Tilg H, Rajilić-Stojanović M, Kump P, Satokari R, et al. European consensus conference on faecal microbiota transplantation in clinical practice. Gut. 2017;66(4):569–80.
Camuesco D, Peran L, Comalada M, Nieto A, Di Stasi LC, Rodriguez-Cabezas ME, et al. Preventative effects of lactulose in the trinitrobenzenesulphonic acid model of rat colitis. Inflamm Bowel Dis. 2005;11(3):265–71.
Cao Y, Zhang B, Wu Y, Wang Q, Wang J, Shen F. The value of fecal microbiota transplantation in the treatment of ulcerative colitis patients: a systematic review and meta-analysis. Gastroenterol Res Pract. 2018;2018:1–12.
Cario E. Bacterial interactions with cells of the intestinal mucosa: toll-like receptors and NOD2. Gut. 2005;54(8):1182–93.
Carroll IM, Chang Y-H, Park J, Sartor RB, Ringel Y. Luminal and mucosal-associated intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome. Gut Pathog. 2010;2(1):19.
Carroll IM, Ringel-Kulka T, TO K, Chang Y-H, Packey CD, Sartor RB, et al. Molecular analysis of the luminal- and mucosal-associated intestinal microbiota in diarrhea-predominant irritable bowel syndrome. Am J Physiol Gastrointest Liver Physiol. 2011;301(5):G799–807.
Carroll IM, Ringel-Kulka T, Siddle JP, Ringel Y. Alterations in composition and diversity of the intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome: alterations in composition and diversity of the intestinal microbiota in D-IBS. Neurogastroenterol Motil. 2012;24(6):521–e248.
Casellas F, Borruel N, Torrejón A, Varela E, Antolin M, Guarner F, et al. Oral oligofructose-enriched inulin supplementation in acute ulcerative colitis is well tolerated and associated with lowered faecal calprotectin. Aliment Pharmacol Ther. 2007;25(9):1061–7.
Cayzeele-Decherf A, Pélerin F, Leuillet S, Douillard B, Housez B, Cazaubiel M, et al. Saccharomyces cerevisiae CNCM I-3856 in irritable bowel syndrome: an individual subject meta-analysis. World J Gastroenterol. 2017;23(2):336.
Cenit M, Olivares M, Codoñer-Franch P, Sanz Y. Intestinal microbiota and celiac disease: cause, consequence or co-evolution? Nutrients. 2015;7(8):6900–23.
Chander AM, Yadav H, Jain S, Bhadada SK, Dhawan DK. Cross-talk between gluten, intestinal microbiota and intestinal mucosa in celiac disease: recent advances and basis of autoimmunity. Front Microbiol. 2018;9:2597.
Chang C, Lin H. Dysbiosis in gastrointestinal disorders. Best Pract Res Clin Gastroenterol. 2016;30(1):3–15.
Chassard C, Dapoigny M, Scott KP, Crouzet L, Del’homme C, Marquet P, et al. Functional dysbiosis within the gut microbiota of patients with constipated-irritable bowel syndrome. Aliment Pharmacol Ther. 2012;35(7):828–38.
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(4):837–41.
Cherbut C, Michel C, Lecannu G. The prebiotic characteristics of fructooligosaccharides are necessary for reduction of TNBS-induced colitis in rats. J Nutr. 2003;133(1):21–7.
Chermesh I, Tamir A, Reshef R, Chowers Y, Suissa A, Katz D, et al. Failure of synbiotic 2000 to prevent postoperative recurrence of Crohn’s disease. Dig Dis Sci. 2007;52(2):385–9.
Chiaro TR, Soto R, Zac Stephens W, Kubinak JL, Petersen C, Gogokhia L, et al. A member of the gut mycobiota modulates host purine metabolism exacerbating colitis in mice. Sci Transl Med. 2017;9(380):eaaf9044.
Chong PP, Chin VK, Looi CY, Wong WF, Madhavan P, Yong VC. The microbiome and irritable bowel syndrome—a review on the pathophysiology, current research and future therapy. Front Microbiol. 2019;10:1136.
Clarke G, Fitzgerald P, Cryan JF, Cassidy EM, Quigley EM, Dinan TG. Tryptophan degradation in irritable bowel syndrome: evidence of indoleamine 2,3-dioxygenase activation in a male cohort. BMC Gastroenterol. 2009;9(1):6.
Clarke G, McKernan DP, Gaszner G, Quigley EM, Cryan JF, Dinan TG. A distinct profile of tryptophan metabolism along the kynurenine pathway downstream of toll-like receptor activation in irritable bowel syndrome. Front Pharmacol. 2012;3:90. https://doi.org/10.3389/fphar.2012.00090/abstract. Accessed 22 Jun 2020.
Coelho A-M, Fioramonti J, Buéno L. Systemic lipopolysaccharide influences rectal sensitivity in rats: role of mast cells, cytokines, and vagus nerve. Am J Physiol Gastrointest Liver Physiol. 2000;279(4):G781–90.
Collado MC, Donat E, Ribes-Koninckx C, Calabuig M, Sanz Y. Specific duodenal and faecal bacterial groups associated with paediatric coeliac disease. J Clin Pathol. 2009;62(3):264–9.
Collins SM, Surette M, Bercik P. The interplay between the intestinal microbiota and the brain. Nat Rev Microbiol. 2012;10(11):735–42.
Colman RJ, Rubin DT. Fecal microbiota transplantation as therapy for inflammatory bowel disease: a systematic review and meta-analysis. J Crohn’s Colitis. 2014;8(12):1569–81.
Conceição-Neto N, Deboutte W, Dierckx T, Machiels K, Wang J, Yinda KC, et al. Low eukaryotic viral richness is associated with faecal microbiota transplantation success in patients with UC. Gut. 2018;67(8):1558–9.
Conte MP, Schippa S, Zamboni I, Penta M, Chiarini F, Seganti L, et al. Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease. Gut. 2006;55(12):1760–7.
Costabile A, Santarelli S, Claus SP, Sanderson J, Hudspith BN, Brostoff J, et al. Effect of breadmaking process on in vitro gut microbiota parameters in irritable bowel syndrome. PLoS One. 2014;9(10):e111225. Smidt H, editor
Costello SP, Soo W, Bryant RV, Jairath V, Hart AL, Andrews JM. Systematic review with meta-analysis: faecal microbiota transplantation for the induction of remission for active ulcerative colitis. Aliment Pharmacol Ther. 2017;46(3):213–24.
Crouzet L, Gaultier E, Del’Homme C, Cartier C, Delmas E, Dapoigny M, et al. The hypersensitivity to colonic distension of IBS patients can be transferred to rats through their fecal microbiota. Neurogastroenterol Motil. 2013;25(4):e272–82.
Cryan JF, Dinan TG. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour. Nat Rev Neurosci. 2012;13(10):701–12.
Cui B, Feng Q, Wang H, Wang M, Peng Z, Li P, et al. Fecal microbiota transplantation through mid-gut for refractory Crohn’s disease: safety, feasibility, and efficacy trial results. J Gastroenterol Hepatol. 2015;30(1):51–8.
Cummings JH, Macfarlane GT. Collaborative JPEN-clinical nutrition scientific publications role of intestinal bacteria in nutrient metabolism. JPEN J Parenter Enteral Nutr. 1997;21(6):357–65.
D’Argenio V, Salvatore F. The role of the gut microbiome in the healthy adult status. Clin Chim Acta. 2015;451:97–102.
Darfeuille-Michaud A, Neut C, Barnich N, Lederman E, Di Martino P, Desreumaux P, et al. Presence of adherent Escherichia coli strains in ileal mucosa of patients with Crohn’s disease. Gastroenterology. 1998;115(6):1405–13.
DʼArgenio V, Casaburi G, Precone V, Pagliuca C, Colicchio R, Sarnataro D, et al. Metagenomics reveals dysbiosis and a potentially pathogenic N. flavescens strain in duodenum of adult celiac patients. Am J Gastroenterol. 2016;111(6):879–90.
de Meij TGJ, Budding AE, Grasman ME, Kneepkens CMF, Savelkoul PHM, Mearin ML. Composition and diversity of the duodenal mucosa-associated microbiome in children with untreated coeliac disease. Scand J Gastroenterol. 2013;48(5):530–6.
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. 2010a;10(1):63.
De Palma G, Cinova J, Stepankova R, Tuckova L, Sanz Y. Pivotal advance: bifidobacteria and gram-negative bacteria differentially influence immune responses in the proinflammatory milieu of celiac disease. J Leukoc Biol. 2010b;87(5):765–78.
De Palma G, Capilla A, Nova E, Castillejo G, Varea V, Pozo T, et al. Influence of milk-feeding type and genetic risk of developing coeliac disease on intestinal microbiota of infants: the PROFICEL study. PLoS One. 2012a;7(2):e30791. Heimesaat MM, editor
De Palma G, Kamanova J, Cinova J, Olivares M, Drasarova H, Tuckova L, et al. Modulation of phenotypic and functional maturation of dendritic cells by intestinal bacteria and gliadin: relevance for celiac disease. J Leukoc Biol. 2012b;92(5):1043–54.
De Preter V, Joossens M, Ballet V, Shkedy Z, Rutgeerts P, Vermeire S, et al. Metabolic profiling of the impact of oligofructose-enriched inulin in Crohnʼs disease patients: a double-blinded randomized controlled trial. Clin Transl Gastroenterol. 2013;4(1):e30.
Deitch EA, Specian RD, Berg RD. Endotoxin-induced bacterial translocation and mucosal permeability: role of xanthine oxidase, complement activation, and macrophage products. Crit Care Med. 1991;19(6):785–91.
Desbonnet L, Garrett L, Clarke G, Kiely B, Cryan JF, Dinan TG. Effects of the probiotic Bifidobacterium infantis in the maternal separation model of depression. Neuroscience. 2010;170(4):1179–88.
Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. Proc Natl Acad Sci U S A. 2011;108(Suppl 1):4554–61.
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(11):e280. Eisen JA, editor
Deuring JJ, Fuhler GM, Konstantinov SR, Peppelenbosch MP, Kuipers EJ, de Haar C, et al. Genomic ATG16L1 risk allele-restricted Paneth cell ER stress in quiescent Crohn’s disease. Gut. 2014;63(7):1081–91.
Dey N, Wagner VE, Blanton LV, Cheng J, Fontana L, Haque R, et al. Regulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel. Cell. 2015;163(1):95–107.
Di Cagno R, De Angelis M, De Pasquale I, Ndagijimana M, Vernocchi P, Ricciuti P, et al. Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization. BMC Microbiol. 2011;11(1):219.
Dimidi E, Christodoulides S, Scott SM, Whelan K. Mechanisms of action of probiotics and the gastrointestinal microbiota on gut motility and constipation. Adv Nutr. 2017;8(3):484–94.
Dinan TG, Stilling RM, Stanton C, Cryan JF. Collective unconscious: how gut microbes shape human behavior. J Psychiatr Res. 2015;63:1–9.
Distrutti E, Monaldi L, Ricci P, Fiorucci S. Gut microbiota role in irritable bowel syndrome: new therapeutic strategies. World J Gastroenterol. 2016;22(7):2219–41.
Dohrman A, Miyata S, Gallup M, Li J-D, Chapelin C, Coste A, et al. Mucin gene (MUC 2 and MUC 5AC) upregulation by Gram-positive and Gram-negative bacteria. Biochim Biophys Acta Mol Basis Dis. 1998;1406(3):251–9.
Dollive S, Chen Y-Y, Grunberg S, Bittinger K, Hoffmann C, Vandivier L, et al. Fungi of the murine gut: episodic variation and proliferation during antibiotic treatment. PLoS One. 2013;8(8):e71806. Jacobsen ID, editor.
Dridi B, Raoult D, Drancourt M. Archaea as emerging organisms in complex human microbiomes. Anaerobe. 2011;17(2):56–63.
Duboc H, Rainteau D, Rajca S, Humbert L, Farabos D, Maubert M, et al. Increase in fecal primary bile acids and dysbiosis in patients with diarrhea-predominant irritable bowel syndrome. Neurogastroenterol Motil. 2012;24(6):513–20, e246-247
Dunlop SP, Hebden J, Campbell E, Naesdal J, Olbe L, Perkins AC, et al. Abnormal intestinal permeability in subgroups of diarrhea-predominant irritable bowel syndromes. Am J Gastroenterol. 2006;101(6):1288–94.
El-Salhy M, Hatlebakk JG, Gilja OH, Bråthen Kristoffersen A, Hausken T. Efficacy of faecal microbiota transplantation for patients with irritable bowel syndrome in a randomised, double-blind, placebo-controlled study. Gut. 2020;69(5):859–67.
Eutamene H, Lamine F, Chabo C, Theodorou V, Rochat F, Bergonzelli GE, et al. Synergy between Lactobacillus paracasei and its bacterial products to counteract stress-induced gut permeability and sensitivity increase in rats. J Nutr. 2007;137(8):1901–7.
Faghfoori Z, Shakerhosseini R, Navai L, Somi MH, Nikniaz Z, Abadi A. Effects of an oral supplementation of germinated barley foodstuff on serum CRP level and clinical signs in patients with ulcerative colitis. Health Promot Perspect. 2014;4(1):116–21. http://journals.tbzmed.ac.ir/HPP/Abstract/HPP_73_20140713172754. Accessed 1 Jul 2020
Faghihi AH, Agah S, Masoudi M, Ghafoori SMS, Eshraghi A. Efficacy of probiotic Escherichia coli Nissle 1917 in patients with irritable bowel syndrome: a double blind placebo-controlled randomized trial. Acta Med Indones. 2015;47(3):201–8.
Fan X, Sellin JH. Review article: small intestinal bacterial overgrowth, bile acid malabsorption and gluten intolerance as possible causes of chronic watery diarrhoea. Aliment Pharmacol Ther. 2009;29(10):1069–77.
Fang H, Fu L, Wang J. Protocol for fecal microbiota transplantation in inflammatory bowel disease: a systematic review and meta-analysis. Biomed Res Int. 2018;2018:1–11.
Fernández-Bañares F, Hinojosa J, Sánchez-Lombraña JL, Navarro E, Martínez-Salmerón JF, García-Pugés A, et al. Randomized clinical trial of Plantago ovata seeds (dietary fiber) as compared with mesalamine in maintaining remission in ulcerative colitis. Spanish Group for the Study of Crohn’s Disease and Ulcerative Colitis (GETECCU). Am J Gastroenterol. 1999;94(2):427–33.
Fitzgerald P, Cassidy Eugene M, Clarke G, Scully P, Barry S, Quigley Eamon MM, et al. Tryptophan catabolism in females with irritable bowel syndrome: relationship to interferon-gamma, severity of symptoms and psychiatric co-morbidity. Neurogastroenterol Motil. 2008;20(12):1291–7.
Flint HJ, Scott KP, Duncan SH, Louis P, Forano E. Microbial degradation of complex carbohydrates in the gut. Gut Microbes. 2012;3(4):289–306.
Ford AC, Quigley EMM, Lacy BE, Lembo AJ, Saito YA, Schiller LR, et al. Efficacy of prebiotics, probiotics, and synbiotics in irritable bowel syndrome and chronic idiopathic constipation: systematic review and meta-analysis. Am J Gastroenterol. 2014;109(10):1547–61; quiz 1546, 1562
Forsythe P, Kunze WA. Voices from within: gut microbes and the CNS. Cell Mol Life Sci. 2013;70(1):55–69.
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. 2007;104(34):13780–5.
Frank DN, Robertson CE, Hamm CM, Kpadeh Z, Zhang T, Chen H, et al. Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases. Inflamm Bowel Dis. 2011;17(1):179–84.
Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat Microbiol. 2019;4(2):293–305.
Fujimori S, Tatsuguchi A, Gudis K, Kishida T, Mitsui K, Ehara A, et al. High dose probiotic and prebiotic cotherapy for remission induction of active Crohn’s disease. J Gastroenterol Hepatol. 2007;22(8):1199–204.
Fujimori S, Gudis K, Mitsui K, Seo T, Yonezawa M, Tanaka S, et al. A randomized controlled trial on the efficacy of synbiotic versus probiotic or prebiotic treatment to improve the quality of life in patients with ulcerative colitis. Nutrition. 2009;25(5):520–5.
Furrie E, Macfarlane S, Kennedy A, Cummings JH, Walsh SV, O’neil DA, et al. Synbiotic therapy (Bifidobacterium longum/Synergy 1) initiates resolution of inflammation in patients with active ulcerative colitis: a randomised controlled pilot trial. Gut. 2005;54(2):242–9.
Furusawa Y, Obata Y, Fukuda S, Endo TA, Nakato G, Takahashi D, et al. Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature. 2013;504(7480):446–50.
Galipeau HJ, McCarville JL, Huebener S, Litwin O, Meisel M, Jabri B, et al. Intestinal microbiota modulates gluten-induced immunopathology in humanized mice. Am J Pathol. 2015;185(11):2969–82.
Gallo A, Passaro G, Gasbarrini A, Landolfi R, Montalto M. Modulation of microbiota as treatment for intestinal inflammatory disorders: an uptodate. World J Gastroenterol. 2016;22(32):7186–202.
Gao J, Gillilland M, Owyang C. Rifaximin, gut microbes and mucosal inflammation: unraveling a complex relationship. Gut Microbes. 2014;5(4):571–5.
Gareau MG, Wine E, Rodrigues DM, Cho JH, Whary MT, Philpott DJ, et al. Bacterial infection causes stress-induced memory dysfunction in mice. Gut. 2011;60(3):307–17.
Garrett WS, Gallini CA, Yatsunenko T, Michaud M, DuBois A, Delaney ML, et al. Enterobacteriaceae act in concert with the gut microbiota to induce spontaneous and maternally transmitted colitis. Cell Host Microbe. 2010;8(3):292–300.
Garrido-Mesa N, Camuesco D, Arribas B, Comalada M, Bailón E, Cueto-Sola M, et al. The intestinal anti-inflammatory effect of minocycline in experimental colitis involves both its immunomodulatory and antimicrobial properties. Pharmacol Res. 2011;63(4):308–19.
Geuking MB, Köller Y, Rupp S, McCoy KD. The interplay between the gut microbiota and the immune system. Gut Microbes. 2014;5(3):411–8.
Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn’s disease. Cell Host Microbe. 2014;15(3):382–92.
Ghiamati Yazdi F, Soleimanian-Zad S, van den Worm E, Folkerts G. Turmeric extract: potential use as a prebiotic and anti-inflammatory compound? Plant Foods Hum Nutr. 2019;74(3):293–9.
Ghoshal UC, Kumar S, Mehrotra M, Lakshmi C, Misra A. Frequency of small intestinal bacterial overgrowth in patients with irritable bowel syndrome and chronic non-specific diarrhea. J Neurogastroenterol Motil. 2010;16(1):40–6.
Ghoshal UC, Srivastava D, Ghoshal U, Misra A. Breath tests in the diagnosis of small intestinal bacterial overgrowth in patients with irritable bowel syndrome in comparison with quantitative upper gut aspirate culture. Eur J Gastroenterol Hepatol. 2014;26(7):753–60.
Giannella RA, Rout WR, Toskes PP. Jejunal brush border injury and impaired sugar and amino acid uptake in the blind loop syndrome. Gastroenterology. 1974;67(5):965–74.
Gibson GR, Hutkins R, Sanders ME, Prescott SL, Reimer RA, Salminen SJ, et al. Expert consensus document: the International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics. Nat Rev Gastroenterol Hepatol. 2017;14(8):491–502.
Gionchetti P, Amadini C, Rizzello F, Venturi A, Poggioli G, Campieri M. Probiotics for the treatment of postoperative complications following intestinal surgery. Best Pract Res Clin Gastroenterol. 2003;17(5):821–31.
Glasser A-L, Darfeuille-Michaud A. Abnormalities in the handling of intracellular bacteria in Crohn’s disease: a link between infectious etiology and host genetic susceptibility. Arch Immunol Ther Exp. 2008;56(4):237–44.
Glassner KL, Abraham BP, Quigley EMM. The microbiome and inflammatory bowel disease. J Allergy Clin Immunol. 2020;145(1):16–27.
Goldenberg JZ, Yap C, Lytvyn L, Lo CK-F, Beardsley J, Mertz D, et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children. Cochrane Database Syst Rev. 2017;12:CD006095.
Golfetto L, de SFD, Hermes J, Beserra BTS, França F da S, Martinello F. Lower bifidobacteria counts in adult patients with celiac disease on a gluten-free diet. Arq Gastroenterol. 2014;51(2):139–43.
Goloshchapov OV, Olekhnovich EI, Sidorenko SV, Moiseev IS, Kucher MA, Fedorov DE, et al. Long-term impact of fecal transplantation in healthy volunteers. BMC Microbiol. 2019;19(1):312.
Gorkiewicz G, Moschen A. Gut microbiome: a new player in gastrointestinal disease. Virchows Arch. 2018;472(1):159–72.
Goverse G, Molenaar R, Macia L, Tan J, Erkelens MN, Konijn T, et al. Diet-derived short chain fatty acids stimulate intestinal epithelial cells to induce mucosal tolerogenic dendritic cells. J Immunol. 2017;198(5):2172–81.
Goyal A, Yeh A, Bush BR, Firek BA, Siebold LM, Rogers MB, et al. Safety, clinical response, and microbiome findings following fecal microbiota transplant in children with inflammatory bowel disease. Inflamm Bowel Dis. 2018;24(2):410–21.
Gueimonde M, Collado MC. Metagenomics and probiotics. Clin Microbiol Infect. 2012;18:32–4.
Guslandi M, Mezzi G, Sorghi M, Testoni PA. Saccharomyces boulardii in maintenance treatment of Crohn’s disease. Dig Dis Sci. 2000;45(7):1462–4.
Guyonnet D, Schlumberger A, Mhamdi L, Jakob S, Chassany O. Fermented milk containing Bifidobacterium lactis DN-173 010 improves gastrointestinal well-being and digestive symptoms in women reporting minor digestive symptoms: a randomised, double-blind, parallel, controlled study. Br J Nutr. 2009a;102(11):1654–62.
Guyonnet D, Woodcock A, Stefani B, Trevisan C, Hall C. Fermented milk containing Bifidobacterium lactis DN-173 010 improved self-reported digestive comfort amongst a general population of adults. A randomized, open-label, controlled, pilot study. J Dig Dis. 2009b;10(1):61–70.
Hafer A, Krämer S, Duncker S, Krüger M, Manns MP, Bischoff SC. Effect of oral lactulose on clinical and immunohistochemical parameters in patients with inflammatory bowel disease: a pilot study. BMC Gastroenterol. 2007;7:36.
Hajjar J, Khuri R, Bikhazi A. Effect of bile salts on amino acid transport by rabbit intestine. Am J Physiol Legacy Content. 1975;229(2):518–23.
Halkjær SI, Boolsen AW, Günther S, Christensen AH, Petersen AM. Can fecal microbiota transplantation cure irritable bowel syndrome? World J Gastroenterol. 2017;23(22):4112–20.
Hallert C, Kaldma M, Petersson BG. Ispaghula husk may relieve gastrointestinal symptoms in ulcerative colitis in remission. Scand J Gastroenterol. 1991;26(7):747–50.
Hallert C, Björck I, Nyman M, Pousette A, Grännö C, Svensson H. Increasing fecal butyrate in ulcerative colitis patients by diet: controlled pilot study. Inflamm Bowel Dis. 2003;9(2):116–21.
Halpern GM, Prindiville T, Blankenburg M, Hsia T, Gershwin ME. Treatment of irritable bowel syndrome with Lacteol Fort: a randomized, double-blind, cross-over trial. Am J Gastroenterol. 1996;91(8):1579–85.
Halvorson HA, Schlett CD, Riddle MS. Postinfectious irritable bowel syndrome-a meta-analysis. Am J Gastroenterol. 2006;101(8):1894–9.
Hamaker BR, Tuncil YE. A perspective on the complexity of dietary fiber structures and their potential effect on the gut microbiota. J Mol Biol. 2014;426(23):3838–50.
Hamer HM, Jonkers D, Venema K, Vanhoutvin S, Troost FJ, Brummer R-J. Review article: the role of butyrate on colonic function: review: role of butyrate on colonic function. Aliment Pharmacol Ther. 2007;27(2):104–19.
Hanai H, Kanauchi O, Mitsuyama K, Andoh A, Takeuchi K, Takayuki I, et al. Germinated barley foodstuff prolongs remission in patients with ulcerative colitis. Int J Mol Med. 2004;13(5):643–7.
Hanai H, Iida T, Takeuchi K, Watanabe F, Maruyama Y, Andoh A, et al. Curcumin maintenance therapy for ulcerative colitis: randomized, multicenter, double-blind. Placebo-Control Trial Clin Gastroenterol Hepatol. 2006;4(12):1502–6.
Hansen R, Mukhopadhya I, Meharg C, Russell R, Berry S, El-Omar E, et al. The role of the fungal microbiota in the pathogenesis of de-novo paediatric inflammatory bowel disease using next generation sequencing. Gut. 2013;62(Suppl 1):A32.1–A32.
Heaton KW, Thornton JR, Emmett PM. Treatment of Crohn’s disease with an unrefined-carbohydrate, fibre-rich diet. BMJ. 1979;2(6193):764–6.
Hofmann AF, Poley JR. Role of bile acid malabsorption in pathogenesis of diarrhea and steatorrhea in patients with ileal resection. I. Response to cholestyramine or replacement of dietary long chain triglyceride by medium chain triglyceride. Gastroenterology. 1972;62(5):918–34.
Holleran G, Lopetuso LR, Ianiro G, Pecere S, Pizzoferrato M, Petito V, et al. Gut microbiota and inflammatory bowel disease: so far so gut! Minerva Gastroenterol Dietol. 2017;63(4):373–84.
Holubar SD, Cima RR, Sandborn WJ, Pardi DS. Treatment and prevention of pouchitis after ileal pouch-anal anastomosis for chronic ulcerative colitis. Cochrane Database Syst Rev. 2010;(6):CD001176.
Holvoet T, Joossens M, Wang J, Boelens J, Verhasselt B, Laukens D, et al. Assessment of faecal microbial transfer in irritable bowel syndrome with severe bloating. Gut. 2017;66(5):980–2.
Huffnagle GB, Noverr MC. The emerging world of the fungal microbiome. Trends Microbiol. 2013;21(7):334–41.
Hunter JO, Tuffnell Q, Lee AJ. Controlled trial of oligofructose in the management of irritable bowel syndrome. J Nutr. 1999;129(7 Suppl):1451S–3S.
Iliev ID, Funari VA, Taylor KD, Nguyen Q, Reyes CN, Strom SP, et al. Interactions between commensal fungi and the C-type lectin receptor dectin-1 influence colitis. Science. 2012;336(6086):1314–7.
Imdad A, Nicholson MR, Tanner-Smith EE, Zackular JP, Gomez-Duarte OG, Beaulieu DB, et al. Fecal transplantation for treatment of inflammatory bowel disease. Cochrane Database Syst Rev. 2018. https://doi.org/10.1002/14651858.CD012774.pub2. Accessed 2 Jul 2020. Cochrane IBD Group, editor.
Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, et al. Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease. Gut. 2018;67(1):108–19.
Ishikawa H, Akedo I, Umesaki Y, Tanaka R, Imaoka A, Otani T. Randomized controlled trial of the effect of bifidobacteria-fermented milk on ulcerative colitis. J Am Coll Nutr. 2003;22(1):56–63.
Ishikawa H, Matsumoto S, Ohashi Y, Imaoka A, Setoyama H, Umesaki Y, et al. Beneficial effects of probiotic bifidobacterium and galacto-oligosaccharide in patients with ulcerative colitis: a randomized controlled study. Digestion. 2011;84(2):128–33.
Ivanov D, Emonet C, Foata F, Affolter M, Delley M, Fisseha M, et al. A serpin from the gut bacterium Bifidobacterium longum inhibits eukaryotic elastase-like serine proteases. J Biol Chem. 2006;281(25):17246–52.
Jacobs JP, Goudarzi M, Singh N, Tong M, McHardy IH, Ruegger P, et al. A disease-associated microbial and metabolomics state in relatives of pediatric inflammatory bowel disease patients. Cell Mol Gastroenterol Hepatol. 2016;2(6):750–66.
Jahng J, Jung IS, Choi EJ, Conklin JL, Park H. The effects of methane and hydrogen gases produced by enteric bacteria on ileal motility and colonic transit time: effects of methane and hydrogen gases on bowel function. Neurogastroenterol Motil. 2012;24(2):185–e92.
Jakobsson HE, Rodríguez-Piñeiro AM, Schütte A, Ermund A, Boysen P, Bemark M, et al. The composition of the gut microbiota shapes the colon mucus barrier. EMBO Rep. 2015;16(2):164–77.
Jalanka-Tuovinen J, Salojärvi J, Salonen A, Immonen O, Garsed K, Kelly FM, et al. Faecal microbiota composition and host–microbe cross-talk following gastroenteritis and in postinfectious irritable bowel syndrome. Gut. 2014;63(11):1737–45.
Jansson J, Willing B, Lucio M, Fekete A, Dicksved J, Halfvarson J, et al. Metabolomics reveals metabolic biomarkers of Crohn’s disease. PLoS One. 2009;4(7):e6386.
Jeffery IB, O’Toole PW, Öhman L, Claesson MJ, Deane J, Quigley EMM, et al. An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota. Gut. 2012;61(7):997–1006.
Jeon SR, Chai J, Kim C, Lee CH. Current evidence for the management of inflammatory bowel diseases using fecal microbiota transplantation. Curr Infect Dis Rep. 2018;20(8):21.
Johnsen PH, Hilpüsch F, Cavanagh JP, Leikanger IS, Kolstad C, Valle PC, et al. Faecal microbiota transplantation versus placebo for moderate-to-severe irritable bowel syndrome: a double-blind, randomised, placebo-controlled, parallel-group, single-centre trial. Lancet Gastroenterol Hepatol. 2018;3(1):17–24.
Jones VA, Dickinson RJ, Workman E, Wilson AJ, Freeman AH, Hunter JO. Crohn’s disease: maintenance of remission by diet. Lancet. 1985;2(8448):177–80.
Jones-Hall YL, Nakatsu CH. The intersection of TNF, IBD and the microbiome. Gut Microbes. 2016;7(1):58–62.
Jones-Hall YL, Kozik A, Nakatsu C. Ablation of tumor necrosis factor is associated with decreased inflammation and alterations of the microbiota in a mouse model of inflammatory bowel disease. PLoS One. 2015;10(3):e0119441.
Joossens M, De Preter V, Ballet V, Verbeke K, Rutgeerts P, Vermeire S. Effect of oligofructose-enriched inulin (OF-IN) on bacterial composition and disease activity of patients with Crohn’s disease: results from a double-blinded randomised controlled trial. Gut. 2012;61(6):958.
Jørgensen J, Mortensen PB. Hydrogen sulfide and colonic epithelial metabolism: implications for ulcerative colitis. Dig Dis Sci. 2001;46(8):1722–32.
Kabouridis PS, Lasrado R, McCallum S, Chng SH, Snippert HJ, Clevers H, et al. Microbiota controls the homeostasis of glial cells in the gut lamina propria. Neuron. 2015;85(2):289–95.
Kajander K, Hatakka K, Poussa T, Farkkila M, Korpela R. A probiotic mixture alleviates symptoms in irritable bowel syndrome patients: a controlled 6-month intervention. Aliment Pharmacol Ther. 2005;22(5):387–94.
Kanamori Y, Hashizume K, Sugiyama M, Morotomi M, Yuki N. Case report: combination therapy with Bifidobacterium breve, Lactobacillus casei, and galactooligosaccharides dramatically improved the intestinal function in a girl with short bowel syndrome: a novel synbiotics therapy for intestinal failure. Dig Dis Sci. 2001;46(9):2010–6.
Kanauchi O, Fujiyama Y, Mitsuyama K, Araki Y, Ishii T, Nakamura T, et al. Increased growth of Bifidobacterium and Eubacterium by germinated barley foodstuff, accompanied by enhanced butyrate production in healthy volunteers. Int J Mol Med. 1999. https://doi.org/10.3892/ijmm.3.2.175. Accessed 1 Jun 2020.
Kanauchi O, Suga T, Tochihara M, Hibi T, Naganuma M, Homma T, et al. Treatment of ulcerative colitis by feeding with germinated barley foodstuff: first report of a multicenter open control trial. J Gastroenterol. 2002;37(S14):67–72.
Kanauchi O, Mitsuyama K, Homma T, Takahama K, Fujiyama Y, Andoh A, et al. Treatment of ulcerative colitis patients by long-term administration of germinated barley foodstuff: multi-center open trial. Int J Mol Med. 2003;12(5):701–4.
Kashyap PC, Marcobal A, Ursell LK, Larauche M, Duboc H, Earle KA, et al. Complex interactions among diet, gastrointestinal transit, and gut microbiota in humanized mice. Gastroenterology. 2013;144(5):967–77.
Kassam Z, Lee CH, Yuan Y, Hunt RH. Fecal microbiota transplantation for Clostridium difficile infection: systematic review and meta-analysis. Am J Gastroenterol. 2013;108(4):500–8.
Kelly JR, Kennedy PJ, Cryan JF, Dinan TG, Clarke G, Hyland NP. Breaking down the barriers: the gut microbiome, intestinal permeability and stress-related psychiatric disorders. Front Cell Neurosci. 2015;9:392. http://journal.frontiersin.org/Article/10.3389/fncel.2015.00392/abstract. Accessed 22 Jun 2020
Kelly CR, Khoruts A, Staley C, Sadowsky MJ, Abd M, Alani M, et al. Effect of fecal microbiota transplantation on recurrence in multiply recurrent Clostridium difficile infection: a randomized trial. Ann Intern Med. 2016;165(9):609.
Kerckhoffs APM, Samsom M, van der Rest ME, de Vogel J, Knol J, Ben-Amor K, et al. Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients. World J Gastroenterol. 2009;15(23):2887–92.
Khan KJ, Ullman TA, Ford AC, Abreu MT, Abadir A, Abadir A, et al. Antibiotic therapy in inflammatory bowel disease: a systematic review and meta-analysis. Am J Gastroenterol. 2011;106(4):661–73.
Kim M-S, Bae J-W. Spatial disturbances in altered mucosal and luminal gut viromes of diet-induced obese mice: mucosal and luminal gut viromes. Environ Microbiol. 2016;18(5):1498–510.
Kim G, Deepinder F, Morales W, Hwang L, Weitsman S, Chang C, et al. Methanobrevibacter smithii is the predominant methanogen in patients with constipation-predominant IBS and methane on breath. Dig Dis Sci. 2012;57(12):3213–8.
King T, Elia M, Hunter J. Abnormal colonic fermentation in irritable bowel syndrome. Lancet. 1998;352(9135):1187–9.
Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, et al. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 2014;6(12):107.
Knox NC, Forbes JD, Peterson C-L, Van Domselaar G, Bernstein CN. The gut microbiome in inflammatory bowel disease: lessons learned from other immune-mediated inflammatory diseases. Am J Gastroenterol. 2019;114(7):1051–70.
Kolho K-L, Pessia A, Jaakkola T, de Vos WM, Velagapudi V. Faecal and serum metabolomics in paediatric inflammatory bowel disease. J Crohns Colitis. 2017;11(3):321–34.
König J, Siebenhaar A, Högenauer C, Arkkila P, Nieuwdorp M, Norén T, et al. Consensus report: faecal microbiota transfer—clinical applications and procedures. Aliment Pharmacol Ther. 2017;45(2):222–39.
Korterink JJ, Ockeloen L, Benninga MA, Tabbers MM, Hilbink M, Deckers-Kocken JM. Probiotics for childhood functional gastrointestinal disorders: a systematic review and meta-analysis. Acta Paediatr. 2014;103(4):365–72.
Krook A, Lindström B, Kjellander J, Järnerot G, Bodin L. Relation between concentrations of metronidazole and Bacteroides spp in faeces of patients with Crohn’s disease and healthy individuals. J Clin Pathol. 1981;34(6):645–50.
Kruis W, Schütz E, Fric P, Fixa B, Judmaier G, Stolte M. Double-blind comparison of an oral Escherichia coli preparation and mesalazine in maintaining remission of ulcerative colitis. Aliment Pharmacol Ther. 1997;11(5):853–8.
La Scaleia R, Barba M, Di Nardo G, Bonamico M, Oliva S, Nenna R, et al. Size and dynamics of mucosal and peripheral IL-17A+ T-cell pools in pediatric age, and their disturbance in celiac disease. Mucosal Immunol. 2012;5(5):513–23.
Laake KO, Line PD, Aabakken L, Løtveit T, Bakka A, Eide J, et al. Assessment of mucosal inflammation and circulation in response to probiotics in patients operated with ileal pouch anal anastomosis for ulcerative colitis. Scand J Gastroenterol. 2003;38(4):409–14.
Labruna G, Nanayakkara M, Pagliuca C, Nunziato M, Iaffaldano L, D’Argenio V, et al. Celiac disease-associated Neisseria flavescens decreases mitochondrial respiration in CaCo-2 epithelial cells: impact of Lactobacillus paracasei CBA L74 on bacterial-induced cellular imbalance. Cell Microbiol. 2019;21(8):e13035. https://doi.org/10.1111/cmi.13035. Accessed 25 Jun 2020
Labus JS, Hollister EB, Jacobs J, Kirbach K, Oezguen N, Gupta A, et al. Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome. Microbiome. 2017;5(1):49.
Lacy BE, Mearin F, Chang L, Chey WD, Lembo AJ, Simren M, et al. Bowel disorders. Gastroenterology. 2016;150(6):1393–1407.e5.
Lamas B, Richard ML, Leducq V, Pham H-P, Michel M-L, Da Costa G, et al. CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands. Nat Med. 2016;22(6):598–605.
Langlands SJ. Prebiotic carbohydrates modify the mucosa associated microflora of the human large bowel. Gut. 2004;53(11):1610–6.
Lee YK, Salminen S. Handbook of probiotics and prebiotics. 2nd ed. Hoboken, NJ: Wiley; 2009. 596 p.
Lee HJ, Choi JK, Ryu HS, Choi CH, Kang EH, Park KS, et al. Therapeutic modulation of gut microbiota in functional bowel disorders. J Neurogastroenterol Motil. 2017;23(1):9–19.
Lembo A, Pimentel M, Rao SS, Schoenfeld P, Cash B, Weinstock LB, et al. Repeat treatment with rifaximin is safe and effective in patients with diarrhea-predominant irritable bowel syndrome. Gastroenterology. 2016;151(6):1113–21.
Lepage P, Häsler R, Spehlmann ME, Rehman A, Zvirbliene A, Begun A, et al. Twin study indicates loss of interaction between microbiota and mucosa of patients with ulcerative colitis. Gastroenterology. 2011;141(1):227–36.
Leung W, Malhi G, Willey BM, McGeer AJ, Borgundvaag B, Thanabalan R, et al. Prevalence and predictors of MRSA, ESBL, and VRE colonization in the ambulatory IBD population. J Crohns Colitis. 2012;6(7):743–9.
Levenstein S, Prantera C, Luzi C, D’Ubaldi A. Low residue or normal diet in Crohn’s disease: a prospective controlled study in Italian patients. Gut. 1985;26(10):989–93.
Levitz SM. Innate recognition of fungal cell walls. PLoS Pathog. 2010;6(4):e1000758. Madhani HD, editor
Levy M, Thaiss CA, Zeevi D, Dohnalová L, Zilberman-Schapira G, Mahdi JA, et al. Microbiota-modulated metabolites shape the intestinal microenvironment by regulating NLRP6 inflammasome signaling. Cell. 2015;163(6):1428–43.
Lewis JD, Chen EZ, Baldassano RN, Otley AR, Griffiths AM, Lee D, et al. Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn’s disease. Cell Host Microbe. 2015;18(4):489–500.
Li J, Kong D, Wang Q, Wu W, Tang Y, Bai T, et al. Niacin ameliorates ulcerative colitis via prostaglandin D2-mediated D prostanoid receptor 1 activation. EMBO Mol Med. 2017;9(5):571–88.
Li P, Zhang T, Xiao Y, Tian L, Cui B, Ji G, et al. Timing for the second fecal microbiota transplantation to maintain the long-term benefit from the first treatment for Crohn’s disease. Appl Microbiol Biotechnol. 2019;103(1):349–60.
Liebregts T, Adam B, Bredack C, Röth A, Heinzel S, Lester S, et al. Immune activation in patients with irritable bowel syndrome. Gastroenterology. 2007;132(3):913–20.
Liguori G, Lamas B, Richard ML, Brandi G, da Costa G, Hoffmann TW, et al. Fungal dysbiosis in mucosa-associated microbiota of Crohn’s disease patients. J Crohns Colitis. 2016;10(3):296–305.
Limon JJ, Tang J, Li D, Wolf AJ, Michelsen KS, Funari V, et al. Malassezia is associated with Crohn’s disease and exacerbates colitis in mouse models. Cell Host Microbe. 2019;25(3):377–388.e6.
Lindsay JO. Clinical, microbiological, and immunological effects of fructo-oligosaccharide in patients with Crohn’s disease. Gut. 2006;55(3):348–55.
Lionetti E, Castellaneta S, Francavilla R, Pulvirenti A, Tonutti E, Amarri S, et al. Introduction of gluten, HLA status, and the risk of celiac disease in children. N Engl J Med. 2014;371(14):1295–303.
Lloyd-Price J, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, et al. Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases. Nature. 2019;569(7758):655–62.
Lopez J, Grinspan A. Fecal microbiota transplantation for inflammatory bowel disease. Gastroenterol Hepatol. 2016;12(6):374–9.
Lotrich FE, El-Gabalawy H, Guenther LC, Ware CF. The role of inflammation in the pathophysiology of depression: different treatments and their effects. J Rheumatol Suppl. 2011;88(0):48–54.
Loubinoux J, Bronowicki J-P, Pereira IAC, Mougenel J-L, Faou AE. Sulfate-reducing bacteria in human feces and their association with inflammatory bowel diseases. FEMS Microbiol Ecol. 2002;40(2):107–12.
Lozupone CA, Stombaugh J, Gonzalez A, Ackermann G, Wendel D, Vazquez-Baeza Y, et al. Meta-analyses of studies of the human microbiota. Genome Res. 2013;23(10):1704–14.
Lupp C, Robertson ML, Wickham ME, Sekirov I, Champion OL, Gaynor EC, et al. Host-mediated inflammation disrupts the intestinal microbiota and promotes the overgrowth of Enterobacteriaceae. Cell Host Microbe. 2007;2(2):119–29.
Lyra A, Rinttilä T, Nikkilä J, Krogius-Kurikka L, Kajander K, Malinen E, et al. Diarrhoea-predominant irritable bowel syndromedistinguishable by 16S rRNA gene phylotype quantifcation. World J Gastroenterol. 2009;15(47):5936.
Lyra A, Krogius-Kurikka L, Nikkilä J, Malinen E, Kajander K, Kurikka K, et al. Effect of a multispecies probiotic supplement on quantity of irritable bowel syndrome-related intestinal microbial phylotypes. BMC Gastroenterol. 2010;10(1):110.
Maccaferri S, Vitali B, Klinder A, Kolida S, Ndagijimana M, Laghi L, et al. Rifaximin modulates the colonic microbiota of patients with Crohn’s disease: an in vitro approach using a continuous culture colonic model system. J Antimicrob Chemother. 2010;65(12):2556–65.
Mack DR. Extracellular MUC3 mucin secretion follows adherence of Lactobacillus strains to intestinal epithelial cells in vitro. Gut. 2003;52(6):827–33.
Mack DR, Michail S, Wei S, McDougall L, Hollingsworth MA. Probiotics inhibit enteropathogenic E. coli adherence in vitro by inducing intestinal mucin gene expression. Am J Physiol Gastrointest Liver Physiol. 1999;276(4):G941–50.
Magnusson MK, Strid H, Sapnara M, Lasson A, Bajor A, Ung K-A, et al. Anti-TNF therapy response in patients with ulcerative colitis is associated with colonic antimicrobial peptide expression and microbiota composition. ECCOJC. 2016;10(8):943–52.
Majeed M, Nagabhushanam K, Natarajan S, Sivakumar A, Ali F, Pande A, et al. Bacillus coagulans MTCC 5856 supplementation in the management of diarrhea predominant irritable bowel syndrome: a double blind randomized placebo controlled pilot clinical study. Nutr J. 2015;15(1):21.
Malchow HA. Crohn’s disease and Escherichia coli. A new approach in therapy to maintain remission of colonic Crohn’s disease? J Clin Gastroenterol. 1997;25(4):653–8.
Malinen E. Association of symptoms with gastrointestinal microbiota in irritable bowel syndrome. World J Gastroenterol. 2010;16(36):4532.
Malinen E, Rinttilä T, Kajander K, Mättö J, Kassinen A, Krogius L, et al. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR. Am J Gastroenterol. 2005;100(2):373–82.
Manichanh C. Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut. 2006;55(2):205–11.
Markowiak P, Śliżewska K. Effects of probiotics, prebiotics, and synbiotics on human health. Nutrients. 2017;9(9):1021.
Marques TM, Wall R, Ross RP, Fitzgerald GF, Ryan CA, Stanton C. Programming infant gut microbiota: influence of dietary and environmental factors. Curr Opin Biotechnol. 2010;21(2):149–56.
Marteau P. Ineffectiveness of Lactobacillus johnsonii LA1 for prophylaxis of postoperative recurrence in Crohn’s disease: a randomised, double blind, placebo controlled GETAID trial. Gut. 2006;55(6):842–7.
Marteau P, Seksik P. Tolerance of probiotics and prebiotics. J Clin Gastroenterol. 2004;38(6 Suppl):S67–9.
Martinez-Medina M, Aldeguer X, Lopez-Siles M, González-Huix F, López-Oliu C, Dahbi G, et al. Molecular diversity of Escherichia coli in the human gut: new ecological evidence supporting the role of adherent-invasive E. coli (AIEC) in Crohnʼs disease. Inflamm Bowel Dis. 2009;15(6):872–82.
Matsuoka K, Kanai T. The gut microbiota and inflammatory bowel disease. Semin Immunopathol. 2015;37(1):47–55.
Mayer EA, Savidge T, Shulman RJ. Brain–gut microbiome interactions and functional bowel disorders. Gastroenterology. 2014;146(6):1500–12.
Mazzawi T, Lied GA, Sangnes DA, El-Salhy M, Hov JR, Gilja OH, et al. The kinetics of gut microbial community composition in patients with irritable bowel syndrome following fecal microbiota transplantation. PLoS One. 2018;13(11):e0194904.
McKernan DP, Gaszner G, Quigley EM, Cryan JF, Dinan TG. Altered peripheral toll-like receptor responses in the irritable bowel syndrome: alterations in toll-like receptor activity in IBS. Aliment Pharmacol Ther. 2011;33(9):1045–52.
Menees S, Chey W. The gut microbiome and irritable bowel syndrome. F1000Res. 2018;7:1029.
Menees SB, Maneerattannaporn M, Kim HM, Chey WD. The efficacy and safety of rifaximin for the irritable bowel syndrome: a systematic review and meta-analysis. Am J Gastroenterol. 2012;107(1):28–35; quiz 36
Mikkelsen HB. Interstitial cells of Cajal, macrophages and mast cells in the gut musculature: morphology, distribution, spatial and possible functional interactions. J Cell Mol Med. 2010;14(4):818–32.
Miquel S, Martín R, Rossi O, Bermúdez-Humarán L, Chatel J, Sokol H, et al. Faecalibacterium prausnitzii and human intestinal health. Curr Opin Microbiol. 2013;16(3):255–61.
Mizuno S, Masaoka T, Naganuma M, Kishimoto T, Kitazawa M, Kurokawa S, et al. Bifidobacterium-rich fecal donor may be a positive predictor for successful fecal microbiota transplantation in patients with irritable bowel syndrome. Digestion. 2017;96(1):29–38.
Moayyedi P, Surette MG, Kim PT, Libertucci J, Wolfe M, Onischi C, et al. Fecal microbiota transplantation induces remission in patients with active ulcerative colitis in a randomized controlled trial. Gastroenterology. 2015;149(1):102–109.e6.
Mohajeri MH, Brummer RJM, Rastall RA, Weersma RK, Harmsen HJM, Faas M, et al. The role of the microbiome for human health: from basic science to clinical applications. Eur J Nutr. 2018;57(S1):1–14.
Mokrowiecka A, Daniel P, Słomka M, Majak P, Malecka-Panas E. Clinical utility of serological markers in inflammatory bowel disease. Hepato-Gastroenterology. 2009;56(89):162–6.
Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13(9):R79.
Morikawa K, Watabe H, Araake M, Morikawa S. Modulatory effect of antibiotics on cytokine production by human monocytes in vitro. Antimicrob Agents Chemother. 1996;40(6):1366–70.
Mortensen PB, Andersen JR, Arffmann S, Krag E. Short-chain fatty acids and the irritable bowel syndrome: the effect of wheat bran. Scand J Gastroenterol. 1987;22(2):185–92.
Mukhopadhya I, Hansen R, El-Omar EM, Hold GL. IBD—what role do Proteobacteria play? Nat Rev Gastroenterol Hepatol. 2012;9(4):219–30.
Muller PA, Koscsó B, Rajani GM, Stevanovic K, Berres M-L, Hashimoto D, et al. Crosstalk between muscularis macrophages and enteric neurons regulates gastrointestinal motility. Cell. 2014;158(5):1210.
Nadal I, Donant E, Ribes-Koninckx C, Calabuig M, Sanz Y. Imbalance in the composition of the duodenal microbiota of children with coeliac disease. J Med Microbiol. 2007;56(12):1669–74.
Naidoo K, Gordon M, Fagbemi AO, Thomas AG, Akobeng AK. Probiotics for maintenance of remission in ulcerative colitis. Cochrane Database Syst Rev. 2011;(12):CD007443.
Narula N, Kassam Z, Yuan Y, Colombel J-F, Ponsioen C, Reinisch W, et al. Systematic review and meta-analysis: fecal microbiota transplantation for treatment of active ulcerative colitis. Inflamm Bowel Dis. 2017;23(10):1702–9.
Neufeld KM, Kang N, Bienenstock J, Foster JA. Reduced anxiety-like behavior and central neurochemical change in germ-free mice: behavior in germ-free mice. Neurogastroenterol Motil. 2011;23(3):255–e119.
Ng SC, Shi HY, Hamidi N, Underwood FE, Tang W, Benchimol EI, et al. Worldwide incidence and prevalence of inflammatory bowel disease in the 21st century: a systematic review of population-based studies. Lancet. 2017;390(10114):2769–78.
Niedzielin K, Kordecki H, Birkenfeld B. A controlled, double-blind, randomized study on the efficacy of Lactobacillus plantarum 299V in patients with irritable bowel syndrome. Eur J Gastroenterol Hepatol. 2001;13(10):1143–7.
Nishida A, Inoue R, Inatomi O, Bamba S, Naito Y, Andoh A. Gut microbiota in the pathogenesis of inflammatory bowel disease. Clin J Gastroenterol. 2018;11(1):1–10.
Nistal E, Caminero A, Herrán AR, Arias L, Vivas S, de Morales JMR, et al. Differences of small intestinal bacteria populations in adults and children with/without celiac disease: effect of age, gluten diet, and disease. Inflamm Bowel Dis. 2012a;18(4):649–56.
Nistal E, Caminero A, Vivas S, Ruiz de Morales JM, Sáenz de Miera LE, Rodríguez-Aparicio LB, et al. Differences in faecal bacteria populations and faecal bacteria metabolism in healthy adults and celiac disease patients. Biochimie. 2012b;94(8):1724–9.
Nobaek S, Johansson ML, Molin G, Ahrné S, Jeppsson B. Alteration of intestinal microflora is associated with reduction in abdominal bloating and pain in patients with irritable bowel syndrome. Am J Gastroenterol. 2000;95(5):1231–8.
Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, et al. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015;160(3):447–60.
Noverr MC, Noggle RM, Toews GB, Huffnagle GB. Role of antibiotics and fungal microbiota in driving pulmonary allergic responses. Infect Immun. 2004;72(9):4996–5003.
Nucera G, Gabrielli M, Lupascu A, Lauritano EC, Santoliquido A, Cremonini F, et al. Abnormal breath tests to lactose, fructose and sorbitol in irritable bowel syndrome may be explained by small intestinal bacterial overgrowth. Aliment Pharmacol Ther. 2005;21(11):1391–5.
Nusbaum DJ, Sun F, Ren J, Zhu Z, Ramsy N, Pervolarakis N, et al. Gut microbial and metabolomic profiles after fecal microbiota transplantation in pediatric ulcerative colitis patients. FEMS Microbiol Ecol. 2018;94(9):fiy133.
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(3):541–51.
Ogura Y, Bonen DK, Inohara N, Nicolae DL, Chen FF, Ramos R, et al. A frameshift mutation in NOD2 associated with susceptibility to Crohn’s disease. Nature. 2001;411(6837):603–6.
Ohkusa T, Koido S. Intestinal microbiota and ulcerative colitis. J Infect Chemother. 2015;21(11):761–8.
Ohkusa T, Kato K, Terao S, Chiba T, Mabe K, Murakami K, et al. Newly developed antibiotic combination therapy for ulcerative colitis: a double-blind placebo-controlled multicenter trial. Am J Gastroenterol. 2010;105(8):1820–9.
Ohland CL, MacNaughton WK. Probiotic bacteria and intestinal epithelial barrier function. Am J Physiol Gastrointest Liver Physiol. 2010;298(6):G807–19.
Öhman L, Törnblom H, Simrén M. Crosstalk at the mucosal border: importance of the gut microenvironment in IBS. Nat Rev Gastroenterol Hepatol. 2015;12(1):36–49.
Olesen M, Gudmand-Hoyer E. Efficacy, safety, and tolerability of fructooligosaccharides in the treatment of irritable bowel syndrome. Am J Clin Nutr. 2000;72(6):1570–5.
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. 2015;64(3):406–17.
Olivares M, Benítez-Páez A, de Palma G, Capilla A, Nova E, Castillejo G, et al. Increased prevalence of pathogenic bacteria in the gut microbiota of infants at risk of developing celiac disease: the PROFICEL study. Gut Microbes. 2018:1–8.
Oświęcimska J, Szymlak A, Roczniak W, Girczys-Połedniok K, Kwiecień J. New insights into the pathogenesis and treatment of irritable bowel syndrome. Adv Med Sci. 2017;62(1):17–30.
Ott SJ, Plamondon S, Hart A, Begun A, Rehman A, Kamm MA, et al. Dynamics of the mucosa-associated flora in ulcerative colitis patients during remission and clinical relapse. J Clin Microbiol. 2008;46(10):3510–3.
Ou G, Hedberg M, Hörstedt P, Baranov V, Forsberg G, Drobni M, et al. Proximal small intestinal microbiota and identification of rod-shaped bacteria associated with childhood celiac disease. Am J Gastroenterol. 2009;104(12):3058–67.
Pace F, Pace M, Quartarone G. Probiotics in digestive diseases: focus on Lactobacillus GG. Minerva Gastroenterol Dietol. 2015;61(4):273–92.
Paineau D, Payen F, Panserieu S, Coulombier G, Sobaszek A, Lartigau I, et al. The effects of regular consumption of short-chain fructo-oligosaccharides on digestive comfort of subjects with minor functional bowel disorders. Br J Nutr. 2008;99(2):311–8.
Pandey KR, Naik SR, Vakil BV. Probiotics, prebiotics and synbiotics—a review. J Food Sci Technol. 2015;52(12):7577–87.
Parada Venegas D, De la Fuente MK, Landskron G, González MJ, Quera R, Dijkstra G, et al. Short chain fatty acids (SCFAs)-mediated gut epithelial and immune regulation and its relevance for inflammatory bowel diseases. Front Immunol. 2019;10:277.
Paramsothy S, Paramsothy R, Rubin DT, Kamm MA, Kaakoush NO, Mitchell HM, et al. Faecal microbiota transplantation for inflammatory bowel disease: a systematic review and meta-analysis. J Crohn’s Colitis. 2017;11(10):1180–99.
Paramsothy S, Nielsen S, Kamm MA, Deshpande NP, Faith JJ, Clemente JC, et al. Specific bacteria and metabolites associated with response to fecal microbiota transplantation in patients with ulcerative colitis. Gastroenterology. 2019;156(5):1440–1454.e2.
Pascal V, Pozuelo M, Borruel N, Casellas F, Campos D, Santiago A, et al. A microbial signature for Crohn’s disease. Gut. 2017;66(5):813–22.
Patel RM, Myers LS, Kurundkar AR, Maheshwari A, Nusrat A, Lin PW. Probiotic bacteria induce maturation of intestinal claudin 3 expression and barrier function. Am J Pathol. 2012;180(2):626–35.
Patton PH, Parker CE, MacDonald JK, Chande N. Anti-tuberculous therapy for maintenance of remission in Crohn’s disease. Cochrane Database Syst Rev. 2016;(7):CD000299.
Peng L, He Z, Chen W, Holzman IR, Lin J. Effects of butyrate on intestinal barrier function in a caco-2 cell monolayer model of intestinal barrier. Pediatr Res. 2007;61(1):37–41.
Peng L, Li Z-R, Green RS, Holzman IR, Lin J. Butyrate enhances the intestinal barrier by facilitating tight junction assembly via activation of AMP-activated protein kinase in Caco-2 cell monolayers. J Nutr. 2009;139(9):1619–25.
Pérez-Brocal V, García-López R, Vázquez-Castellanos JF, Nos P, Beltrán B, Latorre A, et al. Study of the viral and microbial communities associated with Crohnʼs disease: a metagenomic approach. Clin Transl Gastroenterol. 2013;4(6):e36.
Persky SE, Brandt LJ. Treatment of recurrent Clostridium difficile-associated diarrhea by administration of donated stool directly through a colonoscope. Am J Gastroenterol. 2000;95(11):3283–5.
Petnicki-Ocwieja T, Hrncir T, Liu Y-J, Biswas A, Hudcovic T, Tlaskalova-Hogenova H, et al. Nod2 is required for the regulation of commensal microbiota in the intestine. Proc Natl Acad Sci U S A. 2009;106(37):15813–8.
Pimentel M, Chow EJ, Lin HC. Eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome. Am J Gastroenterol. 2000;95(12):3503–6.
Pimentel M, Chow EJ, Lin HC. Normalization of lactulose breath testing correlates with symptom improvement in irritable bowel syndrome: a double-blind, randomized, placebo-controlled study. Am J Gastroenterol. 2003;98(2):412–9.
Pimentel M, Lin HC, Enayati P, van den Burg B, Lee H-R, Chen JH, et al. Methane, a gas produced by enteric bacteria, slows intestinal transit and augments small intestinal contractile activity. Am J Physiol Gastrointest Liver Physiol. 2006;290(6):G1089–95.
Pimentel M, Gunsalus RP, Rao SS, Zhang H. Methanogens in human health and disease. Am J Gastroenterol Suppl. 2012;1(1):28–33.
Pineiro M, Asp N-G, Reid G, Macfarlane S, Morelli L, Brunser O, et al. FAO Technical meeting on prebiotics. J Clin Gastroenterol. 2008;42(Suppl 3 Pt 2):S156–9.
Pinn DM, Aroniadis OC, Brandt LJ. Is fecal microbiota transplantation the answer for irritable bowel syndrome? A single-center experience. Am J Gastroenterol. 2014;109(11):1831–2.
Plaza-Diaz J, Ruiz-Ojeda FJ, Gil-Campos M, Gil A. Mechanisms of action of probiotics. Adv Nutr. 2019;10(suppl_1):S49–66.
Plöger S, Stumpff F, Penner GB, Schulzke J-D, Gäbel G, Martens H, et al. Microbial butyrate and its role for barrier function in the gastrointestinal tract: butyrate and the gastrointestinal barrier. Annal N Y Acad Sci. 2012;1258(1):52–9.
Posserud I, Stotzer P-O, Bjornsson ES, Abrahamsson H, Simren M. Small intestinal bacterial overgrowth in patients with irritable bowel syndrome. Gut. 2007;56(6):802–8.
Pozuelo M, Panda S, Santiago A, Mendez S, Accarino A, Santos J, et al. Reduction of butyrate- and methane-producing microorganisms in patients with irritable bowel syndrome. Sci Rep. 2015;5(1):12693.
Prantera C, Scribano ML, Falasco G, Andreoli A, Luzi C. Ineffectiveness of probiotics in preventing recurrence after curative resection for Crohn’s disease: a randomised controlled trial with Lactobacillus GG. Gut. 2002;51(3):405–9.
Prantera C, Lochs H, Campieri M, Scribano ML, Sturniolo GC, Castiglione F, et al. Antibiotic treatment of Crohn’s disease: results of a multicentre, double blind, randomized, placebo-controlled trial with rifaximin. Aliment Pharmacol Ther. 2006;23(8):1117–25.
Pritchard SE, Marciani L, Garsed KC, Hoad CL, Thongborisute W, Roberts E, et al. Fasting and postprandial volumes of the undisturbed colon: normal values and changes in diarrhea-predominant irritable bowel syndrome measured using serial MRI. Neurogastroenterol Motil. 2014;26(1):124–30.
Pyleris E, Giamarellos-Bourboulis EJ, Tzivras D, Koussoulas V, Barbatzas C, Pimentel M. The prevalence of overgrowth by aerobic bacteria in the small intestine by small bowel culture: relationship with irritable bowel syndrome. Dig Dis Sci. 2012;57(5):1321–9.
Qin J, Raes J, Arumugam M, Burgdorf KS, Manichanh C, Nielsen T, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464(7285):59–65.
Quigley EMM. Gut microbiome as a clinical tool in gastrointestinal disease management: are we there yet? Nat Rev Gastroenterol Hepatol. 2017;14(5):315–20.
Quinton JF, Sendid B, Reumaux D, Duthilleul P, Cortot A, Grandbastien B, et al. Anti-Saccharomyces cerevisiae mannan antibodies combined with antineutrophil cytoplasmic autoantibodies in inflammatory bowel disease: prevalence and diagnostic role. Gut. 1998;42(6):788–91.
Rafii F, Ruseler-Van Embden JGH, LMC VL. Changes in bacterial enzymes and PCR profiles of fecal bacteria from a patient with ulcerative colitis before and after antimicrobial treatments. Dig Dis Sci. 1999;44(3):637–42.
Rahimi R, Nikfar S, Rahimi F, Elahi B, Derakhshani S, Vafaie M, et al. A meta-analysis on the efficacy of probiotics for maintenance of remission and prevention of clinical and endoscopic relapse in Crohn’s disease. Dig Dis Sci. 2008;53(9):2524–31.
Rajilić-Stojanović M, Biagi E, HGHJ H, Kajander K, Kekkonen RA, Tims S, et al. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology. 2011;141(5):1792–801.
Rajilić-Stojanović M. Function of the microbiota. Best Pract Res Clin Gastroenterol. 2013;27(1):5–16.
Rajilić-Stojanović M, Jonkers DM, Salonen A, Hanevik K, Raes J, Jalanka J, et al. Intestinal microbiota and diet in IBS: causes, consequences, or epiphenomena? Am J Gastroenterol. 2015;110(2):278–87.
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(4):541–50.
Rembacken BJ, Snelling AM, Hawkey PM, Chalmers DM, Axon AT. Non-pathogenic Escherichia coli versus mesalazine for the treatment of ulcerative colitis: a randomised trial. Lancet. 1999;354(9179):635–9.
Richard ML, Lamas B, Liguori G, Hoffmann TW, Sokol H. Gut fungal microbiota: the Yin and Yang of inflammatory bowel disease. Inflamm Bowel Dis. 2015;21(3):656–65.
Rigsbee L, Agans R, Shankar V, Kenche H, Khamis HJ, Michail S, et al. Quantitative profiling of gut microbiota of children with diarrhea-predominant irritable bowel syndrome. Am J Gastroenterol. 2012;107(11):1740–51.
Ringel Y. The gut microbiome in irritable bowel syndrome and other functional bowel disorders. Gastroenterol Clin N Am. 2017;46(1):91–101.
Riordan SM, McIver CJ, Thomas DH, Duncombe VM, Bolin TD, Thomas MC. Luminal bacteria and small-intestinal permeability. Scand J Gastroenterol. 1997;32(6):556–63.
Rivière A, Selak M, Geirnaert A, Van den Abbeele P, De Vuyst L. Complementary mechanisms for degradation of inulin-type fructans and arabinoxylan oligosaccharides among bifidobacterial strains suggest bacterial cooperation. Appl Environ Microbiol. 2018;84(9):e02893–17.
Roberfroid M, Gibson GR, Hoyles L, McCartney AL, Rastall R, Rowland I, et al. Prebiotic effects: metabolic and health benefits. Br J Nutr. 2010;104(S2):S1–63.
Rodiño-Janeiro BK, Vicario M, Alonso-Cotoner C, Pascua-García R, Santos J. A review of microbiota and irritable bowel syndrome: future in therapies. Adv Ther. 2018;35(3):289–310.
Roediger WE, Duncan A, Kapaniris O, Millard S. Reducing sulfur compounds of the colon impair colonocyte nutrition: implications for ulcerative colitis. Gastroenterology. 1993;104(3):802–9.
Rolfe VE, Fortun PJ, Hawkey CJ, Bath-Hextall F. Probiotics for maintenance of remission in Crohn’s disease. Cochrane Database Syst Rev. 2006;(4):CD004826.
Rolhion N, Darfeuille-Michaud A. Adherent-invasive Escherichia coli in inflammatory bowel disease. Inflamm Bowel Dis. 2007;13(10):1277–83.
Rossen NG, Fuentes S, van der Spek MJ, Tijssen JG, Hartman JHA, Duflou A, et al. Findings from a randomized controlled trial of fecal transplantation for patients with ulcerative colitis. Gastroenterology. 2015;149(1):110–118.e4.
Rostami Nejad M, Ishaq S, Al Dulaimi D, Zali MR, Rostami K. The role of infectious mediators and gut microbiome in the pathogenesis of celiac disease. Arch Iran Med. 2015;18(4):244–9.
Rousseaux C, Thuru X, Gelot A, Barnich N, Neut C, Dubuquoy L, et al. Lactobacillus acidophilus modulates intestinal pain and induces opioid and cannabinoid receptors. Nat Med. 2007;13(1):35–7.
Rowan F, Docherty NG, Murphy M, Murphy B, Calvin Coffey J, O’Connell PR. Desulfovibrio bacterial species are increased in ulcerative colitis. Dis Colon Rectum. 2010;53(11):1530–6.
Sadaghian Sadabad M, Regeling A, de Goffau MC, Blokzijl T, Weersma RK, Penders J, et al. The ATG16L1-T300A allele impairs clearance of pathosymbionts in the inflamed ileal mucosa of Crohn’s disease patients. Gut. 2015;64(10):1546–52.
Saez-Lara MJ, Gomez-Llorente C, Plaza-Diaz J, Gil A. The role of probiotic lactic acid bacteria and bifidobacteria in the prevention and treatment of inflammatory bowel disease and other related diseases: a systematic review of randomized human clinical trials. Biomed Res Int. 2015;2015:1–15.
Salem AE, Singh R, Ayoub YK, Khairy AM, Mullin GE. The gut microbiome and irritable bowel syndrome: state of art review. Arab J Gastroenterol. 2018;19(3):136–41.
Salonen A, de Vos WM, Palva A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology. 2010;156(11):3205–15.
Sánchez E, Laparra JM, Sanz Y. Discerning the role of Bacteroides fragilis in celiac disease pathogenesis. Appl Environ Microbiol. 2012;78(18):6507–15.
Sánchez E, Donat E, Ribes-Koninckx C, Fernández-Murga ML, Sanz Y. Duodenal-mucosal bacteria associated with celiac disease in children. Appl Environ Microbiol. 2013;79(18):5472–9.
Sánchez B, Delgado S, Blanco-Míguez A, Lourenço A, Gueimonde M, Margolles A. Probiotics, gut microbiota, and their influence on host health and disease. Mol Nutr Food Res. 2017;61(1).
Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology. 2008;134(2):577–94.
Sartor RB. Review article: the potential mechanisms of action of rifaximin in the management of inflammatory bowel diseases. Aliment Pharmacol Ther. 2016;43(Suppl 1):27–36.
Sartor RB, Wu GD. Roles for intestinal bacteria, viruses, and fungi in pathogenesis of inflammatory bowel diseases and therapeutic approaches. Gastroenterology. 2017;152(2):327–339.e4.
Saulnier DM, Riehle K, Mistretta T, Diaz M, Mandal D, Raza S, et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology. 2011;141(5):1782–91.
Sbahi H, Di Palma JA. Faecal microbiota transplantation: applications and limitations in treating gastrointestinal disorders. BMJ Open Gastroenterol. 2016;3(1):e000087.
Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018;3(3):337–46.
Schreiber J, Chapman KA, Summar ML, Mew NA, Sutton VR, MacLeod E, et al. Neurologic considerations in propionic acidemia. Mol Genet Metab. 2012;105(1):10–5.
Schultz M, Timmer A, Herfarth HH, Sartor RB, Vanderhoof JA, Rath HC. Lactobacillus GG in inducing and maintaining remission of Crohn’s disease. BMC Gastroenterol. 2004;4:5.
Schwiertz A, Jacobi M, Frick J-S, Richter M, Rusch K, Köhler H. Microbiota in pediatric inflammatory bowel disease. J Pediatr. 2010;157(2):240–244.e1.
Scoville EA, Allaman MM, Brown CT, Motley AK, Horst SN, Williams CS, et al. Alterations in lipid, amino acid, and energy metabolism distinguish Crohn’s disease from ulcerative colitis and control subjects by serum metabolomic profiling. Metabolomics. 2018;14(1):17.
Scully P, McKernan DP, Keohane J, Groeger D, Shanahan F, Dinan TG, et al. Plasma cytokine profiles in females with irritable bowel syndrome and extra-intestinal co-morbidity. Am J Gastroenterol. 2010;105(10):2235–43.
Selby W, Pavli P, Crotty B, Florin T, Radford-Smith G, Gibson P, et al. Two-year combination antibiotic therapy with clarithromycin, rifabutin, and clofazimine for Crohn’s disease. Gastroenterology. 2007;132(7):2313–9.
Sellitto M, Bai G, Serena G, Fricke WF, Sturgeon C, Gajer P, et al. Proof of concept of microbiome-metabolome analysis and delayed gluten exposure on celiac disease autoimmunity in genetically at-risk infants. PLoS One. 2012;7(3):e33387. Highlander SK, editor
Sen S, Mullan MM, Parker TJ, Woolner JT, Tarry SA, Hunter JO. Effect of Lactobacillus plantarum 299v on colonic fermentation and symptoms of irritable bowel syndrome. Dig Dis Sci. 2002;47(11):2615–20.
Sepehri S, Kotlowski R, Bernstein CN, Krause DO. Microbial diversity of inflamed and noninflamed gut biopsy tissues in inflammatory bowel disease. Inflamm Bowel Dis. 2007;13(6):675–83.
Shen J, Zuo Z-X, Mao A-P. Effect of probiotics on inducing remission and maintaining therapy in ulcerative colitis, Crohn’s disease, and pouchitis: meta-analysis of randomized controlled trials. Inflamm Bowel Dis. 2014;20(1):21–35.
Shepherd S, Parker F, Muir J, Gibson P. Dietary triggers of abdominal symptoms in patients with irritable bowel syndrome: randomized placebo-controlled evidence. Clin Gastroenterol Hepatol. 2008;6(7):765–71.
Shi Y, Dong Y, Huang W, Zhu D, Mao H, Su P. Fecal microbiota transplantation for ulcerative colitis: a systematic review and meta-analysis. PLoS One. 2016;11(6):e0157259. Singh UP, editor
Silk DBA, Davis A, Vulevic J, Tzortzis G, Gibson GR. Clinical trial: the effects of a trans-galactooligosaccharide prebiotic on faecal microbiota and symptoms in irritable bowel syndrome. Aliment Pharmacol Ther. 2009;29(5):508–18.
Silverman MS, Davis I, Pillai DR. Success of self-administered home fecal transplantation for chronic Clostridium difficile infection. Clin Gastroenterol Hepatol. 2010;8(5):471–3.
Simren M. Use and abuse of hydrogen breath tests. Gut. 2006;55(3):297–303.
Simrén M, Barbara G, Flint HJ, Spiegel BMR, Spiller RC, Vanner S, et al. Intestinal microbiota in functional bowel disorders: a Rome foundation report. Gut. 2013;62(1):159–76.
Simren M, Palsson OS, Whitehead WE. Update on Rome IV criteria for colorectal disorders: implications for clinical practice. Curr Gastroenterol Rep. 2017;19(4):15.
Sjöberg V, Sandström O, Hedberg M, Hammarström S, Hernell O, Hammarström M-L. Intestinal T-cell responses in celiac disease – impact of celiac disease associated bacteria. PLoS One. 2013;8(1):e53414. Sestak K, editor
Smirnova MG, Guo L, Birchall JP, Pearson JP. LPS up-regulates mucin and cytokine mRNA expression and stimulates mucin and cytokine secretion in goblet cells. Cell Immunol. 2003;221(1):42–9.
Smith FM, Coffey JC, Kell MR, O’Sullivan M, Redmond HP, Kirwan WO. A characterization of anaerobic colonization and associated mucosal adaptations in the undiseased ileal pouch. Colorect Dis. 2005;7(6):563–70.
Sokol H, Pigneur B, Watterlot L, Lakhdari O, Bermudez-Humaran 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(43):16731–6.
Sokol H, Seksik P, Furet JP, Firmesse O, Nion-Larmurier I, Beaugerie L, et al. Low counts of Faecalibacterium prausnitzii in colitis microbiota. Inflamm Bowel Dis. 2009;15(8):1183–9.
Sokol H, Leducq V, Aschard H, Pham H-P, Jegou S, Landman C, et al. Fungal microbiota dysbiosis in IBD. Gut. 2017;66(6):1039–48.
Sokol H, Seksik P, Berard L, Montil M, Nion-Larmurier I, Bourrier A, et al. Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study. Microbiome. 2020;8(1):12.
Soll DR, Galask R, Schmid J, Hanna C, Mac K, Morrow B. Genetic dissimilarity of commensal strains of Candida spp. carried in different anatomical locations of the same healthy women. J Clin Microbiol. 1991;29(8):1702–10.
Sonnenburg JL, Angenent LT, Gordon JI. Getting a grip on things: how do communities of bacterial symbionts become established in our intestine? Nat Immunol. 2004;5(6):569–73.
Soret R, Chevalier J, De Coppet P, Poupeau G, Derkinderen P, Segain JP, et al. Short-chain fatty acids regulate the enteric neurons and control gastrointestinal motility in rats. Gastroenterology. 2010;138(5):1772–1782.e4.
Spurkland A, Sollid LM, Polanco I, Vartdal F, Thorsby E. HLA-DR and -DQ genotypes of celiac disease patients serologically typed to be non-DR3 or non-DR5/7. Hum Immunol. 1992;35(3):188–92.
Standaert-Vitse A, Sendid B, Joossens M, François N, Vandewalle-El Khoury P, Branche J, et al. Candida albicans colonization and ASCA in familial Crohn’s disease. Am J Gastroenterol. 2009;104(7):1745–53.
Steed H, Macfarlane GT, Blackett KL, Bahrami B, Reynolds N, Walsh SV, et al. Clinical trial: the microbiological and immunological effects of synbiotic consumption—a randomized double-blind placebo-controlled study in active Crohn’s disease. Aliment Pharmacol Ther. 2010;32(7):872–83.
Su JW, Ma JJ, Zhang HJ. Use of antibiotics in patients with Crohn’s disease: a systematic review and meta-analysis. J Dig Dis. 2015;16(2):58–66.
Sudo N, Chida Y, Aiba Y, Sonoda J, Oyama N, Yu X-N, et al. Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice: commensal microbiota and stress response. J Physiol. 2004;558(1):263–75.
Sun D, Li W, Li S, Cen Y, Xu Q, Li Y, et al. Fecal microbiota transplantation as a novel therapy for ulcerative colitis: a systematic review and meta-analysis. Medicine (Baltimore). 2016;95(23):e3765.
Sunkara T, Rawla P, Ofosu A, Gaduputi V. Fecal microbiota transplant—a new frontier in inflammatory bowel disease. J Inflamm Res. 2018;11:321–8.
Suskind DL, Brittnacher MJ, Wahbeh G, Shaffer ML, Hayden HS, Qin X, et al. Fecal microbial transplant effect on clinical outcomes and fecal microbiome in active Crohn’s disease. Inflamm Bowel Dis. 2015;21(3):556–63.
Suzuki T, Yoshida S, Hara H. Physiological concentrations of short-chain fatty acids immediately suppress colonic epithelial permeability. Br J Nutr. 2008;100(2):297–305.
Tailford LE, Crost EH, Kavanaugh D, Juge N. Mucin glycan foraging in the human gut microbiome. Front Genet. 2015;6:81. http://www.frontiersin.org/Nutrigenomics/10.3389/fgene.2015.00081/abstract. Available 22 Jun 2020
Tana C, Umesaki Y, Imaoka A, Handa T, Kanazawa M, Fukudo S. Altered profiles of intestinal microbiota and organic acids may be the origin of symptoms in irritable bowel syndrome. Neurogastroenterol Motil. 2009;22(5):512–9. https://doi.org/10.1111/j.1365-2982.2009.01427.x.
Tap J, Derrien M, Törnblom H, Brazeilles R, Cools-Portier S, Doré J, et al. Identification of an intestinal microbiota signature associated with severity of irritable bowel syndrome. Gastroenterology. 2017;152(1):111–123.e8.
Taverniti V, Guglielmetti S. Methodological issues in the study of intestinal microbiota in irritable bowel syndrome. World J Gastroenterol. 2014;20(27):8821–36.
Thiennimitr P, Winter SE, Winter MG, Xavier MN, Tolstikov V, Huseby DL, et al. Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota. Proc Natl Acad Sci. 2011;108(42):17480–5.
Thijssen AY, Clemens CHM, Vankerckhoven V, Goossens H, Jonkers DMAE, Masclee AAM. Efficacy of Lactobacillus casei Shirota for patients with irritable bowel syndrome. Eur J Gastroenterol Hepatol. 2016;28(1):8–14.
Thorburn AN, Macia L, Mackay CR. Diet, metabolites, and “western-lifestyle” inflammatory diseases. Immunity. 2014;40(6):833–42.
Tjellstrom B, Stenhammar L, Hogberg L, Falth-Magnusson K, Magnusson K-E, Midtvedt T, et al. Gut microflora associated characteristics in children with celiac disease. Am J Gastroenterol. 2005;100(12):2784–8.
Tlaskalová-Hogenová H, Štěpánková R, Kozáková H, Hudcovic T, Vannucci L, Tučková L, et al. The role of gut microbiota (commensal bacteria) and the mucosal barrier in the pathogenesis of inflammatory and autoimmune diseases and cancer: contribution of germ-free and gnotobiotic animal models of human diseases. Cell Mol Immunol. 2011;8(2):110–20.
Tojo R, Suárez A, Clemente MG, de los Reyes-Gavilán CG, Margolles A, Gueimonde M, et al. Intestinal microbiota in health and disease: role of bifidobacteria in gut homeostasis. World J Gastroenterol. 2014;20(41):15163–76.
Tooth D, Garsed K, Singh G, Marciani L, Lam C, Fordham I, et al. Characterisation of faecal protease activity in irritable bowel syndrome with diarrhoea: origin and effect of gut transit. Gut. 2014;63(5):753–60.
Townsend CM, Parker CE, MacDonald JK, Nguyen TM, Jairath V, Feagan BG, et al. Antibiotics for induction and maintenance of remission in Crohn’s disease. Cochrane Database Syst Rev. 2019;2:CD012730.
Treem WR, Ahsan N, Kastoff G, Hyams JS. Fecal short-chain fatty acids in patients with diarrhea-predominant irritable bowel syndrome: in vitro studies of carbohydrate fermentation. J Pediatr Gastroenterol Nutrition. 1996;23(3):280–6.
Turner D, Levine A, Kolho K-L, Shaoul R, Ledder O. Combination of oral antibiotics may be effective in severe pediatric ulcerative colitis: a preliminary report. J Crohn’s Colitis. 2014;8(11):1464–70.
Underhill DM, Iliev ID. The mycobiota: interactions between commensal fungi and the host immune system. Nat Rev Immunol. 2014;14(6):405–16.
Van Gossum A, Dewit O, Louis E, de Hertogh G, Baert F, Fontaine F, et al. Multicenter randomized-controlled clinical trial of probiotics (Lactobacillus johnsonii, LA1) on early endoscopic recurrence of Crohn’s disease after lleo-caecal resection. Inflamm Bowel Dis. 2007;13(2):135–42.
van Nood E, Vrieze A, Nieuwdorp M, Fuentes S, Zoetendal EG, de Vos WM, et al. Duodenal infusion of donor feces for recurrent Clostridium difficile. N Engl J Med. 2013;368(5):407–15.
Van Oudenhove L, McKie S, Lassman D, Uddin B, Paine P, Coen S, et al. Fatty acid–induced gut-brain signaling attenuates neural and behavioral effects of sad emotion in humans. J Clin Invest. 2011;121(8):3094–9.
Vangay P, Ward T, Gerber JS, Knights D. Antibiotics, pediatric dysbiosis, and disease. Cell Host Microbe. 2015;17(5):553–64.
Vanner S. The small intestinal bacterial overgrowth. Irritable bowel syndrome hypothesis: implications for treatment. Gut. 2008;57(9):1315–21.
Vantrappen G, Janssens J, Hellemans J, Ghoos Y. The interdigestive motor complex of normal subjects and patients with bacterial overgrowth of the small intestine. J Clin Invest. 1977;59(6):1158–66.
Vaughn BP, Vatanen T, Allegretti JR, Bai A, Xavier RJ, Korzenik J, et al. Increased intestinal microbial diversity following fecal microbiota transplant for active Crohn’s disease. Inflamm Bowel Dis. 2016;22(9):2182–90.
Verdú EF, Bercík P, Bergonzelli GE, Huang X-X, Blennerhasset P, Rochat F, et al. Lactobacillus paracasei normalizes muscle hypercontractility in a murine model of postinfective gut dysfunction. Gastroenterology. 2004;127(3):826–37.
Verdu EF, Galipeau HJ, Jabri B. Novel players in coeliac disease pathogenesis: role of the gut microbiota. Nat Rev Gastroenterol Hepatol. 2015;12(9):497–506.
Videla S, Vilaseca J, Antolín M, García-Lafuente A, Guarner F, Crespo E, et al. Dietary inulin improves distal colitis induced by dextran sodium sulfate in the rat. Am J Gastroenterol. 2001;96(5):1486–93.
Vriezinga SL, Auricchio R, Bravi E, Castillejo G, Chmielewska A, Crespo Escobar P, et al. Randomized feeding intervention in infants at high risk for celiac disease. N Engl J Med. 2014;371(14):1304–15.
Vulevic J, Tzortzis G, Juric A, Gibson GR. Effect of a prebiotic galactooligosaccharide mixture (B-GOS®) on gastrointestinal symptoms in adults selected from a general population who suffer with bloating, abdominal pain, or flatulence. Neurogastroenterol Motil. 2018;30(11):e13440.
Wacklin P, Kaukinen K, Tuovinen E, Collin P, Lindfors K, Partanen J, et al. The duodenal microbiota composition of adult celiac disease patients is associated with the clinical manifestation of the disease. Inflamm Bowel Dis. 2013;19(5):934–41.
Wacklin P, Laurikka P, Lindfors K, Collin P, Salmi T, Lähdeaho M-L, et al. Altered duodenal microbiota composition in celiac disease patients suffering from persistent symptoms on a long-term gluten-free diet. Am J Gastroenterol. 2014;109(12):1933–41.
Walker AW, Sanderson JD, Churcher C, Parkes GC, Hudspith BN, Rayment N, et al. High-throughput clone library analysis of the mucosa-associated microbiota reveals dysbiosis and differences between inflamed and non-inflamed regions of the intestine in inflammatory bowel disease. BMC Microbiol. 2011;11(1):7.
Walters B, Vanner SJ. Detection of bacterial overgrowth in IBS using the lactulose H2 breath test: comparison with 14C-d-xylose and healthy controls. Am J Gastroenterol. 2005;100(7):1566–70.
Wan YC, Li T, Han Y-D, Zhang H-Y, Lin H, Zhang B. Effect of pregnane xenobiotic receptor activation on inflammatory bowel disease treated with rifaximin. J Biol Regul Homeost Agents. 2015;29(2):401–10.
Wang S-L, Wang Z-R, Yang C-Q. Meta-analysis of broad-spectrum antibiotic therapy in patients with active inflammatory bowel disease. Exp Ther Med. 2012;4(6):1051–6.
Wang S, Xu M, Wang W, Cao X, Piao M, Khan S, et al. Systematic review: adverse events of fecal microbiota transplantation. PLoS One. 2016;11(8):e0161174.
Wang H, Cui B, Li Q, Ding X, Li P, Zhang T, et al. The safety of fecal microbiota transplantation for Crohn’s disease: findings from a long-term study. Adv Ther. 2018;35(11):1935–44.
Warden CC. The toxemic factor in rheumatoid arthritis. Cal State J Med. 1909;7(8):299–301.
Wasilewski A, Zielińska M, Storr M, Fichna J. Beneficial effects of probiotics, prebiotics, synbiotics, and psychobiotics in inflammatory bowel disease. Inflamm Bowel Dis. 2015;21(7):1674–82.
Weissfeld AS, Sonnenwirth AC. Rapid isolation of Yersinia spp. from feces. J Clin Microbiol. 1982;15(3):508–10.
Welters CFM, Heineman E, Thunnissen FBJM, van den Bogaard AEJM, Soeters PB, Baeten CGMI. Effect of dietary inulin supplementation on inflammation of pouch mucosa in patients with an ileal pouch-anal anastomosis. Dis Colon Rectum. 2002;45(5):621–7.
Wheeler ML, Limon JJ, Bar AS, Leal CA, Gargus M, Tang J, et al. Immunological consequences of intestinal fungal dysbiosis. Cell Host Microbe. 2016;19(6):865–73.
Wilkins T, Sequoia J. Probiotics for gastrointestinal conditions: a summary of the evidence. Am Fam Physician. 2017;96(3):170–8.
Wilson B, Rossi M, Dimidi E, Whelan K. Prebiotics in irritable bowel syndrome and other functional bowel disorders in adults: a systematic review and meta-analysis of randomized controlled trials. Am J Clin Nutr. 2019;109(4):1098–111.
Winkler J, Butler R, Symonds E. Fructo-oligosaccharide reduces inflammation in a dextran sodium sulphate mouse model of colitis. Dig Dis Sci. 2007;52(1):52–8.
Yamamoto-Furusho J. Pharmacogenetics in inflammatory bowel disease: understanding treatment response and personalizing therapeutic strategies. Pharmgenomics Pers Med. 2017;10:197–204.
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(7402):222–7.
Yilmaz B, Øyås O, Ramon C, Bravo FD, Franc Y, Fournier N, et al. Microbial network disturbances in relapsing refractory Crohn’s disease. Nat Med. 2019;25(2):323–36.
Yoon H, Park YS, Lee DH, Seo J-G, Shin CM, Kim N. Effect of administering a multi-species probiotic mixture on the changes in fecal microbiota and symptoms of irritable bowel syndrome: a randomized, double-blind, placebo-controlled trial. J Clin Biochem Nutr. 2015;57(2):129–34.
Załęski A, Banaszkiewicz A, Walkowiak J. Butyric acid in irritable bowel syndrome. Prz Gastroenterol. 2013;6:350–3.
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(8):1535–43.
Ze X, Le Mougen F, Duncan SH, Louis P, Flint HJ. Some are more equal than others: the role of “keystone” species in the degradation of recalcitrant substrates. Gut Microbes. 2013;4(3):236–40.
Zhang Y, Li L, Guo C, Mu D, Feng B, Zuo X, et al. Effects of probiotic type, dose and treatment duration on irritable bowel syndrome diagnosed by Rome III criteria: a meta-analysis. BMC Gastroenterol. 2016;16(1):62.
Zhou Q, Zhang B, Verne NG. Intestinal membrane permeability and hypersensitivity in the irritable bowel syndrome. Pain. 2009;146(1):41–6.
Zhuang X, Xiong L, Li L, Li M, Chen M. Alterations of gut microbiota in patients with irritable bowel syndrome: a systematic review and meta-analysis: alterations of gut microbiota. J Gastroenterol Hepatol. 2017;32(1):28–38.
Zimmerman MA, Singh N, Martin PM, Thangaraju M, Ganapathy V, Waller JL, et al. Butyrate suppresses colonic inflammation through HDAC1-dependent Fas upregulation and Fas-mediated apoptosis of T cells. Am J Physiol Gastrointest Liver Physiol. 2012;302(12):G1405–15.
Zinkevich V, Beech IB. Screening of sulfate-reducing bacteria in colonoscopy samples from healthy and colitic human gut mucosa. FEMS Microbiol Ecol. 2000;34(2):147–55.
Zuo T, Ng SC. The gut microbiota in the pathogenesis and therapeutics of inflammatory bowel disease. Front Microbiol. 2018;9:2247.
Zuo T, Lu X-J, Zhang Y, Cheung CP, Lam S, Zhang F, et al. Gut mucosal virome alterations in ulcerative colitis. Gut. 2019;68(7):1169–79.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Evangelia, L., Karanasou, E.A., Gazouli, M. (2021). Gut Microbiome and Gastrointestinal Disorders. In: Gazouli, M., Theodoropoulos, G. (eds) Gut Microbiome-Related Diseases and Therapies. The Microbiomes of Humans, Animals, Plants, and the Environment, vol 1. Springer, Cham. https://doi.org/10.1007/978-3-030-59642-2_3
Download citation
DOI: https://doi.org/10.1007/978-3-030-59642-2_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-59641-5
Online ISBN: 978-3-030-59642-2
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)