Bugs, Stool, and the Irritable Bowel Syndrome: Too Much Is as Bad as Too Little?

Abstract

See “Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome,” by Saulnier DM, Riehle K, Mistretta TA, et al, on page 1782; and “Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,” by Rajilić-Stojanović M, Biagi E, Heilig HG, et al, on page 1792. See “Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome,” by Saulnier DM, Riehle K, Mistretta TA, et al, on page 1782; and “Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome,” by Rajilić-Stojanović M, Biagi E, Heilig HG, et al, on page 1792. Perhaps too much of everything is as bad as too little.—Edna Ferber (1885–1968) The irritable bowel syndrome (IBS) is a common, unexplained disorder, affecting ≥10% of Americans.1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 2Rey E. Talley N.J. Irritable bowel syndrome: novel views on the epidemiology and potential risk factors.Dig Liver Dis. 2009; 41: 772-780Google Scholar The syndrome has been identified around the world, affecting people in all nations studied.1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 2Rey E. Talley N.J. Irritable bowel syndrome: novel views on the epidemiology and potential risk factors.Dig Liver Dis. 2009; 41: 772-780Google Scholar IBS significantly impairs quality of life as manifested by poorer mental and physical function, work productivity, relationships, and sleep.1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 3Koloski N.A. Talley N.J. Boyce P.M. The impact of functional gastrointestinal disorders on quality of life.Am J Gastroenterol. 2000; 95: 67-71Google Scholar No currently available therapy cures IBS; at best therapies provide temporary, symptomatic relief.4Brandt LJ C.W. Foxx-Orenstein A.E. Schiller L.R. et al.An evidence-based position statement on the management of irritable bowel syndrome.Am J Gastroenterol. 2009; 104: S1-S35Google Scholar The IBS phenotype is so characteristic it can usually be recognized in clinical practice without any diagnostic testing, comprising recurrent abdominal pain or discomfort linked to an erratic disturbance of defecation, diarrhea or constipation (or both), and often bloating.5Ford A.C. Talley N.J. Veldhuyzen van Zanten S.J.O. et al.Will the history and physical examination help establish that irritable bowel syndrome is causing this patient's lower gastrointestinal tract symptoms?.JAMA. 2008; 300: 1793-1805Google Scholar Despite the enormous personal and economic costs associated with IBS,1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 2Rey E. Talley N.J. Irritable bowel syndrome: novel views on the epidemiology and potential risk factors.Dig Liver Dis. 2009; 41: 772-780Google Scholar the underlying causal mechanisms are still unknown. However, it is becoming clearer that in genetically predisposed individuals, IBS probably occurs after ≥1 environmental hits (most notably, acute gastroenteritis).1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 6Villani A.-C. Lemire M. Thabane M. et al.Genetic risk factors for post-infectious irritable bowel syndrome following a waterborne outbreak of gastroenteritis.Gastroenterology. 2010; 138: 1502-1513Google Scholar Traditionally, IBS has been conceptualized as a brain–gut disorder, especially because anxiety, depression, and extraintestinal symptoms such as fatigue are strongly comorbid with the condition.1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 7Choung R.S. Locke III, G.R. Zinsmeister A.R. et al.Psychosocial distress and somatic symptoms in community subjects with irritable bowel syndrome: a psychological component is the rule.Am J Gastroenterol. 2009; 104: 1772-1779Google Scholar However, emerging evidence supports the view that at least in a subgroup with IBS, the gut may be the primary driver of the manifestations. There are convincing data that subtle mucosal inflammation in the small bowel and colon, especially mast cell and T-lymphocyte infiltration, occurs in a subset with IBS; the link with mast cells is particularly striking and may represent a mucosal biomarker of disease.1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 8Ford A. Talley N. Mucosal inflammation as a potential etiological factor in irritable bowel syndrome: a systematic review.J Gastroenterol. 2011; 46: 421-431Google Scholar, 9Walker M. Warwick A. Ung C. et al.The role of eosinophils and mast cells in intestinal functional disease.Curr Gastroenterol Rep. 2011; 13: 323-330Google Scholar, 10Cremon C. Carini G. Wang B. et al.Intestinal serotonin release, sensory neuron activation, and abdominal pain in irritable bowel syndrome.Am J Gastroenterol. 2011; 106: 1290-1298Google Scholar Serum cytokines are increased in IBS; significantly higher baseline tumor necrosis factor-α, interleukin (IL)-1β, and IL-6 levels, for example, have been observed.11Liebregts T. Adam B. Bredack C. et al.Immune activation in patients with irritable bowel syndrome.Gastroenterology. 2007; 132: 913-920Abstract Full Text Full Text PDF Scopus (518) Google Scholar It has been speculated that certain cytokine profiles may account for excess somatic symptoms including psychological distress in IBS (because positive correlations have been identified),11Liebregts T. Adam B. Bredack C. et al.Immune activation in patients with irritable bowel syndrome.Gastroenterology. 2007; 132: 913-920Abstract Full Text Full Text PDF Scopus (518) Google Scholar although there is uncertainty surrounding the exact source of the cytokine elevations.8Ford A. Talley N. Mucosal inflammation as a potential etiological factor in irritable bowel syndrome: a systematic review.J Gastroenterol. 2011; 46: 421-431Google Scholar As many as one quarter of people develop IBS after postinfectious gastroenteritis.1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 12Spiller R. Garsed K. Postinfectious irritable bowel syndrome.Gastroenterology. 2009; 136: 1979-1988Google Scholar Other lines of evidence suggest that intestinal permeability is impaired in those with postinfectious IBS, leading to the hypothesis that luminal antigens (eg, from bacteria) may penetrate the mucosa and stimulate abnormal host immune responses in IBS.1Talley N.J. Spiller R. Irritable bowel syndrome: a little understood organic bowel disease?.Lancet. 2002; 360: 555-564Google Scholar, 9Walker M. Warwick A. Ung C. et al.The role of eosinophils and mast cells in intestinal functional disease.Curr Gastroenterol Rep. 2011; 13: 323-330Google Scholar What sets in train the inflammatory cytokine cascade in IBS? One possibility is our own gut flora composition predisposes to IBS, and after another insult initiates disease (Figure 1) . Microorganisms account for a staggering 90% of the cells in our body (many still unculturable); only 10% of each of us is formed by “human” cells.13Sekirov I. Finlay B.B. Human and microbe: united we stand.Nat Med. 2006; 12: 736-737Google Scholar The amazing microbial mass in the intestine is established at birth, with the exact composition likely dependent on our genes and the local environment; it may play a critical role in all inflammatory bowel diseases including IBS. Exciting new technology is allowing a detailed accounting of the vast numbers of microbes that make up the human gut microbiome. Initial reports that have exploited high-throughput methods have found that different people tend to have very different taxa within their gut microbiomes and those differences are somewhat stable over time.14Turnbaugh P.J. Hamady M. Yatsunenko T. et al.A core gut microbiome in obese and lean twins.Nature. 2009; 457: 480-484Google Scholar, 15Spencer M.D. Hamp T.J. Reid R.W. et al.Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency.Gastroenterology. 2011; 140: 976-986Google Scholar It is tempting to speculate that some of these differences between individuals in the gut microbiome may explain why some people develop symptoms of IBS and others do not. Using culture-free techniques such as denaturing gradient gel electrophoresis and quantitative polymerase chain reaction targeting specific taxa, a number of studies have tried to find bacteria that can discriminate case from control in IBS (reviewed in Salonen et al16Salonen A. de Vos W.M. Palva A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives.Microbiology. 2010; 156: 3205-3215Google Scholar). Many of these studies were able to find taxa that seem to be different in cases versus controls. However, signature taxa, which would be consistently associated with IBS across different patient cohorts and different techniques, have not emerged. Now in this issue of Gastroenterology, 2 separate studies have used high-resolution techniques (microarrays and 454 sequencing targeting the 16S rRNA gene) to compare case and control in pediatric17Saulnier D. Riehle K. Mistretta T. et al.Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.Gastroenterology. 2011; 141: 1782-1791Abstract Full Text Full Text PDF Scopus (483) Google Scholar and adult18Rajilić-Stojanović 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 Scopus (713) Google Scholar cohorts. The results are encouraging. In the adult study, the microbial community in 62 patients with IBS and 46 healthy controls was characterized using an Agilent microarray that contained 3699 unique 16S rRNA probes representing 129 distinct “16S rRNA-based genus-like phylogenetic groups.” An attempt to analyze the array by treating each of the 3699 probes independently led to no significant clustering between cases and controls, but when the average signal from the 129 “genus-like” groups was utilized within a constrained multivariate approach to build a model, essentially perfect discrimination between cases from controls was achieved. Variation between human hosts at the species level evidently swamped out the signal associated with the disease, but an analysis at a higher taxonomic level revealed the disease signature. Importantly, a permutation-based test estimated that the odds of seeing such a strong separation of cases and controls by chance was highly unlikely.18Rajilić-Stojanović 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 Scopus (713) Google Scholar In addition, a substantial number of taxa were found that had significantly different signal intensities between cases and controls, even after correcting for multiple hypothesis testing. These robust results confirm that the observed separation of cases and controls is not due to model overfitting and provides further compelling evidence for the hypothesis that differences within the microbial community are associated with IBS. Pediatric IBS is even more poorly understood and understudied than adult IBS, and subgrouping by stool form is controversial. In a pioneering study, Saulnier et al17Saulnier D. Riehle K. Mistretta T. et al.Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.Gastroenterology. 2011; 141: 1782-1791Abstract Full Text Full Text PDF Scopus (483) Google Scholar used next-generation sequencing and microarray platforms to describe differences within the microbial community between IBS and healthy children, and children with different subtypes of IBS. Intriguingly, total microbial load (the 16S rDNA copy number per gram of stool) was not significantly different between healthy children and children with IBS. It will be interesting to see how these observations impact consideration of whether the total number of bacteria present in the gut (the “overgrowth” hypothesis) matters more in IBS than the types of bacteria present, which we can now measure with these high-throughput methods. Despite the considerable progress seen in these papers, great challenges remain. One challenge revolves around the likely existence of microbial niches in the colon and small intestine. Emerging data suggest that there may be differences in the mucosal-associated microbiota (obtained by biopsy) versus the luminal microbiota (from stool sampling) in IBS,19Carroll I.M. Ringel-Kulka T. Keku T.O. 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 July 7; ([Epub ahead of print])Google Scholar although this needs to be confirmed. Differences between small and large intestinal microbiota composition may also be key in disease. The “holy grail” is finding a set of diagnostic taxa in stool that are always, or nearly always, associated with IBS or 1 of its subtypes. Identification of such a set of taxa might have diagnostic use in the clinic and could be evaluated in animal models of IBS for their impact on diarrhea, constipation, and abdominal pain.20Adam B. Liebregts T. Gschossmann J.M. et al.Severity of mucosal inflammation as a predictor for alterations of visceral sensory function in a rat model.Pain. 2006; 123: 179-186Google Scholar The high-throughput methods of the current studies provide the most exhaustive set yet of taxa associated with IBS and there are important similarities between the results of the 2 studies, suggesting that either excess or a deficiency in the microbial composition plays a role. For example, a higher relative abundance of the Firmicutes member Dorea was significantly associated with IBS in both studies. There are, however, also many substantive differences between the results of the 2 studies. For example, in the study from Saulnier et al,17Saulnier D. Riehle K. Mistretta T. et al.Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.Gastroenterology. 2011; 141: 1782-1791Abstract Full Text Full Text PDF Scopus (483) Google Scholar changes between IBS and healthy children were observed in the phylum Proteobacteria; there were, however, no reported significant changes between case and control in Proteobacteria in the study by Rajilić-Stojanović,18Rajilić-Stojanović 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 Scopus (713) Google Scholar although several taxa within Proteobacteria were correlated with IBS symptom scores. Likewise, in the pediatric study,17Saulnier D. Riehle K. Mistretta T. et al.Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.Gastroenterology. 2011; 141: 1782-1791Abstract Full Text Full Text PDF Scopus (483) Google Scholar greater frequency of pain was associated with an increase in the genus Alistipes, but in the adult study,18Rajilić-Stojanović 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 Scopus (713) Google Scholar Alistipes was significantly higher in normal controls. There are, of course, many potential explanations for these sorts of differences. Some of these are biological such as different patient populations (pediatric versus adult) and geographical regions (Houston, TX, versus Helsinki, Finland). Some of the potential explanations are more technical, such as the potential influence of batch effects,21Leek J.T. Scharpf R.B. Bravo H.C. et al.Tackling the widespread and critical impact of batch effects in high-throughput data.Nat Rev Genet. 2010; 11: 733-739Google Scholar the different platforms used in the studies (next-generation sequencing and Affymetrix arrays versus Agilent arrays), different schemes for correction for testing of multiple hypotheses, or other analysis choices made in the very different data pipelines required to analyze these different high-throughput platforms. Clearly, if we are to achieve the goal of a set of reliable and robust set of diagnostic taxa, these kinds of biological and technical issues need to be addressed and standardized. Achieving reproducibility within and across different patient cohorts and different technology platforms remains a central challenge for metagenomic studies,22Zhou J. Wu L. Deng Y. et al.Reproducibility and quantitation of amplicon sequencing-based detection.ISME J. 2011; 5: 1303-1313Google Scholar as in many other areas of genomics.23Boulesteix A.-L. Over-optimism in bioinformatics research.Bioinformatics. 2010; 26: 437-439Google Scholar It is particularly important to study representative, population-based samples in the future to confirm the current findings, notwithstanding the logistical difficulties of undertaking such studies. Despite the considerable challenges, these papers represent encouraging progress, especially because there is growing evidence that the microbial community is involved in and possibly causally linked with IBS based on therapeutic trials.24Moayyedi P. Ford A.C. Talley N.J. et al.The efficacy of probiotics in the treatment of irritable bowel syndrome: a systematic review.Gut. 2010; 59: 325-332Google Scholar, 25Brenner D.M. Moeller M.J. Chey W.D. et al.The utility of probiotics in the treatment of irritable bowel syndrome: a systematic review.Am J Gastroenterol. 2009; 104: 1033-1049Google Scholar, 26Pimentel M. Lembo A. Chey W.D. et al.Rifaximin therapy for patients with Irritable Bowel Syndrome without constipation.N Engl J Med. 2011; 364: 22-32Google Scholar, 27Mendall MA K.D. Antibiotic use, childhood affluence and irritable bowel syndrome.Eur J Gastroenterol Hepatol. 1998; 10: 59-62Google Scholar A meta-analysis reported that probiotics are superior to placebo in IBS, but there remains great uncertainty about optimal therapy, because there is significant heterogeneity in the literature.24Moayyedi P. Ford A.C. Talley N.J. et al.The efficacy of probiotics in the treatment of irritable bowel syndrome: a systematic review.Gut. 2010; 59: 325-332Google Scholar Another review concluded that the best evidence of efficacy in IBS is with Bifidobacterium infantis 35,624 species,25Brenner D.M. Moeller M.J. Chey W.D. et al.The utility of probiotics in the treatment of irritable bowel syndrome: a systematic review.Am J Gastroenterol. 2009; 104: 1033-1049Google Scholar and Rajilić-Stojanović et al observed a 1.5-fold decrease in Bifidobacteria in IBS.18Rajilić-Stojanović 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 Scopus (713) Google Scholar In contrast, 2 randomized, placebo-controlled trials have demonstrated that 2 weeks of therapy with the poorly absorbed antibiotic rifaximin in IBS led to improvement of abdominal pain, loose stools, and bloating (number needed to treat = 10) that persisted for 10 weeks after the antibiotic was ceased.26Pimentel M. Lembo A. Chey W.D. et al.Rifaximin therapy for patients with Irritable Bowel Syndrome without constipation.N Engl J Med. 2011; 364: 22-32Google Scholar Paradoxically, it is also conceivable that antibiotics may precipitate IBS by temporarily suppressing parts of the microbiome. Although more data are needed, a UK study found antibiotic use (adjusted odds ratio. 3.70; 95% confidence interval, 1.80–7.60) to be strongly related to the presence of IBS.27Mendall MA K.D. Antibiotic use, childhood affluence and irritable bowel syndrome.Eur J Gastroenterol Hepatol. 1998; 10: 59-62Google Scholar This is an exciting time as we begin to understand in detail the role of our own microbes in health and gut disease. With these initial applications of high-throughput technology in IBS, we are taking the first steps toward a future where a personalized read-out of the state of the gut microbial community may lead to individualized corrective action in the clinic via probiotics, prebiotics or antibiotics. The authors thank Timm Hamp for technical assistance with manuscript formatting and Sarah Williamson for creation of the figure. We thank Dr Lars Engstrand (Karolinska Institute, Stockholm), Dr Marjorie Walker (Imperial College, London) and Dr Curtis Huttenhower (Harvard School of Public Health, Boston) for helpful comments on the manuscript. Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel SyndromeGastroenterologyVol. 141Issue 5PreviewIrritable bowel syndrome (IBS) has been associated with disruptions to the intestinal microbiota, but studies have had limited power, coverage, and depth of analysis. We aimed to define microbial populations that can be used discriminate the fecal microbiota of patients with IBS from that of healthy subjects and correlate these with IBS intestinal symptom scores. Full-Text PDF Gastrointestinal Microbiome Signatures of Pediatric Patients With Irritable Bowel SyndromeGastroenterologyVol. 141Issue 5PreviewThe intestinal microbiomes of healthy children and pediatric patients with irritable bowel syndrome (IBS) are not well defined. Studies in adults have indicated that the gastrointestinal microbiota could be involved in IBS. Full-Text PDF