Intestinal microbiota: its role in digestive diseases.

WGO REVIEW ARTICLE

Intestinal Microbiota Its Role in Digestive Diseases Luis M. Bustos Fernandez, MD,* Juan S. Lasa, MD,* and Fernando Man, MDw

Abstract: It is now well known that intestinal microbiota exerts not only several physiological functions, but has also been implied in the mechanisms of many conditions, both intestinal and extraintestinal. These advances, to the best of our knowledge, have been made possible by the development of new ways of studying gut flora. Metagenomics, the study of genetic material taken directly from environmental samples, avoiding individual culture, has become an excellent tool to study the human microbiota. Therefore, it has demonstrated an association between an altered intestinal microbiota and inflammatory bowel disease or irritable bowel syndrome, perhaps the most extensively studied conditions associated with this particular subject. However, microbiota has a potential role in the development of other diseases; their manifestations are not confined to the intestine only. In this article, an extensive updated review is conducted on the role intestinal microbiota has in health and in different diseases. Focus is made on the following conditions: inflammatory bowel disease, irritable bowel syndrome, celiac disease, hepatic encephalopathy, and obesity. Key Words: intestinal microbiota, metagenomics, intestinal diseases

(J Clin Gastroenterol 2014;48:657–666)

I

t is well known that the human body is inhabited by an outstandingly vast number of microorganisms including bacteria, archaea, and virus. These microorganisms constitute what is known as microbiota.1 Microorganisms develop through the entire gastrointestinal tract, but their number increase exponentially in the large intestine; the colon contains almost 70% of all the microbes that inhabit the human body.2 Microbial concentration increases aborally from 102 per gram of content in the stomach reaching to a peak of 1011 to 1012 in the cecum and represents a high proportion of the total luminal content, as seen in Table 1. A different composition can be observed according to genetics, diet, and geographical determinants.3 Metagenomics, the study of genetic material taken directly from environmental samples, avoiding individual culture, has provided an excellent tool to study the human microbiota.4 It is a comprehensive approach that gives sequence information from the collective genomes of the microbiota, which can in turn be used to identify the functional contributions and biological roles of intestinal microbiota in human health From the *Instituto Bustos Fernandez; and wGastro, Buenos Aires, Argentina. The authors declare that they have nothing to disclose. Reprints: Luis M. Bustos Fernandez, MD, Echeverria 2771, Zip Code: 1428, Buenos Aires, Argentina (e-mail: luisbustosfernandez@ gmail.com). Copyright r 2014 by Lippincott Williams & Wilkins

J Clin Gastroenterol

and disease. It involves shotgun sequencing, where reads of large cloned fragments isolated from total community DNA (a shotgun read is equivalent to the size of B1 gene) are stitched together into contigs (>1000 bp of contiguous sequence) that are then assembled into scaffolds that approximate whole genomes. According to biological taxonomy, the microbiota is classified following the traditional nomenclature (phylum-class-order-family-genus-species). In the human gut, bacterial predominance is represented by Firmicutes, Bacteroidetes, and Actinobacteria. These advances have shown that intestinal microbiota can be divided into 3 distinct clusters, also called “enterotypes.”5 The existence of these clusters is supported by both phylogenetic and functional analysis. The analysis of these enterotypes derives from a metagenomic study. Each enterotype has specific aspects of species and functional composition that were unique compared with the other 2. It is still unknown which factors determine the segregation of communities into these enterotypes. The majority of intestinal microbiota is composed of anaerobes and, although there have been several bacterial phyla described, 2 of them predominate: the Bacteroidetes and Firmicutes. It is noteworthy that microbial location along the gastrointestinal tract is heterogenous; however, there is also a wide variation in microbial composition when comparing different environments inside the intestine; evidence point toward a difference in bacterial predominance between the intestinal lumen and the mucus layer that separates the latter from the intestinal epithelium.6 Intestinal colonization begins at birth, and the passage through the birth canal constitutes the first contact between microbes and the sterile gut of newborns. Hence, the composition of the mother’s microbiota may have an influence in determining gut flora composition.7,8 In addition, as aforementioned, it has been suggested that host genetics may play a role in the natural selection of coexistent microorganisms.9 Diet can also affect intestinal microbiota, as shown in animal model studies showing the impact of western diet on microbial composition in murine intestine.10 Surprisingly, intestinal microbiota tends to remain unaltered at the phylum level.11 Modulation of the microbiota with Probiotics, Prebiotics, and Symbiotics has been an important tool for the treatment of several diseases. The World Gastroenterology Organisation (WGO) Global Guideline proposed the following definitions: Probiotics: Live microorganisms that confer a health benefit on the host when administered in adequate amounts. Prebiotic: Selectively fermented ingredients that result in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health.

Volume 48, Number 8, September 2014

www.jcge.com |

657


Bustos Fernandez et al


TABLE 1. Variations of Microbial Concentration and Composition Across the Length of the Gastrointestinal Tract

Gastrointestinal Tract Site

Bacterial Concentration (Cells/g)

Stomach Duodenum

10 103

Jejunum Ileum Colon

104 107 1012

Symbiotics: Products that contain both probiotics and prebiotics.

MICROBIOTA IN HEALTH Gut microbes exert a wide variety of physiological functions that have an influential role in intestinal and extraintestinal homeostasis. We will describe the most relevant of them. Table 2 shows a brief synopsis of these functions.

Immunologic Development and Protective Functions Most of the evidence surrounding this particular subject comes from animal model studies using germ-free (GF) mice. In these models, deficits in local and systemic lymphoid structures have been noticed; spleen and lymph nodes are poorly developed, as well as Peyer’s patches.12,13 There is a significant reduction in immunoglobulin secretion and irregularities on cytokine profiles. A notorious defect in GF mice is the lack of expansion of CD4 + T-cell population, which has been shown to be reversed by the exposure to polysaccharide A (PSA) of Bacteroides fragilis.14 GF mice exhibit systemic skewing toward Th2 cytokine profile, a phenotype that can be corrected by the administration of PSA. This evidence shows that bacterial compounds can be critical to promote host immune maturation, both locally and systemically. Peptidoglycan of gram-negative bacteria induces formation of isolated lymphoid follicles through NOD1 signaling, which would later turn into B-cell clusters.12 In contrast, intestinal microbiota seems to be crucial in the avoidance of excessive immune activation due to the mucosal exposure to different microorganisms, through the

TABLE 2. Intestinal Microbiota’s Physiological Functions Immunologic functions Promote host’s local and systemic immune maturation Shaping immune innate response (such as neutrophil activation) Activation of immune tolerance factors Physical barrier against incoming pathogens (competitive exclusion) Stimulation of antimicrobial peptides production (such as defensins) Metabolic functions Production of short-chain fatty acids Useful as colonocyte energy source Useful in prevention of accumulation of toxic compounds Nutrient metabolism Linoleic acid conjugation Dietary oxalates degradation

658 | www.jcge.com

Bacterial Composition Lactobacillus, Veillonella, Helicobacter Bacilli, Streptococcaceae, Actinobacteria, Actinomycinaeae, Corynebacteriaceae Lachnospiraceae, Bacteroidetes

Aerobes

Y

1

Anaerobes

activation of several immune tolerance factors.15,16 Failure in these mechanisms has been suggested as a potential pathophysiological feature in diverse conditions, as will be discussed later. Gut microbiota provides its host with a physical barrier to incoming pathogens by competitive exclusion and production of antibacterial substances. Various intestinal microbiota components have been shown to stimulate the production of antimicrobial peptides, such as defensins or cathedicilins.17,18 Not only microbes induce this production but also microbial metabolites [ie, short-chain fatty acids (SCFA) or lithocolic acid].19–21 The induction of antimicrobial peptides provides protection to the host from invading pathogens and the overgrowth of commensal flora. Overall, it is clear that the interaction between the host immune system and intestinal microbiota is by far a complicated and highly active condition.

Metabolic Functions According to the observation of caloric intake in GF mice, intestinal microbiota seems to maximize caloric availability of ingested nutrients. The mechanisms involved fall into 2 categories: extraction of additional calories from otherwise indigestible oligosaccharides, and promotion of nutrient uptake and utilization. Several bacteria have been related to the production of SCFA, such as butyrate. Production of these are not only relevant as an energy source (ie, for colonocytes), but are also useful to prevent the accumulation of toxic compounds, such as D-lactate.22–24 Gut microbiota has also been shown to regulate the activity of lipoprotein lipase,25 and to upregulate the expression of colipase.26 Clinical studies using quantitative polymerase chain reaction techniques have shown differences in gut microbial composition between obese and nonobese subjects, especially regarding Lactobacillus and Methanobrevibacter smithii.27 Intestinal microbiota also contributes to convert certain nutrients into metabolically active forms. For instance, Bifidobacterium strains conjugate dietary linoleic acid, which has a myriad of physiological effects.28 Oxalobacter formigenes has the ability to degrade dietary oxalates and reducing urinary oxalate excretion, thus preventing oxalate nephrolithiasis.29

MICROBIOTA IN DISEASE Microbiota has a potential role in the development of different diseases. Focus is made on the following conditions: inflammatory bowel disease (IBD), irritable bowel r

2014 Lippincott Williams & Wilkins



syndrome (IBS), celiac disease, hepatic encephalopathy, and obesity.

IBD It has been well established that some components of the microbiota are an essential requirement for full expression of IBD in animal models and in humans.24 The composition of the commensal microbiota of patients with ulcerative colitis (UC) and Crohn’s disease (CD) reflects, in part, the expected microbiota associated with a modern lifestyle in developed countries; however, whether there are additional changes that are specific to or have a causative relationship with these conditions is uncertain. The term “dysbiosis,” introduced many decades ago to highlight some form of microbial disturbance or imbalance, is vague and implies an understanding where none may exist. Neither its biological basis nor the normal microbial balance has been defined. The more consistently observed microbial alterations were linked to CD.24,30–39 Exploration of the microbiota in patients with IBD, though still at an early stage, has already generated interesting insights. Reduced biodiversity has been a particularly consistent but nonspecific observation. Impressive separation of patients with UC and CD by principal component analysis in a metagenomic survey has been reported, but this requires confirmation and was based on only 4 patients with CD.39 Compositional analyses have shown certain microorganisms, such as Faecalibacterium prausnitzii, to have anti-inflammatory properties,36 whereas other microorganisms may contribute to tissue injury because of mucolytic or proteolytic properties.40 In addition, some of the microbial alterations in the microbiota, such as the increases in mucosal-associated bacteria in CD and the increased rates of detection of Mycobacterium avium paratuberculosis and Clostridium difficile, appear to be either secondary to the inflammatory process or because of the defective innate immunity associated with this disorder.24,34 These organisms, however, may have a modifying influence on the clinical course or severity of the disease. In contrast with findings in patients with UC, many independent observations in patients with CD are consistent with reduced clearance of bacteria from the mucosa,41 a fact that has been associated with defective phagocytic-cell function and impaired acute inflammation with compensatory adaptive immunologic responses.42 A diversity of cellular and subcellular components of the commensal microbiota has the potential to engage with the host. These include microbial nucleic acids, secreted proteins, capsular polysaccharides and exopolysaccharides, and cell wall fragments, all of which may have immunomodulatory effects. Host-microbe exchanges occur over a large surface area (approximately 400 m2), with only a single layer of epithelial cells separating the internal milieu from the lumen. Epithelial and dendritic cells are the first to come into contact with the microbiota. Dendritic cells sample the lumen by extending intercellular dendrites across the epithelium and by encountering luminal material that has been transported by M cells overlying the lymphoid follicles. Pattern-recognition receptors such as Toll-like receptors (TLRs), NOD-like receptors (NLRs), and C-type lectins on/in the host cells recognize microorganism-associated molecular patterns on the surface of both commensals and pathogens. A dual-recognition system for commensals versus pathogens does not seem to exist, although 1 commensal, B. fragilis, has been shown to produce “a symbiosis r


Microbiota and Digestive Disease

factor” (PSA) that signals through TLRs directly on regulatory T cells to promote niche-specific mucosal immune tolerance.43 It has been proposed that the production of such symbiotic bacterial molecules may enable the host to discriminate between pathogens and commensals, but this remains to be demonstrated with other organisms. It is noteworthy that the PSA molecule has been reported to have an anti-inflammatory, preventive effect in an animal model of IBD.44 The commensal microbiota is also a rich source of ATP, which is an important immunomodulatory molecule that acts on specific sensors (P2X and P2Y) to generate intestinal T-helper 17 (Th17) cells.45 In susceptible individuals, Th17 cells participate in the pathogenesis of IBD.46 Other commensal-derived immunomodulatory molecules of relevance to IBD include SCFAs that are microbial end-products of the fermentation of dietary polysaccharides. SCFAs not only provide a nutrient source for distal colonocytes but also act on G-protein-coupled receptors (GPR43) and mediate a downregulatory effect on inflammatory responses.47 The production of SCFA such as acetate has also been reported to mediate the protective effect of Bifidobacteria against enteric infection with Escherichia coli.48 Although the microbiota shapes intestinal immunity in health and disease, host-microbe interactions in the gut are bidirectional. Thus, the mucosal immune system influences the composition and proinflammatory potential of the gut microbiota. Disturbances of innate immunity have been linked to aberrant expansion of some components of the microbiota and, in turn, may adversely influence the inflammatory response and risk of disease.49–51 More recently, a mechanism by which the colonic epithelium can sense and regulate the microbiota has been described. This is dependent on the NLRP6 inflammasome, the genetic deletion of which leads to a shift toward a proinflammatory microbiota.52 In summary, why the microbiota provides a protective effect for most individuals, and yet becomes a villain for some who get IBD, may depend on geneticmicrobial-environmental interactions and the timing of these exchanges in early life. Several probiotic preparations have been shown to have beneficial effects in the treatment of IBD, particularly the bacterial mixture VSL#3, the E. coli strain Nissle 1917, and several Lactobacillus species, although other formulations are also available. The bacterial mixture VSL#3 consists of Streptococcus thermophilus, the 4 lactobacilli species L. acidophiles, L. bulgaricus, L. casei, and L. plantarum, and the 3 bifidobaceria species B. breve, B. infantis, and B. longum. Of these, L. casei has been identified as the beneficial strain.53 The E. coli strain Nissle 1917 has been shown to improve intestinal homeostasis.54 In vitro, the E. coli strain Nissle 1917 was shown to prevent the invasion of intestinal epithelia cells by Salmonella dublin, Yersinia enterocolitica, Shigella flexneri, Legionella pneumophila, and Listeria monocytogenes by minimizing the bacteria-induced reduction of the intestinal barrier.55 E. coli strain Nissle 1917 can counter the apoptotic properties of pathogenic bacteria through a secreted soluble factor by a poorly understood, heat shock protein induction-dependent mechanism. The results of probiotic treatment are less promising in CD, with L. rhamnosus GG, L. johnsonii LA1, and Synbiotic2000 (a cocktail of the 4 probiotic lactic acid bacteria: Pediococcus pentosaceus, L. raffinolactis, L. paracasei subsp. paracasei, and L. plantarum, and the 4 prebiotic fermentable fibers : b-glucans, inulin, pectin, and resistant starch) as all were unable to improve symptoms of CD.56 www.jcge.com |

659


However, Saccharomyces boulardii have shown some promise toward improving, but not normalizing, the leaky gut in CD patients.57,58

Pouchitis Proctocolectomy with ileal pouch-anal anastomosis may be required in some UC patients because their disease was medically intractable or they developed secondary dysplasia or cancer. Pouchitis or inflammation of the ileal reservoir created during the procedure may develop between 15% and 50% of patients. It is the most common complication of the surgery, and although the exact etiology is not clear host genetic factors, local pouch issues and the microbiota contained within the pouch are thought to be involved.59,60 Most patients will develop this problem in the first year and antibiotics can be an effective form of therapy in many; however, for those who do not respond, the term antibiotic-resistant is applied and these patients can be chronically active requiring other forms of therapy.60 For some, antibiotics improve the pouchitis, but there is a relapsing course of the pouchitis following the discontinuation of antibiotics. As antibiotics can provide relief for most with pouchitis, a basic assumption has been the importance of the microbiota of the pouch in the development and chronicity of pouchitis. Thus, alteration of the microbiota by addition of probiotics was considered. Subsequently, probiotics for treatment of acute pouchitis, prevention of initial onset of pouchitis, and prevention of relapsing pouchitis have all been evaluated. Kuisma et al61 recruited 20 patients (10 subjects enrolled in the intervention arm) for a trial of L. rhamnosus GG (2 1010 CFU/d) for 3 months. Those patients with chronic, active pouchitis were excluded. The Pouchitis Disease Activity Index62 was utilized for evaluation of clinical effect. In an open-label trial of 51 UC patients, post-ileal pouch-anal anastomosis was performed using a fermented milk product with a blend of probiotic strains (L. acidophilus strain La5 + B. lactis strain Bb12) containing 5 1010 CFU/d.58 However, there was a reported improvement in endoscopic evaluation. In another open-label trial, 23 consecutive patients with mild pouchitis as defined using Pouchitis Disease Activity Index (scores 7 to 12) were treated with 3.6 1012 CFU/d of VSL#3TM for 4 weeks.63 Of 23 patients with mild pouchitis, 16 were in remission after treatment and the median total Pouchitis Disease Activity Index scores reported before therapy improved after therapy. Thus, there is limited evidence for a role of probiotics as monotherapy for mild/moderate pouchitis at the present time. Limiting access of microbiota to the mucosa of the pouch and subsequent development of inflammation may be a key mechanism whereby probiotics provide benefit. Alternatively, changing the composition of the pouch microbiota may be important; although it is interesting that no long-term colonization of probiotic strains is achieved.64

IBS Irritable bowel syndrome (IBS is a highly prevalent disease affecting 10% to 20% of western countries population and accounting for high expenses for medical treatment and loss of work days.65 The proposed mechanisms leading to IBS symptoms include alteration of bowel transit, abnormal rectal

660 | www.jcge.com



evacuation, presence of intraluminal irritants (undigested carbohydrates producing SCFA), excess of biliary acids, gluten intolerance, abnormal susceptibility to inflammation, chronic minimal inflammation, and alteration in the brain-gut axis. More recently, the gut microbiota has gained attention in the pathophysiology of IBS.66 The changes in human gut microbiota have gained recent interest. Qualitative and quantitative changes have been implicated. The occurrence of small intestinal bacterial overgrowth (SIBO) can explain the physiopathology of symptoms in IBS. The studies conducted by Mark Pimentel et al67 using hydrogen-breath tests to measure bacterial hydrogen production attracted scientists’ attention toward microbiota. Although the breath test has been criticized to lack of specificity, culture studies by Pyleris et al68 have proved the relationship between SIBO and IBS. Strictly designed case-controlled studies demonstrated that IBS patients have a higher probability of a positive breath test [odds ratio (OR) = 9.64; 95% confidence interval (CI), 4.26-21.82)].69 The lack of a gold standard to define SIBO70 has created many problems because culture, which is theoretically the best study, is difficult to perform. Jejunal flora is not representative because, by definition, SIBO is the passage of cecal flora to the terminal ileum through a “leaky” ileocecal valve or the rise of cecal pressure because of high of SCFAs fermentation. The cutoff figure of 105 to define SIBO was coined from studies in the 1960s taking Billroth II patients. All the subsequent studies on healthy subjects suggest that the duodenum and proximal ileum almost never have >102 CFU/mL. Using medical convention this should be the definition of SIBO.71 In a recent study by Shah et al,72 the culture of jejunal flora demonstrated that the cutoff value for SIBO was 102 CFU/mL. Comparing IBS patients versus controls, 57% of IBS-D had SIBO versus 30% among those without diarrhea. Considering the risk factors for SIBO, multivariate analysis showed that proton pump inhibitors use was irrelevant. The presence of IBS was the only determinant factor for SIBO (OR = 4.93; 95% CI, 2.46-9.88, P < 0.0001). It must be considered that this result only applies to a subset of IBS patients. The gut microbiota participates in the development and maintenance of gut sensory and motor functions, including propulsive activity. Conversely, the intestinal motility through its sweeping action constitutes one of the major control systems of the microbiota. An alteration in this interplay could explain the pathogenesis of IBS.73 Changes in the composition of gut microflora have also been implicated. A decrease in Bifidobacteria and Lactobacilum and an increase in Firmicutes concentration have been mentioned. An increase in the ratio of Firmicutes to Bacteroidetes has been reported to be associated with longer colonic transit in IBS. Direct evidence for qualitative or quantitative changes in the microbiota has been sought in 2 locations: the colon and the small intestine. Culturebased approaches have suggested the presence of qualitative changes in the colonic flora in IBS, with a relative decrease in the population of Bifidobacteria being the most consistent observation. Nevertheless, studies using a variety of molecular methods have, indeed, confirmed that IBS patients, regardless of subtype, do exhibit a fecal flora that is different from control subjects.74 However, many IBS patients avoid spontaneously dairy products from their diet and this could lead to a biased conclusion. r




The precise nature of these differences, the primacy of these changes in IBS, and their potential to disturb luminal metabolic pathways (be it bile salt deconjugation or carbohydrate fermentation), mucosal responses, or myoneural function in the gut wall, or induce local or systemic immune responses, remain to be defined. A strong piece of evidence supporting a role for changes in microbiota in IBS arises from the use of antibiotics in SIBO. Two well-designed randomized controlled trials (RCT), TARGET 1 and 2,75 have recently demonstrated the benefit of rifaximin, a poorly absorbed antibiotic given 550 mg tid for 2 weeks, in the relief of bloating, abdominal pain, and consistence of feces. The effect was still present 10 weeks later after finishing the treatment. Even though the number necessary to treat was 11, the number necessary to harm was >700, suggesting that rifaximin is indeed a good choice for a situation in which treatment options are scarce.76 There is also experience with retreatment with rifaximin without any major side effects reported.77 In the last few years, attention has driven to the development of IBS symptoms in patients who suffered a recent past gastrointestinal infection, mostly bacterial, the so-called postinfectious-IBS (PI-IBS), highlighting the link between these apparent unconnected diseases. The duration of symptoms is shorter and less intense than in noninfectious IBS. PI-IBS provided the first hint of an association between a persistent low-grade inflammatory response and this common disorder,78 a concept that has subsequently been extended to IBS in general.79 The assessment of circulating anti-flagellin antibodies80 found increased levels of defensin-2 in stool,81 and the upregulation of TLR4 in the colonic mucosa82 in IBS may relate to interactions with the microbiota. These inflammatory responses have been identified in the gut mucosa and/or the systemic circulation. The pathophysiological sequence might be as follows: Altered microbiota-Immune mucosal responseEnhanced permeability-Activation of nociceptive pathways-Alteration of brain gut axis.

PI-IBS Among 7% to 31% of patients with history of recent gastrointestinal bacterial (mainly Salmonella, Campylobacter, or Shigella) or rarely, viral infection will develop PIIBS or dyspepsia. The risk factors include prolonged duration of initial infection, female sex, use of antibiotics, smoking habit, toxicity of the bacterial strain, and anxiety/ depression. A recent meta-analysis pooling 18 studies indicated a relative increased risk of developing IBS 1 year after bacterial gastroenteritis (RR = 6.5; 95% CI, 2.6-15.4), an effect still apparent at 36 months (RR = 3.9; 95% CI, 3.0-5.0).83

Microbiota and IBS Constipation Type (IBS-C) Incomplete sugar digestion can also produce methane due to bacterial metabolism in patients with IBS-C. Kunkel et al84 reported in a meta-analysis a positive relationship between methane production and IBS-C; 1277 subjects were examined by breath testing (N = 319 methane producers and N = 958 methane nonproducers). Pooling all studies, a significant association was found between methane on breath test and constipation (OR = 3.51; 95% CI, 2.00-6.16). Among adults only, methane excretion was significantly associated with constipation (OR = 3.47; 95% r



CI, 1.84-6.54). As shown by Kim et al,85 the responsible strain in these patients was the M. smithii. The combination of rifaximin plus neomycin proved to be effective in these cases.

Diet, Microbiota, and IBS Food can play an important modulating role in gut microbiota, even more than genetics. According to van Hycklama Vlieg et al,86 the shaping effect of food is responsible for 60% of gut microbiota variability and genetics only 10%. Metagenomics sequencing analysis reveals an extensive assemblage of microbiota for the digestion of diverse food components, especially complex sugars. These carbohydrates represent the energy source for the host and microbiota. In contrast, the anaerobic digestion of carbohydrates can produce some toxic metabolic products such as alcohols, acids, and ketones, which might account for extraintestinal symptoms such as headache.87 A reduction in fermentable food, that is, fiber or FODMAPs (Fermentable oligo-di-mono-saccharides and polyols), has been advocated in the treatment of IBS, bearing in mind that these foods may promote higher levels of fermentation in the gut lumen due to incomplete digestion. FODMAPs include fruits with more fructose than glucose: apples, pears, and watermelon; fructan-containing vegetables: onion, leeks, asparagus, and artichokes; wheatbased products; sorbitol, lactose-containing foods, and raffinose-containing foods: legumes, soya beans, lentils, cabbages, broccoli, and cauliflower. These exclusion diets have proved some benefits, but further studies are needed.88

Probiotics and Microbiota Since long ago, probiotics have been advocated as possible modulators of gut microbiota. The great amount of studies published is very heterogenous, including different types of patients, many uncontrolled, and using different strains, which makes it difficult to draw a single conclusion upon this subject. At present, it is still unknown which organisms are most effective, bearing in mind that some mainly reduce bloating and flatulence, whereas others improve bowel frequency or ameliorate global symptom scores. Brenner et al,89 in an elegant systematic review, retrieved 4648 articles. Among 21 probiotic studies that met inclusion criteria, 16 were RCTs in adults with IBS defined by Rome II or Manning criteria. Primary outcome was improvement of IBS symptoms and/or decrease in frequency of adverse events reported. They concluded that B. infantis 35624 demonstrated efficacy in 2 well-designed RCTs. No other probiotic showed significant improvement of symptoms. Microbiota has undoubtedly a great responsibility in IBS pathophysiology, although no uniform pattern has been described. Also no biomarker has been described to help diagnosis. Different alterations may account for different types of IBS. Nonabsorbable antibiotics and probiotics have proved some efficacy in subsets of IBS patients. Future well-designed RCTs are needed to improve our knowledge in such a vast issue.

Celiac Disease Celiac disease [or celiac sprue (CS)] is a chronic inflammatory disorder of the small intestine caused by the lack of oral tolerance to wheat-gluten proteins (eg, gliadins) and other related prolamins in genetically predisposed www.jcge.com |

661


individuals. The abnormal intestinal immune response to gluten peptides is a key feature of this pathology, involving both adaptive and innate immunity. In CS patients, some gliadin peptides activate Th1 and Th17 inflammatory responses of adaptive immunity with the production of inflammatory cytokines (eg, INF-g, TNF-a, IL-21) within the mucosa, causing severe inflammation.90 Gliadin peptides also activate the zonulin pathway, leading to cytoskeleton reorganization, tight-junction opening, and an increase in intestinal permeability.91 Intestinal tissue lesion of active CS patients is characterized by flattening of the villi, crypt hyperplasia, and intraepithelial lymphocytosis. This leads to the typical manifestation of CS, characterized by malabsorption syndrome with chronic diarrhea, weight loss, abdominal distension, and impaired growth. Environmental factors, such as milk-feeding type, duration of breast-feeding, and gastrointestinal infections, have also been suggested to play a role in the risk and timing CS onset.92–94 These factors are known to influence the composition of the gut microbiota and could thereby modify its role in the proper development of the immune system and oral tolerance. Furthermore, several studies have consistently shown that intestinal dysbiosis is associated with CS.95 Studies investigating the composition of the intestinal microbiota in CS patients and control subjects have been primarily conducted to identify associations between specific microbial groups and this disorder. The microbiota of feces and duodenal biopsies from CS children (untreated or treated with a gluten-free diet) were compared with those of healthy controls in the Spanish pediatric population, using different molecular techniques.96–99 A comparative analysis of the duodenal-associated microbiota of CS patients and controls was carried out by fluorescent in situ hybridization coupled with flow cytometry.100 This study showed that the ratio of harmless (Lactobacillus-Bifidobacterium) to potentially harmful bacteria (Bacteroides/Prevotella-E. coli) was significantly inferior in CS patients than in controls, regardless of whether CS was active or inactive.101 Alterations in the composition of fecal SCFA generated from microbial fermentation have also been reported in CS patients and first-degree relatives. Feces of CS patients showed increased levels of total SCFA and acetic, valeric, and butyric acids compared with those of healthy controls.101 SIBO is also known to affect most CS patients with persistence of gastrointestinal symptoms after gluten withdrawal. This has been investigated as a cause of nonresponsive CS and, for example, plate-counting analyses of intestinal aspirates indicated that both symptomatic treated or untreated CS were affected by bacterial overgrowth.102 The associations between intestinal dysbiosis and CS have encouraged studies of possible links between the microbiota and CS pathogenesis. The mucous layer that covers epithelial cells prevents direct contact between enteric pathogens and epithelial cell surfaces and contains binding sites for indigenous commensal microbes.103 The possible role of TLRs in CS has also been evaluated in recent studies. Szebeni et al104 reported that TLR2 and TLR4 mRNA expression and protein levels were higher in the duodenal mucosa of children with treated CS and untreated CS, compared with controls. Another study reported an increase of TLR4-positive cells in the duodenal mucosa of active CS patients in comparison with controls, although the differences in expression of TLR4mRNA were

662 | www.jcge.com



not significant. In contrast, differences in TLR2-positive cells between CS patients and controls were not significant, whereas the expression of TLR2 mRNA was significantly lower in CS mucosal samples than in control samples.105 Therefore, gluten peptides and harmful microbes could interact with common molecular targets of innate immune system and activate similar pathogenic pathways, damaging the intestinal mucosal barrier and favoring inflammation and, therefore, could probably influence CS expression. The association of CS with intestinal dysbiosis and the evidence supporting a role for the microbiota and specific bacteria in regulating key aspects of innate and acquired immunity106 have led to the evaluation of possible benefits of potentially probiotic strains in this disorder. Strains of the Bifidobacterium genus B. longum CECT 7347 (IATAES1) and B. bifidum CECT 7365 (IATA-ES2) have been shown to offer protection against the inflammatory response and mucosal damage caused by gliadin peptides in vitro and in intestinal loops of GF rats.107 Another research group reported that a strain of B. lactis, but not L. fermentum, inhibited the gliadin-induced increase of epithelial permeability in vitro, modified the ZO-1 expression pattern, and inhibited membrane ruffle formation induced by gliadins on Caco-2 cells.108 Although intervention studies with potential probiotic strains in humans are necessary to prove that specific strains could play protective roles in CS, so far in vitro and in situ animal studies support this notion, thus it deserves further in vivo investigations. Several studies consistently prove that intestinal dysbiosis is associated with this disorder. This evidence has also encouraged investigation into the potential roles played by specific bacteria in this disorder, indicating that such influence could be relevant to the disease and thus help redefine how it is investigated.

Hepatic Encelophalopathy Evidence point toward a major role intestinal microbiota may have on the development of systemic complications related to cirrhosis. Studies on cirrhotic rats have shown that the administration of insulin-like growth factor (IGF-I), responsible for gut barrier maintenance, is able to limit the development of liver cirrhosis by enhancing intestinal barrier function and reducing levels of bacterial translocation.109 Fecal flora analysis of cirrhosis patients revealed reduced levels of Bifidobacteria.110 According to the experience by Liu and colleagues, where subjects with minimal hepatic encephalopathy were randomized to receive either a synbiotic, a prebiotic, or placebo, minimal hepatic encephalopathy was reversed in 50% of patients who received the synbiotic and in some who received the prebiotic alone. This was accompanied by a significant increase in nonurease-producing lactobacilli.111 Oral antibiotics such as neomycin, paromomycin, vancomycin, and metronidazole have been effectively used to reduce ammonia-producing enteric bacteria112; however, these alternatives are not recommended for long-term use due to their side effects. Rifaximin seems to be a promising option due to its proved effectiveness and safety profile.113 Question arises on the consequences that chronic administration of a nonabsorbable antibiotic could have on the induction of microbial resistance. Nevertheless, the clinical utility of antibiotics and probiotics in hepatic encephalopathy shows that intestinal microbiota is deeply involved in its genesis. r




Obesity As pointed out elsewhere, intestinal microbiota has an important metabolic function that can exert a crucial influence on the development of metabolic disorders such as obesity. Analysis of >5000 16S rRNA sequences revealed that genetically obese mice (ob/ob, characterized by a mutation in the leptin gene) had a 50% reduction in the abundance of Bacteroidetes, and a correspondent increase in the proportion of Firmicutes, compared with lean (ob/ + and &Ob + /Ob + ) mice.114 Comparisons of obese and lean distal gut microbiotas from mice and humans indicate that the community structures are very similar at the division level.9 Microbiota profiling in humans indicates that the Bacteroidetes-to-Firmicutes ratio in obese individuals puts on a “lean” diet increase toward that which is expected in a “lean” individual. As over 90% of phylogenetic types (phylo-types) present in the gut microbiota belong to the Firmicutes and the Bacteroidetes divisions, the marked shift in microbiota composition seen in obese individuals indicates that substantial changes are being made to the functional gut ecosystem. Indeed, characterization of the gut microbiome of obese mice (ob/ob) and their lean (ob/ + and &Ob + / Ob + ) littermates showed that compared with the “lean” microbiome, the obesity-associated microbiome harbors a substantial increase in genes encoding enzymes involved in the breakdown of dietary polysaccharides.115 In agreement with this, a significantly lower amount of energy remained in the feces of obese mice, relative to their lean counterparts, highlighting the increased capacity of the obese microbiome for energy extraction from the diet. Backhed et al25 found that the mice raised in the absence of microorganisms (GF) had about 40% less total body fat than mice with a normal gut microbiota, even though the latter ate 30% less diet than did the GF mice. To get more insight into those findings, the authors conducted a key experiment: they conventionalized GF mice with a normal gut microbiota harvested from the cecum of a “normal” mouse, and found that this conventionalization produced a 60% increase in body fat content and insulin resistance within 2 weeks, despite a significant lower food intake. The mechanisms of the apparent weight gain implied an increase in the intestinal glucose absorption, energy extraction from nondigestible food component, and concomitant higher glycemia and insulinemia, 2 key metabolic factors regulating lipogenesis. Ridaura et al116 transplanted fecal microbiota from adult female twin pairs discordant for obesity into GF mice fed with low-fat mouse chow, as well as different levels of saturated fat; they found out that increased total body and fat mass were transmissible with uncultured fecal communities and with their corresponding fecal bacterial culture collections. Moreover, cohousing mice with an obese twin’s microbiota with mice containing the lean co-twin’s microbiota prevented the development of increased body mass and metabolic phenotypes in Ob cage mates. This very interesting study highlights the influence that intestinal microbiota may exert on the development of obesity.

CONCLUSIONS As it has been reviewed, an increasing amount of evidence shows the relevance intestinal microbiota has in the development of several diseases. However, we are still r



far from understanding the complete nexus between the microorganisms that inhabit human intestine and their relationship with normal intestinal function and the aforementioned conditions. Future work will be crucial to the understanding of this relationship and its therapeutic relevance. REFERENCES 1. Kunz C, Kuntz S, Rudloff S. Intestinal flora. Adv Exp Med Biol. 2009;639:67–79. 2. Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA. 1998;95:6578–6583. 3. Simren M, Barbara G, Flint HJ, et al. Intestinal microbiota in functional bowel disorders: a Rome Foundation Report. Gut. 2013;62:159–176. 4. Frank DN, Pace NR. Gastrointestinal microbiology enters the metagenomics era. Curr Opin Gastroenterol. 2008;24:4–10. 5. Arumugam M, Raes J, Pelletier E, et al. Enterotypes of the human gut microbiome. Nature. 2011;473:174–180. 6. Swidsinski A, Loening-Baucke V, Lochs H, et al. Spatial organization of bacterial flora in normal and inflamed intestine: a fluorescence in situ hybridization study in mice. World J Gastroenterol. 2005;11:1131–1140. 7. Huurre A, Kalliomaki M, Rautava S, et al. Mode of delivery: effects on gut microbiota and humoral immunity. Neonatology. 2008;93:236–240. 8. Mandar R, Mikelsaar M. Transmission of mother’s microflora to the newborn at birth. Biol Neonate. 1996;69:30–35. 9. Ley RE, Backhed F, Turnbaugh P, et al. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA. 2005;102: 11070–11075. 10. Turnbaugh PJ, Backhed F, Fulton L, et al. Diet-induced obesity is linked to marked but reversible alterations in the mouse distal gut microbiome. Cell Host Microbe. 2008;3:213–223. 11. Gill SR, Pop M, Deboy RT, et al. Metagenomic analysis of the human distal gut microbiome. Science. 2006;312:1355–1359. 12. Bouskra D, Brezillon C, Berard M, et al. Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis. Nature. 2008;456:507–510. 13. Macpherson AJ, Harris NL. Interactions between commensal intestinal bacteria and the immune system. Nat Rev Immunol. 2004;4:478–485. 14. Mazmanian SK, Liu CH, Tzianabos AO, et al. An immunomodulatory molecule of symbiotic bacteria directs maturation of the host immune system. Cell. 2005;122:107–118. 15. Lee J, Mo JH, Katakura K, et al. Maintenance of colonic homeostasis by distinctive apical TLR9 signalling in intestinal epithelial cells. Nat Cell Biol. 2006;8:1327–1336. 16. Zeuthen LH, Fink LN, Frokiaer H. Epithelial cells prime the immune response to an array of gut-derived commensals towards a tolerogenic phenotype through distinct actions of thymic stromal lymphopoietin and transforming growth factor-beta. Immunology. 2008;123:197–208. 17. Hooper LV. Do symbiotic bacteria subvert host immunity? Nat Rev Microbiol. 2009;7:367–374. 18. Salzman NH, Underwood MA, Bevins CL. Paneth cells, defensins, and the commensal microbiota: a hypothesis on intimate interplay at the intestinal mucosa. Semin Immunol. 2007;19:70–83. 19. Kida Y, Shimizu T, Kuwano K. Sodium butyrate up-regulates cathelicidin gene expression via activator protein-1 and histone acetylation at the promoter region in a human lung epithelial cell line, EBC-1. Mol Immunol. 2006;43:1972–1981. 20. Termen S, Tollin M, Rodriguez E, et al. PU1 and bacterial metabolites regulate the human gene CAMP encoding antimicrobial peptide LL-37 in colon epithelial cells. Mol Immunol. 2008;45:3947–3955. 21. Schauber J, Svanholm C, Termen S, et al. Expression of the cathelicidin LL-37 is modulated by short chain fatty acids in

www.jcge.com |

663


22.

23. 24. 25.

26.

27.

28.

29.

30.

31.

32.

33.

34.

35.

36.

37.

38.

39.

40.

41.

colonocytes: relevance of signaling pathways. Gut. 2003;52: 735–741. Duncan SH, Louis P, Flint HJ. Lactate-utilizing bacteria, isolated from human feces, that produce butyrate as a major fermentation product. Appl Environ Microbiol. 2004;70: 5810–5817. Macfarlane S, Macfarlane GT. Regulation of short-chain fatty acid production. Proc Nutr Soc. 2003;62:67–72. Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology. 2008;134:577–594. Backhed F, Ding H, Wang T, et al. The gut microbiota as an environmental factor that regulates fat storage. Proc Natl Acad Sci USA. 2004;101:15718–15723. Hooper LV, Wong MH, Thelin A, et al. Molecular analysis of commensal host-microbial relationships in the intestine. Science. 2001;291:881–884. Scanlan PD, Shanahan F, Marchesi JR. Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis. BMC Microbiol. 2008;8:79. Oh DK, Hong GH, Lee Y, et al. Production of conjugated linoleic acid by isolate Bifidobacterium strains. World J Microbiol Biotechnol. 2003;19:907–912. Sidhu H, Allison MJ, Chow JM, et al. Rapid reversal of hyperoxaluria in a rat model after probiotic administration of Oxalobacter formigenes. J Urol. 2001;166:1487–1491. Sartor RB. Genetics and environmental interactions shape the intestinal microbiome to promote inflammatory bowel disease versus mucosal homeostasis. Gastroenterology. 2010;139: 1816–1833. Swidsinski A, Ladhoff A, Pernthaler A, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology. 2002;122: 44–54. Abubakar I, Myhill D, Aliyu SH, et al. Detection of Mycobacterium avium subspecies paratuberculosis from patients with Crohn’s disease using nucleic acid-based techniques: a systematic review and meta-analysis. Inflamm Bowel Dis. 2008;14:401–410. Darfeuille-Michaud A, Boudeau J, Bulois P, et al. High prevalence of adherent-invasive Escherichia coli associated with ileal mucosa in Crohn’s disease. Gastroenterology. 2004;127:412–421. Clayton EM, Rea MC, Shanahan F, et al. The vexed relationship between Clostridium difficile and inflammatory bowel disease: an assessment of carriage in an outpatient setting among patients in remission. Am J Gastroenterol. 2009;104:1162–1169. Peterson DA, Frank DN, Pace NR, et al. Metagenomic approaches for defining the pathogenesis of inflammatory bowel diseases. Cell Host Microbe. 2008;3:417–427. Sokol H, Pigneur B, Watterlot L, et al. Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn’s disease patients. Proc Natl Acad Sci USA. 2008;105:16731–16736. Schwiertz A, Jacobi M, Frick J-S, et al. Microbiota in pediatric inflammatory bowel disease. J Pediatr. 2010; 157:240–244. Frank DN, St Amand AL, Feldman RA, et al. Molecularphylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci USA. 2007;104:13780–13785. Qin J, Li R, Raes J, et al. A human gut microbial gene catalogue established by metagenomic sequencing. Nature. 2010;464:59–65. Pruteanu M, Hyland NP, Clarke DJ, et al. Degradation of the extracellular matrix components by bacterial-derived metalloproteases: implications for inflammatory bowel diseases. Inflamm Bowel Dis. 2011;17:1189–1200. Knight P, Campbell BJ, Rhodes JM. Host-bacteria interaction in inflammatory bowel disease. Br Med Bull. 2008; 88:95–113.

664 | www.jcge.com



42. Sewell GW, Marks DJB, Segal AW. The immunopathogenesis of Crohn’s disease: a three-stage model. Curr Opin Immunol. 2009;21:506–513. 43. Round JL, Lee SM, Li J, et al. The Toll-like receptor 2 pathway establishes colonization by a commensal of the human microbiota. Science. 2011;332:974–977. 44. Mazmanian SK, Round JL, Kasper DL. A microbial symbiosis factor prevents intestinal inflammatory disease. Nature. 2008;453:620–625. 45. Atarashi K, Nishimura J, Shima T, et al. ATP drives lamina propria TH17 cell differentiation. Nature. 2008;455:808–812. 46. MacDonald TT, Monteleone I, Fantini MC, et al. Regulation of homeostasis and inflammation in the intestine. Gastroenterology. 2011;140:1768–1775. 47. Maslowski KM, Vieira AT, Ng A, et al. Regulation of immunomodulatory responses by gut microbiota and chemoattractant receptor GPR43. Nature. 2009;461:1282–1286. 48. Fukuda S, Toh H, Hase K, et al. Bifidobacteria can protect from enteropathogenic infection through production of acetate. Nature. 2011;469:543–547. 49. Suzuki K, Meek B, Doi Y, et al. Aberrant expansion of segmented filamentous bacteria in IgA-deficient gut. Proc Natl Acad Sci USA. 2004;101:1981–1986. 50. Wen L, Ley RE, Volchkov PV, et al. Innate immunity and intestinal microbiota in the development of type 1 diabetes. Nature. 2008;455:1109–1113. 51. Vijay-Kumar M, Aitken JD, Carvalho FA, et al. Metabolic syndrome and altered gut microbiota in mice lacking Toll-like receptor 5. Science. 2010;328:228–231. 52. Elinav E, Strowig T, Kau AL, et al. NLRP6 inflammasome regulates colonic microbial ecology and risk for colitis. Cell. 2011;145:1–13. 53. von Schillde MA, Ho¨rmannsperger G, Weiher M, et al. Lactocepin secreted by Lactobacillus exerts anti-inflammatory effects by selectively degrading proinflammatory chemokines. Cell Host Microbe. 2012;11:387–396. 54. Petersen AM, Schjørring S, Gerstrøm SC, et al. Treatment of inflammatory bowel disease associated E. coli with ciprofloxacin and E. coli Nissle in the streptomycin-treated mouse intestine. PLoS One. 2011;6:e22823. 55. Altenhoefer A, Oswald S, Sonnenborn U, et al. The probiotic Escherichia coli strain Nissle 1917 interferes with invasion of human intestinal epithelial cells by different enteroinvasive bacterial pathogens. FEMS Immunol Med Microbiol. 2004;40:223–229. 56. Scaldaferri F, Gerardi V, Lopetuso LR, et al. Gut microbial flora, prebiotics, and probiotics in IBD: their current usage and utility. Biomed Res Int. 2013;2013:435268. 57. Reiff C, Kelly D. Inflammatory bowel disease, gut bacteria and probiotic therapy. Int J Med Microbiol. 2010;300: 25–33. 58. Hormannsperger G, Haller D. Molecular crosstalk of probiotic bacteria with the intestinal immune system: clinical relevance in the context of inflammatory bowel disease. Int J Med Microbiol. 2010;300:63–73. 59. Elahi B, Nikfar S, Derakhshani S, et al. On the benefit of probiotics in the management of pouchitis in patients underwent ileal pouch anal anastomosis: a meta-analysis of controlled clinical trials. Dig Dis Sci. 2008;53:1278–1284. 60. Pardi DS, D’Haens G, Shen B, et al. Clinical guidelines for the management of pouchitis. Inflamm Bowel Dis. 2009;15: 1424–1431. 61. Kuisma J, Mentula S, Jarvinen H, et al. Effect of Lactobacillus rhamnosus GG on ileal pouch inflammation and microbial flora. Aliment Pharmacol Ther. 2003;17:509–515. 62. Laake KO, Bjorneklett A, Aamodt G, et al. Outcome of four weeks’ intervention with probiotics on symptoms and endoscopic appearance after surgical reconstruction with a J- configuration ileal-pouch-anal-anastomosis in ulcerative colitis. Scand J Gastroenterol. 2005;40:43–51. r




63. Gionchetti P, Rizzello F, Morselli C, et al. High-dose probiotics for the treatment of active pouchitis. Dis Colon Rectum. 2007;50:2075–2078. 64. Mimura T, Rizzello F, Helwig U, et al. Once daily high dose probiotic therapy (VSL#3) for maintaining remission in recurrent or refractory pouchitis. Gut. 2004;53:108–114. 65. Longstreth Gf, Thompson WG, Chey WD, et al. Functional bowel disorders. Gastroenterology. 2006;130:1480–1491. 66. Camilieri M. Peripheral mechanisms in irritable bowel syndrome. N Engl J Med. 2012;367:1626–1635. 67. Pimentel M, Chow EJ, Lin HC. Eradication of small intestinal bacterial overgrowth reduces symptoms in irritable bowel syndrome. Am J Gastroenterol. 2000;95:3503–3506. 68. Pyleris E, Giamarellos-Bourboulis EJ, Tzivras D, et al. The prevalence of overgrowth by aerobic bacteria in the small intestine by small bowel culture: relationship with irritable bowel syndrome. Dig Dis Sci. 2012;57:1321–1329. 69. Ford AC, Spiegel BM, Talley NJ, et al. Small intestinal bacterial overgrowth in irritable bowel syndrome: systematic review and meta-analysis. Clin Gastroenterol Hepatol. 2009;7: 1729–1786. 70. Khoshini R, Dai SC, Lezcano S, et al. A systematic review of diagnostic tests for small intestinal bacterial overgrowth. Dig Dis Sci. 2008;53:1443–1454. 71. Pimentel M. 2011 Spring Post Graduate Course Syllabus Digestive Disease Week. 2011. 72. Shah ED, Basseri RJ, Chong K, et al. Abnormal breath testing in IBS: a meta-analysis. Dig Dis Sci. 2010;55: 2441–2449. 73. Barbara G, Stanghellini V, Brandi G, et al. Interactions between commensal bacteria and gut sensorimotor function in health and disease. Am J Gastroenterol. 2005;100: 2560–2568. 74. Malinen E, Rinttila E, Kajander K, et al. Analysis of the fecal microbiota of irritable bowel syndrome patients and healthy control with real-time PCR. Am J Gastroenterol. 2005;100: 373–382. 75. Pimentel M, Lembo A, Chey WD, et al. Rifaximin therapy for patients with irritable bowel syndrome without constipation. N Engl J Med. 2011;364:22–32. 76. Menees SB, Maneerattannaporn M, Kim HM, et al. The efficacy and safety of rifaximin for the irritable bowel syndrome: a systematic review and meta-analysis. Am J Gastroenterol. 2012;107:28–35. 77. Pimentel M, Morales W, Chua K, et al. Effects of rifaximin treatment and retreatment in nonconstipated IBS subjects. Dig Dis Sci. 2011;56:2067–2072. 78. Spiller RC. Postinfectious irritable bowel syndrome. Gastroenterology. 2003;124:1662–1671. 79. Barbara G, Stanghellini V, De Giorgio R, et al. Activated mast cells in proximity to colonic nerves correlate with abdominal pain in irritable bowel syndrome. Gastroenterology. 2004;126:693–702. 80. Schoepfer AM, Schaffer T, Seibold-schmid B, et al. Antibodies to flagellin indicate reactivity to bacterial antigens in IBS patients. Neurogastroenterol Motil. 2008;20:1110–1118. 81. Langhorst J, Junge A, Rueffer A, et al. Elevated human Bdefensin-2 levels indicate an activation of the innate immune system in patients with irritable bowel syndrome. Am J Gastroenterol. 2009;104:404–410. 82. Brint EK, MacSharry J, Fanning A, et al. Differential expression of Toll-like receptors in patients with irritable bowel syndrome. Am J Gastroenterol. 2011;106:329–336. 83. Thabane M, Kottachchi DT, Marshall JK. Systematic review and meta-analysis: the incidence and prognosis of postinfectious irritable bowel syndrome. Aliment Pharmacol Ther. 2007;26:535–544. 84. Kunkel D, Brasseri RJ, Makhani MD, et al. Methane on breath testing is associated with constipation: a systematic review and meta-analysis. Dig Dis Sci. 2011;56:1612–1618. 85. Kim G, Weitsman S, Choy JY, et al. Methanobrevibacter smithii is prominent in stool of subjects with constipation r



86.

87.

88.

89. 90. 91.

92. 93.

94.

95. 96. 97.

98. 99. 100. 101.

102.

103. 104. 105.

predominant IBS and methane on lactulose breath test. Dig Dis Week. 2010. Abstract. van Hycklama Vlieg JE, Veiga P, Zhang C, et al. Impact of microbial transformation of food on health- from fermented foods to fermentation in the gastrointestinal tract. Curr Opin Biotech. 2011;22:211–215. Shepherd SJ, Parker FC, Muir JG, et al. Dietary triggers of abdominal symptoms in patients with irritable bowel syndrome: randomized placebo-controlled evidence. Clin Gastroenterol Hepatol. 2008;6:765–769. Staudacher HM, Whelan K, Irving PM, et al. Comparison of symptom (FODMAPs) versus standard dietary advice in patients with irritable bowel syndrome. J Hum Nutr Diet. 2011;24:487–495. 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;104:1033–1049. Monteleone I, Sarra M, Del Vecchio Blanco G, et al. Characterization of IL-17A-producing cells in celiac disease mucosa. J Immunol. 2010;184:2211–2218. Drago S, El Asmar R, Di Pierro M, et al. Gliadin, zonulin and gut permeability: effects on celiac and non-celiac intestinal mucosa and intestinal cell lines. Scand J Gastroenterol. 2006;41:408–419. Ivarsson A, Hernell O, Stenlund H, et al. Breast-feeding protects against coeliac disease. Am J Clin Nutr. 2002;75: 914–921. Stene LC, Honeyman MC, Hoffenberg EJ, et al. Rotavirus infection frequency and risk of celiac disease autoimmunity in early childhood: a longitudinal study. Am J Gastroenterol. 2006;101:2333–2340. Akobeng AK, Ramanan AV, Buchan I, et al. Effect of breast feeding on risk of coeliac disease: a systematic review and meta-analysis of observational studies. Arch Dis Child. 2006; 91:39–43. Sanz Y. Gut microbes in coeliac disease pathogenesis and therapy. In: Eduards MA, ed. Celiac Disease: Etiology, Diagnosis, and Treatment. New York: Nova Science; 2009. Nadal I, Donat E, Ribes-Koninckx C, et al. Imbalance in the composition of the duodenal microbiota of children with coeliac disease. J Med Microbiol. 2007;56:1669–1674. Collado MC, Donat E, Ribes-Koninckx C, et al. Imbalances in faecal and duodenal Bifidobacterium species composition inactive and non-active coeliac disease. BMC Microbiol. 2008;22:232. Collado MC, Donat E, Ribes-Koninckx C, et al. Specific duodenal and faecal bacterial groups associated with paediatric coeliac disease. J Clin Pathol. 2009;62:264–269. De Palma G, Nadal I, Medina M, et al. Intestinal dysbiosis and reduced immunoglobulin-coated bacteria associated with coeliac disease in children. BMC Microbiol. 2010;10:63. Tjellstrom B, Stenhammar L, Hogberg L, et al. Gut microflora associated characteristics in children with CD. Am J Gastroenterol. 2005;100:2784–2788. Tjellstrom B, Stenhammar L, Hogberg L, et al. Gut microflora associated characteristics in first-degree relatives of children with CD. Scand J Gastroenterol. 2007;42: 1204–1208. Rubio-Tapia A, Barton SH, Rosenblatt JE, et al. Prevalence of small intestine bacterial overgrowth diagnosed by quantitative culture of intestinal aspirate in celiac disease. J Clin Gastroenterol. 2009;43:157–161. Cinova J, De Palma G, Stepankova R, et al. Role of intestinal bacteria in gliadin-induced changes in intestinal mucosa: study in germ-free rats. PLoS One. 2011;6:161–169. Szebeni B, Veres G, Dezsofi A, et al. Increased mucosal expression of Toll-like receptor (TLR)2 and TLR4 in coeliac disease. J Pediatr Gastroenterol Nutr. 2007;45:187–193. Westerholm-Ormio M, Vaarala O, Tiittanen M, et al. Infiltration of Foxp3- and Toll-like receptor-4-positive cells in the intestines of children with food allergy. J Pediatr Gastroenterol Nutr. 2010;50:367–376.

www.jcge.com |

665


106. Tlaskalova-Hogenova H, Stepankova R, Kozakova H, 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;8:110–120. 107. Medina M, De Palma G, Ribes-Koninckx C, et al. Bifidobacterium strains suppress in vitro the pro-inflammatory milieu triggered by the large intestinal microbiota of coeliac patients. J Inflamm (Lond). 2008;5:19. 108. Lindfors K, Blomqvist T, Juuti-Uusitalo K, et al. Live probiotic Bifidobacterium lactis bacteria inhibit the toxic effects induced by wheat gliadin in epithelial cell culture. Clin Exp Immunol. 2008;152:552–558. 109. Lorenzo-Zuniga V, Rodriguez-Ortigosa CM, Bartoli R, et al. Insulin-like growth factor I improves intestinal barrier function in cirrhotic rats. Gut. 2006;55:1306–1312. 110. Zhao HY, Wang HJ, Lu Z, et al. Intestinal microflora in patients with liver cirrhosis. Chin J Dig Dis. 2004;5:64–67.

666 | www.jcge.com



111. Liu Q, Duan ZP, Ha DK, et al. Synbiotic modulation of gut flora: effect on minimal hepatic encephalopathy in patients with cirrhosis. Hepatology. 2004;39: 1441–1449. 112. Morgan MY, Blei A, Grungreiff K. The treatment of hepatic encephalopathy. Metab Brain Dis. 2007;22:389–405. 113. Bass NM, Mullen KD, Sanyal A, et al. Rifaximin treatment in hepatic encephalopathy. N Engl J Med. 2010;362: 1071–1081. 114. Ley RE, Turnbaugh PJ, Klein S, et al. Microbial ecology: human gut microbes associated with obesity. Nature. 2006;444:1022–1023. 115. Turnbaugh PJ, Ley RE, Mahowald MA, et al. An obesityassociated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027–1031. 116. Ridaura VK, Faith JJ, Rey FE, et al. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 2013;341:1–22.

r


Review article: fungal microbiota and digestive diseases.

Gut microbiota: its role in hepatic encephalopathy.

The multifaceted role of the intestinal microbiota in colon cancer.

Diet-Intestinal Microbiota Axis in Osteoarthritis: A Possible Role.

Intestinal microbiota and its effects on the immune system.

Pathogenic role of the gut microbiota in gastrointestinal diseases.

Fecal microbiota transplantation broadening its application beyond intestinal disorders.

PPARγ and Its Role in Cardiovascular Diseases.

Role of microbiota on lung homeostasis and diseases.

The digestive and defensive basis of carcass utilization by the burying beetle and its microbiota.

Digestive Enzyme Supplementation in Gastrointestinal Diseases.

Intestinal microbiota in metabolic diseases: from bacterial community structure and functions to species of pathophysiological relevance.

Therapeutic potential of curcumin in digestive diseases.

Gut Microbiota and Metagenomic Advancement in Digestive Disease.

Autophagy, microbiota and intestinal oncogenesis.

Intestinal microbiota and chronic constipation.

Effects of dietary supplementation of multi-enzyme on growth performance, nutrient digestibility, small intestinal digestive enzyme activities, and large intestinal selected microbiota in weanling pigs.

Autism and our intestinal microbiota.

Lymphoma caused by intestinal microbiota.

Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases.

Intestinal Microbiota Metabolism and Atherosclerosis.

LGR4 and Its Role in Intestinal Protection and Energy Metabolism.

Intestinal IgA production and its role in host-microbe interaction.

The intestinal microbiota and microenvironment in liver.