The irritable bowel syndrome (IBS) is a common,

Size: px

Start display at page:

Download "The irritable bowel syndrome (IBS) is a common,"

Rachel Mathews
5 years ago
Views:

1 faecal occult blood test in a colorectal cancer screening programme. Br J Cancer 2009;101: Levi Z, Rozen P, Hazazi R, et al. A quantitative immunochemical fecal occult blood test for colorectal neoplasia. Ann Intern Med 2007;146: Lansdorp-Vogelaar I, van Ballegooijen M, Zauber AG, et al. Effect of rising chemotherapy costs on the cost savings of colorectal cancer screening. J Natl Cancer Inst 2009;101: Parekh M, Fendrick AM, Ladabaum U. As tests evolve and costs of cancer care rise: reappraising stool-based screening for colorectal neoplasia. Aliment Pharmacol Ther 2008;27: Reprint requests Address requests for reprints to: Theodore R. Levin, MD, Associate Chief of Gastroenterology, Kaiser Permanente Medical Center, Walnut Creek, California Theodore.Levin@kp.org Conflicts of interest The author discloses no conflicts by the AGA Institute /$36.00 doi: /j.gastro Bugs, Stool, and the Irritable Bowel Syndrome: Too Much Is as Bad as Too Little? 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 Perhaps too much of everything is as bad as too little. Edna Ferber ( ) The irritable bowel syndrome (IBS) is a common, unexplained disorder, affecting 10% of Americans. 1,2 The syndrome has been identified around the world, affecting people in all nations studied. 1,2 IBS significantly impairs quality of life as manifested by poorer mental and physical function, work productivity, relationships, and sleep. 1,3 No currently available therapy cures IBS; at best therapies provide temporary, symptomatic relief. 4 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. 5 Despite the enormous personal and economic costs associated with IBS, 1,2 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). 1,6 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. 1,7 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. 1,8-10 Serum cytokines are increased in IBS; significantly higher baseline tumor necrosis factor-, interleukin (IL)-1, and IL-6 levels, for example, have been observed. 11 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), 11 although there is uncertainty surrounding the exact source of the cytokine elevations. 8 As many as one quarter of people develop IBS after postinfectious gastroenteritis. 1,12 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. 1,9 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. 13 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 highthroughput methods have found that different people tend to have very different taxa within their gut microbiomes and those differences are somewhat stable over time. 14,15 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 discrim- 1555

2 Figure 1. Intestinal bacteria and IBS. Different people have distinct gut microbiota; the hypothesis is that the differences set in motion an inflammatory cascade in those who are genetically predisposed and subject to a specific environmental hit. A new insult (eg, acute infectious gastroenteritis) may damage intestinal permeability, leading to a cascade of microbes upregulating mast cells through the Th2 pathway. Toll-like receptors (TLR) on mast cells may interact directly with relevant microbes. Mast cells accumulate in the lamina propria and release histamine (that interacts with H1-4 receptors), proteases (PAR1 receptor), and probably serotonin (5HT3 and 5HT4 receptors). Chemical signaling via receptors results in neural excitation and smooth muscle contraction, leading to abdominal pain, abnormal intestino-abdominal reflex responses (that combined with fermentation by gas-producing bacteria in the lumen triggers bloating), and disturbed intestinal transit (manifest as diarrhea or constipation, or both, depending on the balance of up- and down-regulatory responses). Cytokines and chemokines are released into the circulation inducing extra-intestinal symptoms. (Adapted from Walker MM, Warwick A, Ung C, Talley NJ. The role of eosinophils and mast cells in intestinal functional disease. Curr Gastroenterol Rep 2011;13: ) 1556

3 inate case from control in IBS (reviewed in Salonen et al 16 ). 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 pediatric 17 and adult 18 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. 18 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 al 17 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, 19 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. 20 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, 17 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, 18 although several taxa within Proteobacteria were correlated with IBS symptom scores. Likewise, in the pediatric study, 17 greater frequency of pain was associated with an increase in the genus Alistipes, but in the adult study, 18 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, 21 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, 22 as in many other areas of genomics. 23 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 1557

4 and possibly causally linked with IBS based on therapeutic trials 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. 24 Another review concluded that the best evidence of efficacy in IBS is with Bifidobacterium infantis 35,624 species, 25 and Rajilić-Stojanović et al observed a 1.5- fold decrease in Bifidobacteria in IBS. 18 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. 26 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, ) to be strongly related to the presence of IBS. 27 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 highthroughput 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. NICHOLAS J. TALLEY Department of Health University of Newcastle Callaghan, New South Wales, Australia and The Mayo Clinic and University of North Carolina and Karolinska Institute Stockholm, Sweden ANTHONY A. FODOR Bioinformatics and Genomics Department The University of North Carolina at Charlotte Charlotte, North Carolina References 1. Talley NJ, Spiller R. Irritable bowel syndrome: a little understood organic bowel disease? Lancet 2002;360: Rey E, Talley NJ. Irritable bowel syndrome: novel views on the epidemiology and potential risk factors. Dig Liver Dis 2009;41: Koloski NA, Talley NJ, Boyce PM. The impact of functional gastrointestinal disorders on quality of life. Am J Gastroenterol 2000; 95: Brandt LJ CW, Foxx-Orenstein AE, Schiller LR, et al. An evidencebased position statement on the management of irritable bowel syndrome. Am J Gastroenterol 2009;104:S Ford AC, Talley NJ, Veldhuyzen van Zanten SJO, 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: Villani 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: Choung RS, Locke GR III, Zinsmeister AR, 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: Ford A, Talley N. Mucosal inflammation as a potential etiological factor in irritable bowel syndrome: a systematic review. J Gastroenterol 2011;46: Walker M, Warwick A, Ung C, et al. The role of eosinophils and mast cells in intestinal functional disease. Curr Gastroenterol Rep 2011;13: Cremon 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: Liebregts T, Adam B, Bredack C, et al. Immune activation in patients with irritable bowel syndrome. Gastroenterology 2007; 132: Spiller R, Garsed K. Postinfectious irritable bowel syndrome. Gastroenterology 2009;136: Sekirov I, Finlay BB. Human and microbe: united we stand. Nat Med 2006;12: Turnbaugh PJ, Hamady M, Yatsunenko T, et al. A core gut microbiome in obese and lean twins. Nature 2009;457: Spencer MD, Hamp TJ, Reid RW, et al. Association between composition of the human gastrointestinal microbiome and development of fatty liver with choline deficiency. Gastroenterology 2011;140: Salonen A, de Vos WM, Palva A. Gastrointestinal microbiota in irritable bowel syndrome: present state and perspectives. Microbiology 2010;156: Saulnier D, Riehle K, Mistretta T, et al. Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome. Gastroenterology 2011;141: Rajilić-Stojanović M, Biagi E, Heilig HG, et al. Global and deep molecular analysis of microbiota signatures in fecal samples from patients with irritable bowel syndrome. Gastroenterology 2011; 141: Carroll IM, Ringel-Kulka T, Keku TO, 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]. 20. Adam B, Liebregts T, Gschossmann JM, et al. Severity of mucosal inflammation as a predictor for alterations of visceral sensory function in a rat model. Pain 2006;123: Leek JT, Scharpf RB, Bravo HC, et al. Tackling the widespread and critical impact of batch effects in high-throughput data. Nat Rev Genet 2010;11: Zhou J, Wu L, Deng Y, et al. Reproducibility and quantitation of amplicon sequencing-based detection. ISME J 2011;5: Boulesteix A-L. Over-optimism in bioinformatics research. Bioinformatics 2010;26: Moayyedi P, Ford AC, Talley NJ, et al. The efficacy of probiotics in the treatment of irritable bowel syndrome: a systematic review. Gut 2010;59: Brenner DM, Moeller MJ, Chey WD, et al. The utility of probiotics in the treatment of irritable bowel syndrome: a systematic review. Am J Gastroenterol 2009;104:

5 26. Pimentel M, Lembo A, Chey WD, et al. Rifaximin therapy for patients with Irritable Bowel Syndrome without constipation. N Engl J Med 2011;364: Mendall MA KD. Antibiotic use, childhood affluence and irritable bowel syndrome. Eur J Gastroenterol Hepatol 1998;10: Reprint requests Address requests for reprints to: Anthony A. Fodor, Bioinformatics and Genomics Department, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC, afodor@uncc.edu. Acknowledgments 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. Conflicts of Interest NJT has consulted for Salix. The remaining author discloses no conflicts by the AGA Institute /$36.00 doi: /j.gastro Editorials Molecular Gastronomy: How to Make the Critical Intestinal Foxp3 Treg Cell See Intestinal dendritic cells specialize to activate transforming growth factor- and induce Foxp3 regulatory T cells via integrin v 8, by Worthington JJ, Czajkowska BI, and Melton AC, et al, on page 1802; and Preferential expression of integrin v 8 promotes generation of regulatory T cells by mouse CD103 dendritic cells, by Paidassi H, Acharya M, Zhang A, et al on page The gastrointestinal tract is constantly exposed to food proteins, commensal bacteria, and occasionally pathogenic microorganisms. 1,2 Despite enormous bacterial challenge, the host intestine establishes a mutualistic relationship with the microbiota, with which it lives in harmony. Among the multiple mechanisms which have evolved to regulate this relationship, regulatory T (Treg) cells have been implicated as a dominant element, because mice with deficient Treg cells or deficient cytokines mediating Treg cell function develop chronic intestinal inflammation that can be suppressed by adoptively transferred Treg cells. 3 These Treg cells constitutively express high levels of the transcription factor Foxp3, which is critical for initiating and maintaining a genetic program for the differentiation and function of Treg cells. Foxp3 can be induced during thymic differentiation under the influence of relatively high avidity interactions of the T-cell receptor with self-antigens (termed natural Treg cells [ntreg]), or post-thymically in conventional mature T cells when they are activated in vitro or in vivo in the presence of transforming growth factor (TGF)- (termed induced Treg cells [itreg]). The specific local environment greatly influences itreg cell development, function, preservation of integrity, and trafficking. Peripheral tissues with such properties are uncommon, and the majority of Treg cells present in most sites are of thymic origin, and thus mostly ntreg. In contrast, the intestines contain local factors that preferentially promote itreg differentiation. This property balances the fact that the intestines are under conditions of chronic antigen exposure, which is crucial for the maintenance of intestinal homeostasis. Recent research has begun to clarify the cells and factors that drive differentiation and function of Foxp3 Treg cells in the intestines. Intestinal dendritic cells (DCs), which are located throughout the lamina propria (LP), have been shown to be crucial in the maintenance of intestinal immune homeostasis. 4 Several functional properties have recently been ascribed to murine intestinal DCs, including induction of gut-homing receptors (CCR9 and 4 7) on responding T cells and B cells, an enhanced ability to promote FoxP3 Treg cell development, and immunoglobulin (Ig)A-secreting B-cell differentiation. Based on the expression of the CD103 ( E integrin) and the chemokine receptor CX3CR1, intestinal DCs have been identified as 2 major populations. 5,6 CD11c high CD103 DCs share developmental origins with lymphoid tissue DCs and are derived from pre-dcs without a monocyte intermediate, whereas intestinal CD11c high CD103 CX3CR1 DCs develop from monocytes. CD103 DCs are dispersed throughout the LP and migrate from the LP to the mesenteric lymph nodes (MLNs) in a CCR7-dependent manner. CD103 DCs can induce 4 7 integrin and CCR9 expression on naive lymphocytes to establish gut tropism, as well as promote IgA class-switch recombination by intestinal B cells in a TGF- - and retinoic acid (RA)-dependent manner. They express the retinal-metabolizing enzyme genes aldh1a1 and aldh1a2, although it is not known whether CD103 DCs are an essential functional source of RA in vivo. 7,8 It has also been shown recently that CD103 DCs induce Foxp3 Treg cells, which has been linked to their ability to produce enhanced levels of RA 1559

The role of gut microbiome in IBS

The role of gut microbiome in IBS Chung Owyang, MD H. Marvin Pollard Professor of Internal Medicine Professor of Molecular and Integrative Physiology Chief, Division of Gastroenterology Director, Pollard