Title: Brain–Gut Microbiome Interactions and Functional Bowel Disorders
Abstract: Alterations in the bidirectional interactions between the intestine and the nervous system have important roles in the pathogenesis of irritable bowel syndrome (IBS). A body of largely preclinical evidence suggests that the gut microbiota can modulate these interactions. A small and poorly defined role for dysbiosis in the development of IBS symptoms has been established through characterization of altered intestinal microbiota in IBS patients and reported improvement of subjective symptoms after its manipulation with prebiotics, probiotics, or antibiotics. It remains to be determined whether IBS symptoms are caused by alterations in brain signaling from the intestine to the microbiota or primary disruption of the microbiota, and whether they are involved in altered interactions between the brain and intestine during development. We review the potential mechanisms involved in the pathogenesis of IBS in different groups of patients. Studies are needed to better characterize alterations to the intestinal microbiome in large cohorts of well-phenotyped patients, and to correlate intestinal metabolites with specific abnormalities in gut–brain interactions. Alterations in the bidirectional interactions between the intestine and the nervous system have important roles in the pathogenesis of irritable bowel syndrome (IBS). A body of largely preclinical evidence suggests that the gut microbiota can modulate these interactions. A small and poorly defined role for dysbiosis in the development of IBS symptoms has been established through characterization of altered intestinal microbiota in IBS patients and reported improvement of subjective symptoms after its manipulation with prebiotics, probiotics, or antibiotics. It remains to be determined whether IBS symptoms are caused by alterations in brain signaling from the intestine to the microbiota or primary disruption of the microbiota, and whether they are involved in altered interactions between the brain and intestine during development. We review the potential mechanisms involved in the pathogenesis of IBS in different groups of patients. Studies are needed to better characterize alterations to the intestinal microbiome in large cohorts of well-phenotyped patients, and to correlate intestinal metabolites with specific abnormalities in gut–brain interactions. Tor SavidgeView Large Image Figure ViewerDownload Hi-res image Download (PPT)Robert J. ShulmanView Large Image Figure ViewerDownload Hi-res image Download (PPT) Alterations in bidirectional brain–gut interactions are believed to be involved in the pathogenesis of irritable bowel syndrome (IBS) and related functional gastrointestinal (GI) disorders.1Mayer E.A. 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Barbara G. Flint H.J. et al.Intestinal microbiota in functional bowel disorders: a Rome foundation report.Gut. 2013; 62: 159-176Crossref PubMed Scopus (59) Google Scholar activating the mucosal immune response,10Camilleri M. Lasch K. Zhou W. Irritable bowel syndrome: methods, mechanisms, and pathophysiology. The confluence of increased permeability, inflammation, and pain in irritable bowel syndrome.Am J Physiol Gastrointest Liver Physiol. 2012; 303: G775-G785Crossref PubMed Scopus (20) Google Scholar, 11Matricon J. Meleine M. Gelot A. et al.Review article: associations between immune activation, intestinal permeability and the irritable bowel syndrome.Aliment Pharmacol Ther. 2012; 36: 1009-1031Crossref PubMed Scopus (18) Google Scholar, 12Simren M. Barbara G. Flint H.J. et al.Intestinal microbiota in functional bowel disorders: a Rome foundation report.Gut. 2013; 62: 159-176Crossref PubMed Scopus (59) Google Scholar, 13Ringel Y. Maharshak N. 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Flint H.J. et al.Intestinal microbiota in functional bowel disorders: a Rome foundation report.Gut. 2013; 62: 159-176Crossref PubMed Scopus (59) Google Scholar There is also controversy regarding the beneficial effects of manipulating the microbiome with prebiotics, probiotics, or antibiotics in patients with IBS. Furthermore, it is not clear whether alterations observed in the microbiome of patients with IBS arise from altered intestinal function, physiology, and/or changes in brain signaling. For example, there are multiple mechanisms by which the brain, via the hypothalamic pituitary axis, the autonomic nervous system (ANS), and ANS modulation of the enteric nervous system affect the environment of the intestinal microbiota. They can alter motility patterns in different regions of the intestine, as well as epithelial permeability, luminal secretion, mucosal immune function, and possibly intraluminal release of neurotransmitters from enteroendocrine and other cells in the gut (reviewed by Mayer1Mayer E.A. Gut feelings: the emerging biology of gut-brain communication.Nat Rev Neurosci. 2011; 12: 453-466Crossref PubMed Scopus (82) Google Scholar and Rhee et al2Rhee S.H. Pothoulakis C. Mayer E.A. Principles and clinical implications of the brain-gut-enteric microbiota axis.Nat Rev Gastroenterol Hepatol. 2009; 6: 306-314Crossref PubMed Scopus (95) Google Scholar). Several intriguing preclinical studies have described the effects of the gut microbiota on the developing and adult brain and associated behavioral responses,6Sudo N. Chida Y. Aiba Y. et al.Postnatal microbial colonization programs the hypothalamic-pituitary-adrenal system for stress response in mice.J Physiol. 2004; 558: 263-275Crossref PubMed Scopus (154) Google Scholar, 17Diaz Heijtz R. Wang S. Anuar F. et al.Normal gut microbiota modulates brain development and behavior.Proc Natl Acad Sci U S A. 2011; 108: 3047-3052Crossref PubMed Scopus (191) Google Scholar, 18Neufeld K.M. Kang N. Bienenstock J. et al.Reduced anxiety-like behavior and central neurochemical change in germ-free mice.Neurogastroenterol Motil. 2011; 23 (e119): 255-264Crossref PubMed Scopus (80) Google Scholar, 19Gareau M.G. Wine E. Rodrigues D.M. et al.Bacterial infection causes stress-induced memory dysfunction in mice.Gut. 2011; 60: 307-317Crossref PubMed Scopus (51) Google Scholar and have characterized neuroactive metabolites that might mediate these effects.8Cryan J.F. Dinan T.G. Mind-altering microorganisms: the impact of the gut microbiota on brain and behaviour.Nat Rev Neurosci. 2012; 13: 701-712Crossref PubMed Scopus (66) Google Scholar A recent study reported that alteration of the intestinal microbiota with a probiotic affected brain function in healthy individuals.20Tillisch K. Labus J. Kilpatrick L. et al.Consumption of fermented milk product with probiotic modulates brain activity.Gastroenterology. 2013; 144 (1401 e1–e4): 1394-1401Abstract Full Text Full Text PDF PubMed Scopus (15) Google Scholar Our knowledge of the healthy human microbiome is advancing rapidly; reference data sets will enable scientists to distinguish physiologic from pathologic changes in the intestinal microbiome.21Backhed F. Fraser C.M. Ringel Y. et al.Defining a healthy human gut microbiome: current concepts, future directions, and clinical applications.Cell Host Microbe. 2012; 12: 611-622Abstract Full Text Full Text PDF PubMed Scopus (10) Google Scholar We review the associations between alterations to the intestinal microbiota and the development and symptoms of IBS—the most prevalent and best-studied functional GI disorder. Interactions between the brain and intestinal microbiota are conserved among species, so it should be possible to use findings from different systems to determine relationships among the microbiota, intestinal function, and brain, and to determine how they contribute to IBS. New technologies to characterize the microbiome, its metabolic products, and brain structure and function will help us better understand how the intestinal microbiota and brain interact in health and how specific disruptions to these processes may contribute to the symptoms of functional GI disorders. Advances in analytic techniques have helped to better characterize different aspects of the gut microbiome.22Le Chatelier E. Nielsen T. Qin J. et al.Richness of human gut microbiome correlates with metabolic markers.Nature. 2013; 500: 541-546Crossref PubMed Scopus (30) Google Scholar, 23Methe B.A. Nelson K.E. Pop M. et al.A framework for human microbiome research.Nature. 2012; 486: 215-221Crossref PubMed Scopus (160) Google Scholar, 24Li K. Bihan M. Yooseph S. et al.Analyses of the microbial diversity across the human microbiome.PLoS One. 2012; 7: e32118Crossref PubMed Scopus (28) Google Scholar Only 20%–30% of microbes identified in the human colon can be cultured (mostly Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria); these new techniques can be used to assess diversity and functional groups.12Simren M. Barbara G. Flint H.J. et al.Intestinal microbiota in functional bowel disorders: a Rome foundation report.Gut. 2013; 62: 159-176Crossref PubMed Scopus (59) Google Scholar Culture-independent approaches include 16S ribosomal RNA gene-based analyses (to identify microbes in the GI tract), metagenomic approaches (to determine which microbial genes are present), as well as metatranscriptomic, metaproteonomic, and metabolomic techniques (to study transcription, protein production, and metabolism in the microbiome, respectively). Studies of subjects with IBS have used a variety of these techniques12Simren M. Barbara G. Flint H.J. et al.Intestinal microbiota in functional bowel disorders: a Rome foundation report.Gut. 2013; 62: 159-176Crossref PubMed Scopus (59) Google Scholar (Table 1).Table 1Reported Changes in Gut Microbiota in IBS PatientsQuantification methodChangeStudy (subjects)Culture↓ Bifidobacteria (part of the phylum Actinobacteria), Lactobaccili (part of the phylum Firmicutes), AnaerobesBalsari et al, 1982126Balsari A. Ceccarelli A. Dubini F. et al.The fecal microbial population in the irritable bowel syndrome.Microbiologica. 1982; 5: 185-194PubMed Google Scholar (20 with IBS, 20 controls); Si et al, 2004127Si J.M. Yu Y.C. Fan Y.J. et al.Intestinal microecology and quality of life in irritable bowel syndrome patients.World J Gastroenterol. 2004; 10: 1802-1805Crossref PubMed Google Scholar (25 with IBS, 25 controls); Matto et al, 2005128Matto J. Maunuksela L. Kajander K. et al.Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome–a longitudinal study in IBS and control subjects.FEMS Immunol Med Microbiol. 2005; 43: 213-222Crossref PubMed Scopus (112) Google Scholar (26 with IBS, 25 controls; Carroll et al, 2010129Carroll I.M. Chang Y.H. Park J. et al.Luminal and mucosal-associated intestinal microbiota in patients with diarrhea-predominant irritable bowel syndrome.Gut Pathog. 2010; 2: 19Crossref PubMed Scopus (22) Google Scholar (10 with IBS-D, 10 controls)↑ Enterobacteria, AerobesPCR-DGGE/qPCR↓ Anaerobes, Lactobaccilli in IBS-DMatto et al, 2005128Matto J. Maunuksela L. Kajander K. et al.Composition and temporal stability of gastrointestinal microbiota in irritable bowel syndrome–a longitudinal study in IBS and control subjects.FEMS Immunol Med Microbiol. 2005; 43: 213-222Crossref PubMed Scopus (112) Google Scholar (26 with IBS, 25 controls); Malinen et al, 2005130Malinen E. Rinttila T. Kajander K. et al.Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy controls with real-time PCR.Am J Gastroenterol. 2005; 100: 373-382Crossref PubMed Scopus (275) Google Scholar (27 with IBS, 22 controls)↑ AerobesFISH↓ BifidobacteriaKerckhoffs et al, 2009131Kerckhoffs A.P. Samsom M. van der Rest M.E. et al.Lower Bifidobacteria counts in both duodenal mucosa-associated and fecal microbiota in irritable bowel syndrome patients.World J Gastroenterol. 2009; 15: 2887-2892Crossref PubMed Scopus (56) Google Scholar (41 with IBS, 26 controls)↑ Firmicutes (phylum that includes Lactobacilli)Microarray↓ Bacteroidetes (phylum that includes Bacteroides), BifidobacteriaRajilic-Stojanovic et al, 2011132Rajilic-Stojanovic M. Biagi E. Heilig H.G. et al.Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome.Gastroenterology. 2011; 141: 1792-1801Abstract Full Text Full Text PDF PubMed Scopus (92) Google Scholar (62 with IBS, 42 controls); Saulnier et al, 2011133Saulnier D.M. Riehle K. Mistretta T.A. et al.Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.Gastroenterology. 2011; 141: 1782-1791Abstract Full Text Full Text PDF PubMed Scopus (72) Google Scholar (22 with pediatric IBS, 22 controls)↑ Firmicutes16S-Pyrosequencing↓ Bacteroidetes, Bifidobacteria, ActinobacteriaKrogius-Kurikka et al, 2009134Krogius-Kurikka L. Lyra A. Malinen E. 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: 95Crossref PubMed Scopus (53) Google Scholar (10 with IBS-D, 23 controls), Rajilic-Stojanovic et al, 2011132Rajilic-Stojanovic M. Biagi E. Heilig H.G. et al.Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome.Gastroenterology. 2011; 141: 1792-1801Abstract Full Text Full Text PDF PubMed Scopus (92) Google Scholar (62 with IBS, 42 controls); Saulnier et al, 2011133Saulnier D.M. Riehle K. Mistretta T.A. et al.Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.Gastroenterology. 2011; 141: 1782-1791Abstract Full Text Full Text PDF PubMed Scopus (72) Google Scholar (22 with pediatric IBS, 22 controls); Jeffery, 201243Jeffery I.B. O'Toole P.W. Ohman L. et al.An irritable bowel syndrome subtype defined by species-specific alterations in faecal microbiota.Gut. 2012; 61: 997-1006Crossref PubMed Scopus (58) Google Scholar (37 with IBS, 20 controls)↑ Firmicutes, ProteobacteriaNOTE. Changes in bacterial genus and phyla in stool samples from adult and pediatric patients with IBS, measured by different methods. Data were derived from reports for which a general consensus was reached on changes in the microbiota. Direction of arrows indicates increases/decreases in microbial numbers.DGGE, denaturing gradient gel electrophoresis; FISH, fluorescence in situ hybridization; qPCR, quantitative polymerase chain reaction. Open table in a new tab NOTE. Changes in bacterial genus and phyla in stool samples from adult and pediatric patients with IBS, measured by different methods. Data were derived from reports for which a general consensus was reached on changes in the microbiota. Direction of arrows indicates increases/decreases in microbial numbers. DGGE, denaturing gradient gel electrophoresis; FISH, fluorescence in situ hybridization; qPCR, quantitative polymerase chain reaction. Seven studies have evaluated shifts in the composition of microbial communities in the upper bowel (summarized by Simren et al12Simren M. Barbara G. Flint H.J. et al.Intestinal microbiota in functional bowel disorders: a Rome foundation report.Gut. 2013; 62: 159-176Crossref PubMed Scopus (59) Google Scholar and Wang and Yang25Wang Z.K. Yang Y.S. Upper gastrointestinal microbiota and digestive diseases.World J Gastroenterol. 2013; 19: 1541-1550Crossref PubMed Scopus (4) Google Scholar), in a total of 314 subjects who met the criteria for the diagnosis of IBS, based on culture results; 2 additional studies reported results from molecular studies.26Kerckhoffs A.P. Ben-Amor K. Samsom M. et al.Molecular analysis of faecal and duodenal samples reveals significantly higher prevalence and numbers of Pseudomonas aeruginosa in irritable bowel syndrome.J Med Microbiol. 2011; 60: 236-245Crossref PubMed Scopus (18) Google Scholar, 27Pimentel M.F. Giamarellos-Bourboulis E.J. Pyleris E. et al.The first large scale deep sequencing of the duodenal microbiome in irritable bowel syndrome reveals striking differences compared to healthy controls.Gastroenterology. 2013; 144: S59Abstract Full Text Full Text PDF PubMed Scopus (4) Google Scholar Twenty-two studies, comprising 827 subjects, have reported significant changes in the microbial communities of healthy individuals (controls) vs patients with different subtypes of IBS (IBS with diarrhea [IBS-D], constipation [IBS-C], or both), ages (pediatric vs adult), or compartments (mucosa vs stool).12Simren M. Barbara G. Flint H.J. et al.Intestinal microbiota in functional bowel disorders: a Rome foundation report.Gut. 2013; 62: 159-176Crossref PubMed Scopus (59) Google Scholar Despite a lack of consensus on the exact microbial differences between patients with IBS and controls, or the specific microbial changes associated with disease outcome, some general trends are emerging. In contrast to culture-based studies of small-bowel microbiota, which have shown no consistent differences between IBS and controls, recent molecular analyses of mucosal brush samples or luminal aspirates have indicated decreased diversity in small-bowel microbiota of patients with IBS, with increased abundance of gram-negative organisms.26Kerckhoffs A.P. Ben-Amor K. Samsom M. et al.Molecular analysis of faecal and duodenal samples reveals significantly higher prevalence and numbers of Pseudomonas aeruginosa in irritable bowel syndrome.J Med Microbiol. 2011; 60: 236-245Crossref PubMed Scopus (18) Google Scholar, 27Pimentel M.F. 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Maternal separation disrupts the integrity of the intestinal microflora in infant rhesus monkeys.Dev Psychobiol. 1999; 35: 146-155Crossref PubMed Scopus (80) Google Scholar, 29Bailey M.T. Karaszewski J.W. Lubach G.R. et al.In vivo adaptation of attenuated Salmonella typhimurium results in increased growth upon exposure to norepinephrine.Physiol Behav. 1999; 67: 359-364Crossref PubMed Scopus (18) Google Scholar, 30Bailey M.T. Lubach G.R. Coe C.L. Prenatal stress alters bacterial colonization of the gut in infant monkeys.J Pediatr Gastroenterol Nutr. 2004; 38: 414-421Crossref PubMed Google Scholar On the other hand, Firmicutes is the dominant phylum in the microbiota of adults who consume Western diets (high in animal fat and protein), whereas Bacteroidetes is dominant in the microbiota of children who consume fiber–based, agrarian diets.31De Filippo C. Cavalieri D. Di Paola M. et al.Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.Proc Natl Acad Sci U S A. 2010; 107: 14691-14696Crossref PubMed Scopus (378) Google Scholar The dominant genera within Bacteroidetes may differ among groups; Prevotella was more abundant in an African population consuming a plant-based diet, whereas Bacteroides was more abundant in a North American population consuming a different plant-based diet.32Wu G.D. Chen J. Hoffmann C. et al.Linking long-term dietary patterns with gut microbial enterotypes.Science. 2011; 334: 105-108Crossref PubMed Scopus (392) Google Scholar In addition to the evidence that long-term food preferences appear to shape predominant enterotypes (defined by bacterial genera), recent evidence also has shown that short dietary changes are able to produce similar microbial changes.33David L.A. Maurice C.F. Carmody R.N. et al.Diet rapidly and reproducibly alters the human gut microbiome.Nature. 2014; 505: 559-563Crossref PubMed Scopus (4) Google Scholar Considered together with reported phylum-level shifts in the intestinal microbiota of pediatric and adult patients with IBS, the finding of an increased ratio of Firmicutes:Bacteroidetes might arise from factors related to the typical Western diet.34Jeffery I.B. O'Toole P.W. Diet-microbiota interactions and their implications for healthy living.Nutrients. 2013; 5: 234-252Crossref PubMed Scopus (5) Google Scholar However, even though the reported prevalence of IBS is higher in some countries with Western diets (particularly the United States, United Kingdom, and Italy), there are few reliable data to support the concept that IBS prevalence differs significantly among countries or cultural settings (urban vs rural) with Western vs agrarian diets.35Gwee K.A. Irritable bowel syndrome in developing countries–a disorder of civilization or colonization?.Neurogastroenterol Motil. 2005; 17: 317-324Crossref PubMed Scopus (88) Google Scholar There is also no firm evidence that dietary patterns differ significantly between patients with and without IBS36Williams E.A. Nai X. Corfe B.M. Dietary intakes in people with irritable bowel syndrome.BMC Gastroenterol. 2011; 11: 9Crossref PubMed Scopus (13) Google Scholar, 37Bohn L. Storsrud S. Simren M. Nutrient intake in patients with irritable bowel syndrome compared with the general population.Neurogastroenterol Motil. 2013; 25: 23-30.e1Crossref PubMed Scopus (5) Google Scholar, 38El-Salhy M. Ostgaard H. Gundersen D. et al.The role of diet in the pathogenesis and management of irritable bowel syndrome (review).Int J Mol Med. 2012; 29: 723-731PubMed Google Scholar, 39Jarrett M. Heitkemper M.M. 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Jimenez-Hernandez N. et al.Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome.Environ Microbiol Rep. 2012; 4: 242-247Crossref PubMed Scopus (3) Google Scholar A better understanding of the mucosal microbiota in IBS is critical because of the closer communication of signaling systems between mucosa-associated microbiota and the epithelium and the nervous system.2Rhee S.H. Pothoulakis C. Mayer E.A. Principles and clinical implications of the brain-gut-enteric microbiota axis.Nat Rev Gastroenterol Hepatol. 2009; 6: 306-314Crossref PubMed Scopus (95) Google Scholar A number of significant variables likely contribute to the widely conflicting reports of microbial dysbiosis in patients with IBS. This limits our understanding of the collective literature. Many clinical studies used markedly different approaches to define microbial communities. These studies included poorly defined clinical cohorts, patients with psychologic comorbidities, and inadequate numbers of subjects; some studies were repeated in the same patient study population. They did not collect stool samples or compare data among samples from subjects with symptoms. Most studies did not consider dietary variations or use of drugs (eg, antibiotics or proton pump inhibitors) that directly could affect the composition of the microbial community, or indirectly affect it by altering intestinal or immune activity, or other functions such as mucosal permeability. A recent study in a cohort of well-phenotyped IBS patients highlighted these complexities. IBS subgroups were identified based on hierarchical clustering of operational taxonomic unit information from 16S RNA analyses.42Durban A. Abellan J.J. Jimenez-Hernandez N. et al.Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome.Environ Microbiol Rep. 2012; 4: 242-247Crossref PubMed Scopus (3) Google Scholar The weighted UniFrac principal coordinates analysis showed that 2 IBS clusters were clearly separated from each other, from the normal-like IBS sample and from the healthy control sample. For example, the normal-like IBS sample showed normal diversity and a normal Firmicutes:Ba