Gastroenterology
Volume 141, Issue 5 , Pages 1555-1559, November 2011

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

  • Anthony A. Fodor

      Affiliations

    • Corresponding Author InformationReprint 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, 28223

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

Bioinformatics and Genomics Department, The University of North Carolina at Charlotte, Charlotte, North Carolina

published online 26 September 2011.

Article Outline

 

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.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, 9, 10 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.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 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.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 discriminate case from control in IBS (reviewed in Salonen et al16). 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.

  • View full-size image.
  • 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;13:323–330.)

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 pediatric17 and adult18 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 al17 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 and possibly causally linked with IBS based on therapeutic trials.24, 25, 26, 27 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, 1.80–7.60) 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 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.

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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.

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References 

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 Conflicts of Interest NJT has consulted for Salix. The remaining author discloses no conflicts.

PII: S0016-5085(11)01254-6

doi:10.1053/j.gastro.2011.09.019

Refers to article:

  • Editorial Accompanies this Article Global and Deep Molecular Analysis of Microbiota Signatures in Fecal Samples From Patients With Irritable Bowel Syndrome , 08 August 2011

    Mirjana Rajilić–Stojanović, Elena Biagi, Hans G.H.J. Heilig, Kajsa Kajander, Riina A. Kekkonen, Sebastian Tims, Willem M. de Vos
    Gastroenterology November 2011 (Vol. 141, Issue 5, Pages 1792-1801)

  • Editorial Accompanies this ArticleAdditional Online Content Available Gastrointestinal Microbiome Signatures of Pediatric Patients With Irritable Bowel Syndrome , 11 July 2011

    Delphine M. Saulnier, Kevin Riehle, Toni–Ann Mistretta, Maria–Alejandra Diaz, Debasmita Mandal, Sabeen Raza, Erica M. Weidler, Xiang Qin, Cristian Coarfa, Aleksandar Milosavljevic, Joseph F. Petrosino, Sarah Highlander, Richard Gibbs, Susan V. Lynch, Robert J. Shulman, James Versalovic
    Gastroenterology November 2011 (Vol. 141, Issue 5, Pages 1782-1791)

Gastroenterology
Volume 141, Issue 5 , Pages 1555-1559, November 2011

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