Best Practice & Research Clinical Gastroenterology 28 (2014) 995e1002
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Best Practice & Research Clinical Gastroenterology
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The gastrointestinal microbiome e Functional interference between stomach and intestine Loris R. Lopetuso, MD, PhD, Research Fellow *, Franco Scaldaferri, MD, PhD, Research Fellow, Francesco Franceschi, MD, Professor, Antonio Gasbarrini, MD, Professor Department of Internal Medicine, Gastroenterology Division, Catholic University of Rome, Policlinico “A. Gemelli” Hospital, Roma 00168, Italy
a b s t r a c t Keywords: Gastric microbiota Gut microbiota Helicobacter pylori Clostridia Gastric intestinal interference Gastric modulation of Gut microbiota
The gastrointestinal (GI) tract is a complex and dynamic network with interplay between various gut mucosal cells and their defence molecules, the immune system, food particles, and the resident microbiota. This ecosystem acts as a functional unit organized as a semipermeable multi-layer system that allows the absorption of nutrients and macromolecules required for human metabolic processes and, on the other hand, protects the individual from potentially invasive microorganisms. Commensal microbiota and the host are a unique entity in a continuum along the GI tract, every change in one of these players is able to modify the whole homeostasis. In the stomach, Helicobacter pylori is a gram-negative pathogen that is widespread all over the world, infecting more than 50% of the world's population. In this scenario, H. pylori infection is associated with changes in the gastric microenvironment, which in turn affects the gastric microbiota composition, but also might trigger large intestinal microbiota changes. It is able to influence all the vital pathways of human system and also to influence microbiota composition along the GI tract. This can cause a change in the normal functions exerted by intestinal commensal microorganisms leading to a new gastrointestinal physiological balance. This review focuses and speculates on the possible
* Corresponding author. Largo Gemelli, 1, 00168 Rome, Italy. Tel./fax: þ39 06 30156018. E-mail addresses: [email protected] (L.R. Lopetuso), [email protected] (F. Scaldaferri), francesco.franceschi@ rm.unicatt.it (F. Franceschi), [email protected] (A. Gasbarrini).
http://dx.doi.org/10.1016/j.bpg.2014.10.004 1521-6918/© 2014 Elsevier Ltd. All rights reserved.
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L.R. Lopetuso et al. / Best Practice & Research Clinical Gastroenterology 28 (2014) 995e1002
interactions between gastric microorganisms and intestinal microbiota and on the consequences of this interplay in modulating gut health. © 2014 Elsevier Ltd. All rights reserved.
Introduction The gastrointestinal (GI) tract, human most widely exposed organ system to the external environment with a global surface of 200 m2, is a complex and dynamic network with interplay between various gut mucosal cells and their defence molecules, the immune system, food particles, and the resident microbiota. This ecosystem acts as a functional unit organized as a semipermeable multi-layer system that allows the absorption of nutrients and macromolecules required for human metabolic processes and, on the other hand, protects the individual from potentially invasive microorganisms [1,2]. These basic functions are carried out in a dynamic environment inhabited by 1 kg of commensal microbes that include more than 3 million of genes [3,4]. They belong to the three domains of life, Bacteria, Archaea and Eukarya [5e7], as well as to viral particles [8,9]. Recent advances in cultureindependent molecular techniques, by the analysis of phylogenetic arrays, next generation 16S rRNA sequencing and metagenome sequencing derived from human mucosal biopsies, luminal contents and feces, have shown that four major microbial phyla, (Firmicutes, Bacteroides, Proteobacteria and Actinobacteria), represent 98% of the intestinal microbiota and fall into three main groups of strict extremophile anaerobes: Bacteroides, Clostridium cluster XIVa (also known as the Clostridium Coccoides group), and Clostridium cluster IV (also known as the Clostridium leptum group) [5,6,10e17]. An intricate and mutualistic symbiosis modulates the relationship between the host and the gut microbiota [11,18,19]. This relationship is constantly challenged with several factors such as rapid turnover of the intestinal epithelium and overlaying mucus, exposure to peristaltic activity, food molecules, gastric, pancreatic and biliary secretions, defence molecules, drugs, pH and redox potential variations, and exposure to transient bacteria from the oral cavity and oesophagus, and can lead to the collapse of the microbial community structure [17]. On the other hand, resident microbes perform several useful functions, including maintaining barrier function, synthesis and metabolism of nutrients, drug and toxin metabolism, and behavioural conditioning [20]. Gut microbiota is also involved in the digestion of energy substrates, production of vitamins and hormones [21], protection from pathogenic bacteria by consuming nutrients and producing molecules that inhibit their growth [22e24], production of nutrients for mucosal cells [25e27], augmenting total and pathogen-specific mucosal IgA levels upon infection [28,29], and in modulating immune system development and immunological tolerance [30]. Unfavorable alteration of microbiota composition, known as dysbiosis, has been implicated in chronic, and perhaps also systemic, immune disorders of the gut, such as in the pathogenesis of inflammatory bowel diseases (IBD), and other gastrointestinal disorders, including gastritis, peptic ulcer, irritable bowel syndrome [31] and even gastric and colon cancer [14,32e34]. This review focuses and speculates on the possible interactions between gastric microorganisms (i.e., Helicobacter pylori) and intestinal microbiota and on the consequences of this interplay in modulating gut health. Regional microbiota colonization In healthy gut, a distinct and stable microbial community populates each gastrointestinal region and shapes many of its functions. In particular, at the gastric level, there is a concentration of 103 colony-forming units (CFU)/mL, in the small intestine between 102 and 109CFU/mL and in the large intestine between 104 and 1012 CFU/mL. The high density of the colon is mainly due to the slow transit of ingested material and to the low redox potential. Only in this part of the GI tract the intestinal flora is stable [35]. However, there is not only a well-defined geography of the microbial flora along the digestive tract, but also a specific spatial organization for each group, in particular in the colon. This is organized as a
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functional unit with a physical and a functional barrier. The first one prevents bacterial adhesion and regulates the paracellular diffusion to the underlying host tissues. The second barrier, organized in a complex specialized and compartmentalized network of immune cells, known as ‘gut associated lymphoid tissue’ or GALT, is able to recognize commensal and pathogenic flora, modulating the immunologic tolerance and response to pathogens [36]. The microbiota is in close contact with the mucus layer and the intestinal epithelium. These three entities constitute the superficial physical barrier. In particular, the mucus, organized around the highly glycosylated mucin, MUC2, consists of two layers: an inner layer, very dense, tightly adherent to the epithelial cells and not inhabited by bacteria, and a less dense outer layer, which is an ideal habitat for the commensal flora. In this mucus layer the microbiota is distributed with a precise functional compartmentalization, on the base of the different role played by the various microbial species. This compartmentalization seems to be essential for intestinal homeostasis. Gastric microbiota The gastrointestinal system, from the oral cavity to the distal colon, consists of a wide variety of habitats including the stomach that represents the most extreme. Few bacterial species are able to survive in the high acidic environmental of the gastric mucosa. Moreover, the constitution of the mucus is peculiar. In fact, the mucin MUC5AC is specific for the gastric mucus and makes this habitat very different from others. In the past, several studies tried to grown in culture organisms isolated from gastric juices or mucosal biopsies. Culture-independent studies were also conducted to identify and quantify specific pathogens such as Helicobacter pylori (H. pylori), which is an important member of the gastric microbiota and is associated with the development of progressively more serious pathological conditions such as gastritis, peptic ulcer, gastric cancer and gastric lymphoma. This represents the most important component of the gastric microflora, is specific for this region, and also the most studied. Temperature gradient gel electrophoresis (TGGE) analysis performed on gastric biopsies also identified Enterococcus, Streptococcus, Staphylococcus and Stomatococcus, which belong to the normal microbial population of the respiratory tract and oral cavity. Furthermore, these analyses showed the presence of species belonging to Pseudomonas, which is not commonly associated with this habitat. This species has also been isolated from gastric aspirates from individuals with gastroesophageal reflux disease. However, the role and the presence of Pseudomonas in the gastric mucosa are not yet perfectly clear. Another recent study was not able to isolate it in the stomach. This study, using cultureindependent methods identified 128 different phyla with only five dominant: Proteobacteria, Firmicutes, Bacteroides, Actinobacteria and Fusobacteria. Among these 128 phyla, bacteria that cannot grow in culture media represent the 50%, while the 67% is also present in the oral cavity, suggesting the possibility of a gastric colonization by oro-esophageal species. Finally it showed, for the first time in humans, the presence of sequences belonging to the phylum Deinococcus/Thermus, which could be specifically adapted to live in the stomach. Overall, further evidences are needed to verify whether there is a specific gastric microbiota, excluding the H. pylori, and not a contamination coming from the upper regions [17,21]. Gut barrier and commensal microbiota The intestinal barrier is a functional unit, organized as a multi-layer system, in which it is possible to recognize two main parts: a superficial physical barrier, which prevents bacterial adhesion and regulates paracellular diffusion to the underlying host tissues, and a deeper functional barrier, which is able to discriminate commensal bacteria from pathogens and is responsible for immunological tolerance to commensal and immune response to pathogen microorganisms [20]. Everyday, thousands of compounds derived from food and microorganisms come in contact with the intestinal mucosa. This interaction requires a complex defence system that separates intestinal contents from the host tissues, regulates nutrient absorption, and allows tolerance between the resident bacterial flora and the mucosal immune system, while inhibiting translocation of infectious agents to the inner tissues. Commensal gut microbiota constitutes the anatomical barrier, along with the mucous layer and the
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intestinal epithelial monolayer. The deeper, inner layer is represented by GALT. GALT represents both isolated and aggregated lymphoid follicles and is one of the largest lymphoid organs, containing up to 70% of the body's total number of immunocytes and is involved in responding to pathogenic microorganisms, as well as providing immune tolerance to commensal bacteria. The ability of GALT to interact with the luminal antigens rests on specific mucosal immune cells (i.e., dendritic cells and Mcells), primarily localized to Peyer's patches within the ileum that are intimately positioned at the mucosal-environmental interface and internalize microorganisms and macromolecules. These specialized immune cells have the ability to present antigen to naïve T-lymphocytes, which subsequently produce cytokines and activate mucosal immune responses, when needed. Thus, the mucosal immune system participates in the maintenance of gut microbial communities by directly monitoring the luminal environment through the constant sampling through M-cells that overlie lymphoid follicles and by dendritic cells that resides within the lamina propria. The interaction of these cellular components sustains the delicate equilibrium to maintain intestinal homeostasis, establishing a state of immunological tolerance towards antigens from food and commensal bacteria. Many factors can alter this balance, including alterations in the gut microflora, modifications of the mucus layer, and epithelial damage, leading to increased intestinal permeability and translocation of luminal contents to the underlying mucosa. Dysregulation of any of the aforementioned components have been implicated, not only in the pathogenesis of IBD, but in many other GI disorders, including infectious enterocolitis, IBS, small intestinal bowel overgrowth, celiac sprue, hepatic fibrosis, atopic manifestations and food intolerance [37e39]. The gut microbiota is an essential actor in the aforementioned defence mechanisms and in the resistance to infection. It plays a crucial role, both by acting indirectly, for example in immune system development and modulating immunological tolerance [40], and also directly, by preventing potentially deleterious and pathogenic organisms from taking up residence. This phenomenon is known as colonization resistance [17]. The interplay between gastric and intestinal microbiota Since commensal microbiota and the host are a unique entity in a continuum along the GI tract, every change in one of these players is able to modify the whole homeostasis. In the stomach, H. pylori is a gram-negative pathogen that is widespread all over the world, infecting more than 50% of the world's population. It is aetiologically associated with non-atrophic and atrophic gastritis, peptic ulcer and shows a deep association with primary gastric B-cell lymphoma and gastric adenocarcinoma. H. pylori colonizes the entire gastric epithelium, and has an important urease activity, that leads to the ammonia production in order to protect itself from gastric acidity. It produces also other enzymes, such as phospholipase A2 and C, and glycosulfatase, which play a role in the development of the gastric mucosal damage [41]. Indeed, H. pylori induces an inflammatory response through the gastric epithelium, with production of pro-inflammatory cytokines, such as interleukin 1b and interleukin 8. Some H. pylori genotypes, especially those Vac-A (vacuolating toxin A) and Cag-A (cytotoxin-associated gene A) positive, are associated with greater pathogenicity and more severe disease. Cag-A positive strains induce a stronger inflammatory response of gastric mucosa, with increased production of proinflammatory cytokines. The VacA gene, which leads to vacuolization and apoptosis of gastric epithelial cells, is genetically expressed in every H. pylori strain, even if is phenotypically present in only 60% of them [42]. There is a deep association between H. pylori and primary gastric B-cell lymphoma (MucosaAssociated-Lymphatic-Tissue or MALTelymphoma) and gastric adenocarcinoma. H. pylori has been therefore classified by IARC/WHO as ‘group 1 carcinogen’ [43]. Finally, over the last years, many authors investigated the relationship between H. pylori infection and extra-digestive diseases, following the rationale that it may act as an immunological trigger. The strongest association has been found with idiopathic thrombocytopenic purpura, while other studies seems to connect H. pylori infection with autoimmune diseases (Schonlein-Henoch purpura, Sjogren syndrome, autoimmune thrombocytopenia), skin diseases (urticaria, rosacea, and alopecia areata), and cardiovascular diseases (chronic ischaemic heart disease and chronic ischaemic cerebrovascular disease) [44,45]. Recently, many studies focused on the modification of the gastric environment induced by H. pylori infection, possibly affecting
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the absorption of nutrients and drugs as well as the production of hormones strongly implicated in the metabolic syndrome and in the regulation of appetite and growth. Interestingly, the absorption of iron and vitamin B12 is impaired by H. pylori infection, while infected subjects have lower basal and fasting serum levels of ghrelin and higher concentration of leptin compared to controls. Since leptin is an anorexigenic hormone, and ghrelin stimulates the release of growth hormone in humans, H. pylori infection may finally induce growth retardation if acquired very early in the childhood and in malnourished children. Furthermore, idiopathic sideropenic anaemia is strongly related to H. pylori infection [46,47]. In this scenario, H. pylori infection is associated with changes in the gastric microenvironment, which in turn affects the gastric microbiota composition. Indeed, it has been demonstrated that following H. pylori infection, bacterial species usually restricted to the lower intestinal tract (such as Bacteroides/Prevotella spp. and Clostridia, among others) were present in stomach samples of H. pylori infected mice, whereas Lactobacillus spp. were predominant in control animals [48]. Furthermore, in a previous report Mongolian gerbils with gastritis and duodenitis harboured significantly higher Bacteroides spp. numbers at sites of inflammation 12 weeks following H. pylori infection [49]. Interestingly, Heimesaat et al investigated potential changes of the microbiota composition distal to the inflammatory process, particularly in long-term H. pylori infection [50]. This study demonstrated that longterm infection with a H. pylori WT strain displaying an intact type IV secretion system leads to distinct shifts of the microbiota composition in the distal uninflamed, but not proximal inflamed GI tract. Hence, H. pylori induced immunopathogenesis of the stomach, including hypochlorhydria and hypergastrinemia, might trigger large intestinal microbiota changes whereas the exact underlying mechanisms need to be further unraveled [50]. Overall, we can speculate that H. pylori has an exceptional impact on GI system. It is able to influence all the vital pathways of human system and also to influence microbiota composition along the GI tract. This can cause a change in the normal functions exerted by intestinal commensal microorganisms leading to a new physiological balance. On the other side, H. pylori eradication could also remodel and affect the equilibrium of gut ecosystem. Beside this, long term protein pump inhibitor (PPI) therapy is able to continuously reduce gastric acidity, blocking one of the most important microbiota-modulating agents. For example, it has been demonstrated that PPIs increase the risk of infection in cirrhosis and should not be prescribed in these patients without specific indications [51]. Additional studies to elucidate the real impact of long-term PPI use with or without H. pylori eradication on all the components of gut barrier should be encouraged. In this scenario Clostridia, contributing to a significant portion of indigenous bacteria in the large intestine, are strongly involved in the maintenance of overall gut function. From an experimental point of view, this thesis has been strongly strengthened in a very recent paper [52]. Maurice et al, studying the role of xenobiotics in shaping the physiology and gene expression of the active humane gut microbiota, showed that a distinctive subset of microorganisms, enriched for Clostridia, tends to dominate the active fraction of the gut microbiota [52]. The position of Clostridia, in close relationship with intestinal cells, allows them to participate as crucial factors in modulating physiologic, metabolic and immune processes in the gut, and appears to be necessary for the welfare of maintaining normal gut immune homeostasis and, on the basis of their influence on the neuroenteric system, of the braingut axis. Based on this new information, novel pathogenic hypotheses can be formed that have important translational implications in regard to the prevention and treatment of dysbiosis that can be implicated in many gastrointestinal disorders, including chronic intestinal inflammation, colorectal cancer and irritable bowel syndrome. It will be fascinating to elucidate the underlying mechanisms for xenobiotic resistance and metabolism in the active human gut microbiota in order to provide indications for unexplained patient-to-patient variations in drug efficacy and toxicity. Conclusions Overall, the GI tract is a complex and dynamic network with interplay between various gut mucosal cells and their defence molecules, the immune system, food particles, and the resident microbiota. An intricate and mutualistic symbiosis modulates the relationship between the host and the gut microbiota. Since commensal microbiota and the host are a unique entity in a continuum along the GI tract,
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every change in one of these players is able to modify the whole homeostasis. In this scenario, H. pylori infection is associated with changes in the gastric microenvironment, which in turn affects the gastric microbiota composition, but also might trigger large intestinal microbiota changes. It is able to influence all the vital pathways of human system and also to influence microbiota composition along the GI tract. This can cause a change in the normal functions exerted by intestinal commensal microorganisms (i.e., Clostridia) leading to a new gastrointestinal physiological balance. Furthermore, increasing evidences are focussing on its role also in pathological aspects not immediately related to the GI tract, such as metabolic syndrome and gynaecological diseases. This new approach in studying gut microbiota has obvious therapeutic implications and could lead to perform detailed mechanistic studies to improve the development of microbial therapies that may modulate the composition of the gut microflora with the end goal of promoting gut health.
Practice Points The GI tract is a complex and dynamic network with interplay between host cells and commensal microbiota. H. pylori infection is associated with changes in the gastric microenvironment, but also might trigger large intestinal microbiota changes leading to a new gastrointestinal physiological balance. Clostridia, contributing to a significant portion of indigenous bacteria in the large intestine, are strongly involved in the maintenance of overall gut function and could be influenced by H. pylori colonization.
Research agenda Detailed studies are necessary to understand if H. pylori colonization is associated to a functional modulation of the intestinal microbiota. Design of additional mechanistic studies to evaluate the overall impact of H. pylori eradication on the human health is required. It will be fascinating to elucidate the underlying mechanisms for xenobiotic resistance and metabolism in the active human gut microbiota. Detailed mechanistic studies are needed to improve the development of microbial therapies that may modulate the whole composition and function of the gut microflora.
Conflict of interest statement None. References [1] Walker WA, Wu M, Isselbacher KJ, Bloch KJ. Intestinal uptake of macromolecules. III. Studies on the mechanism by which immunization interferes with antigen uptake. J Immunol 1975;115:854e61. [2] Walker WA, Wu M, Isselbacher KJ, Bloch KJ. Intestinal uptake of macromolecules. IV e The effect of pancreatic duct ligation on the breakdown of antigen and antigen-antibody complexes on the intestinal surface. Gastroenterology 1975;69: 1223e9. [3] Leser TD, Molbak L. Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host. Environ Microbiol 2009;11:2194e206. [4] Neish AS. Microbes in gastrointestinal health and disease. Gastroenterology 2009;136:65e80.
L.R. Lopetuso et al. / Best Practice & Research Clinical Gastroenterology 28 (2014) 995e1002
1001
[5] Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science 2005;308:1635e8. [6] Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science 2006;312:1355e9. [7] Scanlan PD, Marchesi JR. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J 2008;2:1183e93. [8] Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, Soh SW, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 2006;4:e3. [9] Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, et al. Viral diversity and dynamics in an infant gut. Res Microbiol 2008;159:367e73. [10] Hold GL, Pryde SE, Russell VJ, Furrie E, Flint HJ. Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 2002;39:33e9. [11] Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307:1915e20. [12] Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 2005;102:11070e5. [13] Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006;124:837e48. [14] Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 2007;104:13780e5. [15] Rajilic-Stojanovic M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007;9:2125e36. [16] Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 2009;11:2574e84. [17] Manson JM, Rauch M, Gilmore MS. The commensal microbiology of the gastrointestinal tract. Adv Exp Med Biol 2008;635: 15e28. [18] McCracken VJ, Lorenz RG. The gastrointestinal ecosystem: a precarious alliance among epithelium, immunity and microbiota. Cell Microbiol 2001;3:1e11. [19] Lievin-Le Moal V, Servin AL. The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota. Clin Microbiol Rev 2006;19:315e37. [20] Scaldaferri F, Pizzoferrato M, Gerardi V, Lopetuso L, Gasbarrini A. The gut barrier: new acquisitions and therapeutic approaches. J Clin Gastroenterol 2012;46(Suppl.):S12e7. [21] Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut mircobiota in health and disease. Physiol Rev 2010;90:859e904. [22] Silva AM, Barbosa FH, Duarte R, Vieira LQ, Arantes RM, Nicoli JR. Effect of Bifidobacterium longum ingestion on experimental salmonellosis in mice. J Appl Microbiol 2004;97. [23] Truusalu K, Rea M. Eradication of Salmonella typhimurium infection in a murine model of typhoid fever with the cimbination of probiotic Lactobacillus fermentum ME-3 and ofloxacin. BMC Microbiol 2008;8. [24] Searle LE, Best A, Nunez A, Salguero FJ, Johnson L, Weyer U, et al. A mixture containing galactooligosaccharide, produced by the enzymic activity of Bifidobacterium bifidum, reduces Salmonella enterica serovar Typhimurium infection in mice. J Med Microbiol 2009;58:37e48. [25] Martens EC, R Rea. Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent gut symbiont. J Biol Chem 2009;284. [26] Burger van Paassen N, V Aea. The regulation of intestinal mucin MUC2 expression by short chain fatty acid: implications for epithelial protection. Biochem J 2009;420. [27] Dharmani P, S Vea. Role of intestinal mucins in annate host defense mechanisms against pathogens. J Innate Immun 2009;1. [28] Galdeano CM, Perdigon G. The probiotic bacterium Lactobacillus casei induces activation of the gut mucosal immune system through innate immunity. Clin Vaccine Immunol 2006;13:219e26. [29] Leblanc J, Fliss I, Matar C. Induction of a humoral immune response following an Escherichia coli O157:H7 infection with an immunomodulatory peptidic fraction derived from Lactobacillus helveticus-fermented milk. Clin Diagn Lab Immunol 2004;11:1171e81. [30] Allen CA, Torres AG. Host-microbe communication within the GI tract. Adv Exp Med Biol 2008;635:93e101. [31] Parashar UD, Gibson CJ, Bresee JS, Glass RI. Rotavirus and severe childhood diarrhea. Emerg Infect Dis 2006;12:304e6. [32] Swidsinski A, Ladhoff A, Pernthaler A, Swidsinski S, Loening-Baucke V, Ortner M, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology 2002;122:44e54. [33] Hill DA, Artis D. Intestinal bacteria and the regulation of immune cell homeostasis. Annu Rev Immunol 2010;28:623e67. [34] Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology 2008;134:577e94. [35] Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220e30. [36] Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A. Commensal Clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog 2013;5:23. [37] Camilleri M, Madsen K, Spiller R, Greenwood-Van Meerveld B, Verne GN. Intestinal barrier function in health and gastrointestinal disease. Neurogastroenterol Motil 2012;24:503e12. [38] Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol 2012;42:71e8. [39] Fasano A. Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer. Physiol Rev 2011;91:151e75. [40] Kelly D, Conway S, Aminov R. Commensal gut bacteria: mechanisms of immune modulation. Trends Immunol 2005;26: 326e33. [41] Dzierzanowska-Fangrat K, Dzierzanowska D. Helicobacter pylori: microbiology and interactions with gastrointestinal microflora. J Physiol Pharmacol e Off J Pol Physiol Soc 2006;57(Suppl. 3):5e14. [42] Yamaoka Y. Mechanisms of disease: Helicobacter pylori virulence factors. Nat Rev Gastroenterol Hepatol 2010;7:629e41.
1002
L.R. Lopetuso et al. / Best Practice & Research Clinical Gastroenterology 28 (2014) 995e1002
[43] Pandey R, Misra V, Misra SP, Dwivedi M, Kumar A, Tiwari BK. Helicobacter pylori and gastric cancer. Asian Pac J Cancer Prev e APJCP 2010;11:583e8. [44] Gasbarrini A, Franceschi F, Armuzzi A, Ojetti V, Candelli M, Torre ES, et al. Extradigestive manifestations of Helicobacter pylori gastric infection. Gut 1999;45(Suppl. 1):I9e12. [45] Solnick JV, Franceschi F, Roccarina D, Gasbarrini A. Extragastric manifestations of Helicobacter pylori infectioneother Helicobacter species. Helicobacter 2006;11(Suppl. 1):46e51. [46] Capurso G, Marignani M, Delle Fave G, Annibale B. Iron-deficiency anemia in premenopausal women: why not consider atrophic body gastritis and Helicobacter pylori role? Am J Gastroenterol 1999;94:3084e5. [47] Akcam M, Ozdem S, Yilmaz A, Gultekin M, Artan R. Serum ferritin, vitamin B(12), folate, and zinc levels in children infected with Helicobacter pylori. Dig Dis Sci 2007;52:405e10. [48] Aebischer T, Fischer A, Walduck A, Schlotelburg C, Lindig M, Schreiber S, et al. Vaccination prevents Helicobacter pyloriinduced alterations of the gastric flora in mice. FEMS Immunol Med Microbiol 2006;46:221e9. [49] Yin YN, Wang CL, Liu XW, Cui Y, Xie N, Yu QF, et al. Gastric and duodenum microflora analysis after long-term Helicobacter pylori infection in Mongolian Gerbils. Helicobacter 2011;16:389e97. [50] Heimesaat MM, Fischer A, Plickert R, Wiedemann T, Loddenkemper C, Gobel UB, et al. Helicobacter pylori induced gastric immunopathology is associated with distinct microbiota changes in the large intestines of long-term infected Mongolian gerbils. PloS One 2014;9:e100362. [51] Merli M, Lucidi C, Di Gregorio V, Giannelli V, Giusto M, Ceccarelli G, et al. The chronic use of beta-blockers and proton pump inhibitors may affect the rate of bacterial infections in cirrhosis. Liver Int 2014 May 17. http://dx.doi.org/10.1111/liv. 12593 [Epub ahead of print]. [52] Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 2013;152:39e50.
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Best Practice & Research Clinical Gastroenterology
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The gastrointestinal microbiome e Functional interference between stomach and intestine Loris R. Lopetuso, MD, PhD, Research Fellow *, Franco Scaldaferri, MD, PhD, Research Fellow, Francesco Franceschi, MD, Professor, Antonio Gasbarrini, MD, Professor Department of Internal Medicine, Gastroenterology Division, Catholic University of Rome, Policlinico “A. Gemelli” Hospital, Roma 00168, Italy
a b s t r a c t Keywords: Gastric microbiota Gut microbiota Helicobacter pylori Clostridia Gastric intestinal interference Gastric modulation of Gut microbiota
The gastrointestinal (GI) tract is a complex and dynamic network with interplay between various gut mucosal cells and their defence molecules, the immune system, food particles, and the resident microbiota. This ecosystem acts as a functional unit organized as a semipermeable multi-layer system that allows the absorption of nutrients and macromolecules required for human metabolic processes and, on the other hand, protects the individual from potentially invasive microorganisms. Commensal microbiota and the host are a unique entity in a continuum along the GI tract, every change in one of these players is able to modify the whole homeostasis. In the stomach, Helicobacter pylori is a gram-negative pathogen that is widespread all over the world, infecting more than 50% of the world's population. In this scenario, H. pylori infection is associated with changes in the gastric microenvironment, which in turn affects the gastric microbiota composition, but also might trigger large intestinal microbiota changes. It is able to influence all the vital pathways of human system and also to influence microbiota composition along the GI tract. This can cause a change in the normal functions exerted by intestinal commensal microorganisms leading to a new gastrointestinal physiological balance. This review focuses and speculates on the possible
* Corresponding author. Largo Gemelli, 1, 00168 Rome, Italy. Tel./fax: þ39 06 30156018. E-mail addresses: [email protected] (L.R. Lopetuso), [email protected] (F. Scaldaferri), francesco.franceschi@ rm.unicatt.it (F. Franceschi), [email protected] (A. Gasbarrini).
http://dx.doi.org/10.1016/j.bpg.2014.10.004 1521-6918/© 2014 Elsevier Ltd. All rights reserved.
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interactions between gastric microorganisms and intestinal microbiota and on the consequences of this interplay in modulating gut health. © 2014 Elsevier Ltd. All rights reserved.
Introduction The gastrointestinal (GI) tract, human most widely exposed organ system to the external environment with a global surface of 200 m2, is a complex and dynamic network with interplay between various gut mucosal cells and their defence molecules, the immune system, food particles, and the resident microbiota. This ecosystem acts as a functional unit organized as a semipermeable multi-layer system that allows the absorption of nutrients and macromolecules required for human metabolic processes and, on the other hand, protects the individual from potentially invasive microorganisms [1,2]. These basic functions are carried out in a dynamic environment inhabited by 1 kg of commensal microbes that include more than 3 million of genes [3,4]. They belong to the three domains of life, Bacteria, Archaea and Eukarya [5e7], as well as to viral particles [8,9]. Recent advances in cultureindependent molecular techniques, by the analysis of phylogenetic arrays, next generation 16S rRNA sequencing and metagenome sequencing derived from human mucosal biopsies, luminal contents and feces, have shown that four major microbial phyla, (Firmicutes, Bacteroides, Proteobacteria and Actinobacteria), represent 98% of the intestinal microbiota and fall into three main groups of strict extremophile anaerobes: Bacteroides, Clostridium cluster XIVa (also known as the Clostridium Coccoides group), and Clostridium cluster IV (also known as the Clostridium leptum group) [5,6,10e17]. An intricate and mutualistic symbiosis modulates the relationship between the host and the gut microbiota [11,18,19]. This relationship is constantly challenged with several factors such as rapid turnover of the intestinal epithelium and overlaying mucus, exposure to peristaltic activity, food molecules, gastric, pancreatic and biliary secretions, defence molecules, drugs, pH and redox potential variations, and exposure to transient bacteria from the oral cavity and oesophagus, and can lead to the collapse of the microbial community structure [17]. On the other hand, resident microbes perform several useful functions, including maintaining barrier function, synthesis and metabolism of nutrients, drug and toxin metabolism, and behavioural conditioning [20]. Gut microbiota is also involved in the digestion of energy substrates, production of vitamins and hormones [21], protection from pathogenic bacteria by consuming nutrients and producing molecules that inhibit their growth [22e24], production of nutrients for mucosal cells [25e27], augmenting total and pathogen-specific mucosal IgA levels upon infection [28,29], and in modulating immune system development and immunological tolerance [30]. Unfavorable alteration of microbiota composition, known as dysbiosis, has been implicated in chronic, and perhaps also systemic, immune disorders of the gut, such as in the pathogenesis of inflammatory bowel diseases (IBD), and other gastrointestinal disorders, including gastritis, peptic ulcer, irritable bowel syndrome [31] and even gastric and colon cancer [14,32e34]. This review focuses and speculates on the possible interactions between gastric microorganisms (i.e., Helicobacter pylori) and intestinal microbiota and on the consequences of this interplay in modulating gut health. Regional microbiota colonization In healthy gut, a distinct and stable microbial community populates each gastrointestinal region and shapes many of its functions. In particular, at the gastric level, there is a concentration of 103 colony-forming units (CFU)/mL, in the small intestine between 102 and 109CFU/mL and in the large intestine between 104 and 1012 CFU/mL. The high density of the colon is mainly due to the slow transit of ingested material and to the low redox potential. Only in this part of the GI tract the intestinal flora is stable [35]. However, there is not only a well-defined geography of the microbial flora along the digestive tract, but also a specific spatial organization for each group, in particular in the colon. This is organized as a
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functional unit with a physical and a functional barrier. The first one prevents bacterial adhesion and regulates the paracellular diffusion to the underlying host tissues. The second barrier, organized in a complex specialized and compartmentalized network of immune cells, known as ‘gut associated lymphoid tissue’ or GALT, is able to recognize commensal and pathogenic flora, modulating the immunologic tolerance and response to pathogens [36]. The microbiota is in close contact with the mucus layer and the intestinal epithelium. These three entities constitute the superficial physical barrier. In particular, the mucus, organized around the highly glycosylated mucin, MUC2, consists of two layers: an inner layer, very dense, tightly adherent to the epithelial cells and not inhabited by bacteria, and a less dense outer layer, which is an ideal habitat for the commensal flora. In this mucus layer the microbiota is distributed with a precise functional compartmentalization, on the base of the different role played by the various microbial species. This compartmentalization seems to be essential for intestinal homeostasis. Gastric microbiota The gastrointestinal system, from the oral cavity to the distal colon, consists of a wide variety of habitats including the stomach that represents the most extreme. Few bacterial species are able to survive in the high acidic environmental of the gastric mucosa. Moreover, the constitution of the mucus is peculiar. In fact, the mucin MUC5AC is specific for the gastric mucus and makes this habitat very different from others. In the past, several studies tried to grown in culture organisms isolated from gastric juices or mucosal biopsies. Culture-independent studies were also conducted to identify and quantify specific pathogens such as Helicobacter pylori (H. pylori), which is an important member of the gastric microbiota and is associated with the development of progressively more serious pathological conditions such as gastritis, peptic ulcer, gastric cancer and gastric lymphoma. This represents the most important component of the gastric microflora, is specific for this region, and also the most studied. Temperature gradient gel electrophoresis (TGGE) analysis performed on gastric biopsies also identified Enterococcus, Streptococcus, Staphylococcus and Stomatococcus, which belong to the normal microbial population of the respiratory tract and oral cavity. Furthermore, these analyses showed the presence of species belonging to Pseudomonas, which is not commonly associated with this habitat. This species has also been isolated from gastric aspirates from individuals with gastroesophageal reflux disease. However, the role and the presence of Pseudomonas in the gastric mucosa are not yet perfectly clear. Another recent study was not able to isolate it in the stomach. This study, using cultureindependent methods identified 128 different phyla with only five dominant: Proteobacteria, Firmicutes, Bacteroides, Actinobacteria and Fusobacteria. Among these 128 phyla, bacteria that cannot grow in culture media represent the 50%, while the 67% is also present in the oral cavity, suggesting the possibility of a gastric colonization by oro-esophageal species. Finally it showed, for the first time in humans, the presence of sequences belonging to the phylum Deinococcus/Thermus, which could be specifically adapted to live in the stomach. Overall, further evidences are needed to verify whether there is a specific gastric microbiota, excluding the H. pylori, and not a contamination coming from the upper regions [17,21]. Gut barrier and commensal microbiota The intestinal barrier is a functional unit, organized as a multi-layer system, in which it is possible to recognize two main parts: a superficial physical barrier, which prevents bacterial adhesion and regulates paracellular diffusion to the underlying host tissues, and a deeper functional barrier, which is able to discriminate commensal bacteria from pathogens and is responsible for immunological tolerance to commensal and immune response to pathogen microorganisms [20]. Everyday, thousands of compounds derived from food and microorganisms come in contact with the intestinal mucosa. This interaction requires a complex defence system that separates intestinal contents from the host tissues, regulates nutrient absorption, and allows tolerance between the resident bacterial flora and the mucosal immune system, while inhibiting translocation of infectious agents to the inner tissues. Commensal gut microbiota constitutes the anatomical barrier, along with the mucous layer and the
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intestinal epithelial monolayer. The deeper, inner layer is represented by GALT. GALT represents both isolated and aggregated lymphoid follicles and is one of the largest lymphoid organs, containing up to 70% of the body's total number of immunocytes and is involved in responding to pathogenic microorganisms, as well as providing immune tolerance to commensal bacteria. The ability of GALT to interact with the luminal antigens rests on specific mucosal immune cells (i.e., dendritic cells and Mcells), primarily localized to Peyer's patches within the ileum that are intimately positioned at the mucosal-environmental interface and internalize microorganisms and macromolecules. These specialized immune cells have the ability to present antigen to naïve T-lymphocytes, which subsequently produce cytokines and activate mucosal immune responses, when needed. Thus, the mucosal immune system participates in the maintenance of gut microbial communities by directly monitoring the luminal environment through the constant sampling through M-cells that overlie lymphoid follicles and by dendritic cells that resides within the lamina propria. The interaction of these cellular components sustains the delicate equilibrium to maintain intestinal homeostasis, establishing a state of immunological tolerance towards antigens from food and commensal bacteria. Many factors can alter this balance, including alterations in the gut microflora, modifications of the mucus layer, and epithelial damage, leading to increased intestinal permeability and translocation of luminal contents to the underlying mucosa. Dysregulation of any of the aforementioned components have been implicated, not only in the pathogenesis of IBD, but in many other GI disorders, including infectious enterocolitis, IBS, small intestinal bowel overgrowth, celiac sprue, hepatic fibrosis, atopic manifestations and food intolerance [37e39]. The gut microbiota is an essential actor in the aforementioned defence mechanisms and in the resistance to infection. It plays a crucial role, both by acting indirectly, for example in immune system development and modulating immunological tolerance [40], and also directly, by preventing potentially deleterious and pathogenic organisms from taking up residence. This phenomenon is known as colonization resistance [17]. The interplay between gastric and intestinal microbiota Since commensal microbiota and the host are a unique entity in a continuum along the GI tract, every change in one of these players is able to modify the whole homeostasis. In the stomach, H. pylori is a gram-negative pathogen that is widespread all over the world, infecting more than 50% of the world's population. It is aetiologically associated with non-atrophic and atrophic gastritis, peptic ulcer and shows a deep association with primary gastric B-cell lymphoma and gastric adenocarcinoma. H. pylori colonizes the entire gastric epithelium, and has an important urease activity, that leads to the ammonia production in order to protect itself from gastric acidity. It produces also other enzymes, such as phospholipase A2 and C, and glycosulfatase, which play a role in the development of the gastric mucosal damage [41]. Indeed, H. pylori induces an inflammatory response through the gastric epithelium, with production of pro-inflammatory cytokines, such as interleukin 1b and interleukin 8. Some H. pylori genotypes, especially those Vac-A (vacuolating toxin A) and Cag-A (cytotoxin-associated gene A) positive, are associated with greater pathogenicity and more severe disease. Cag-A positive strains induce a stronger inflammatory response of gastric mucosa, with increased production of proinflammatory cytokines. The VacA gene, which leads to vacuolization and apoptosis of gastric epithelial cells, is genetically expressed in every H. pylori strain, even if is phenotypically present in only 60% of them [42]. There is a deep association between H. pylori and primary gastric B-cell lymphoma (MucosaAssociated-Lymphatic-Tissue or MALTelymphoma) and gastric adenocarcinoma. H. pylori has been therefore classified by IARC/WHO as ‘group 1 carcinogen’ [43]. Finally, over the last years, many authors investigated the relationship between H. pylori infection and extra-digestive diseases, following the rationale that it may act as an immunological trigger. The strongest association has been found with idiopathic thrombocytopenic purpura, while other studies seems to connect H. pylori infection with autoimmune diseases (Schonlein-Henoch purpura, Sjogren syndrome, autoimmune thrombocytopenia), skin diseases (urticaria, rosacea, and alopecia areata), and cardiovascular diseases (chronic ischaemic heart disease and chronic ischaemic cerebrovascular disease) [44,45]. Recently, many studies focused on the modification of the gastric environment induced by H. pylori infection, possibly affecting
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the absorption of nutrients and drugs as well as the production of hormones strongly implicated in the metabolic syndrome and in the regulation of appetite and growth. Interestingly, the absorption of iron and vitamin B12 is impaired by H. pylori infection, while infected subjects have lower basal and fasting serum levels of ghrelin and higher concentration of leptin compared to controls. Since leptin is an anorexigenic hormone, and ghrelin stimulates the release of growth hormone in humans, H. pylori infection may finally induce growth retardation if acquired very early in the childhood and in malnourished children. Furthermore, idiopathic sideropenic anaemia is strongly related to H. pylori infection [46,47]. In this scenario, H. pylori infection is associated with changes in the gastric microenvironment, which in turn affects the gastric microbiota composition. Indeed, it has been demonstrated that following H. pylori infection, bacterial species usually restricted to the lower intestinal tract (such as Bacteroides/Prevotella spp. and Clostridia, among others) were present in stomach samples of H. pylori infected mice, whereas Lactobacillus spp. were predominant in control animals [48]. Furthermore, in a previous report Mongolian gerbils with gastritis and duodenitis harboured significantly higher Bacteroides spp. numbers at sites of inflammation 12 weeks following H. pylori infection [49]. Interestingly, Heimesaat et al investigated potential changes of the microbiota composition distal to the inflammatory process, particularly in long-term H. pylori infection [50]. This study demonstrated that longterm infection with a H. pylori WT strain displaying an intact type IV secretion system leads to distinct shifts of the microbiota composition in the distal uninflamed, but not proximal inflamed GI tract. Hence, H. pylori induced immunopathogenesis of the stomach, including hypochlorhydria and hypergastrinemia, might trigger large intestinal microbiota changes whereas the exact underlying mechanisms need to be further unraveled [50]. Overall, we can speculate that H. pylori has an exceptional impact on GI system. It is able to influence all the vital pathways of human system and also to influence microbiota composition along the GI tract. This can cause a change in the normal functions exerted by intestinal commensal microorganisms leading to a new physiological balance. On the other side, H. pylori eradication could also remodel and affect the equilibrium of gut ecosystem. Beside this, long term protein pump inhibitor (PPI) therapy is able to continuously reduce gastric acidity, blocking one of the most important microbiota-modulating agents. For example, it has been demonstrated that PPIs increase the risk of infection in cirrhosis and should not be prescribed in these patients without specific indications [51]. Additional studies to elucidate the real impact of long-term PPI use with or without H. pylori eradication on all the components of gut barrier should be encouraged. In this scenario Clostridia, contributing to a significant portion of indigenous bacteria in the large intestine, are strongly involved in the maintenance of overall gut function. From an experimental point of view, this thesis has been strongly strengthened in a very recent paper [52]. Maurice et al, studying the role of xenobiotics in shaping the physiology and gene expression of the active humane gut microbiota, showed that a distinctive subset of microorganisms, enriched for Clostridia, tends to dominate the active fraction of the gut microbiota [52]. The position of Clostridia, in close relationship with intestinal cells, allows them to participate as crucial factors in modulating physiologic, metabolic and immune processes in the gut, and appears to be necessary for the welfare of maintaining normal gut immune homeostasis and, on the basis of their influence on the neuroenteric system, of the braingut axis. Based on this new information, novel pathogenic hypotheses can be formed that have important translational implications in regard to the prevention and treatment of dysbiosis that can be implicated in many gastrointestinal disorders, including chronic intestinal inflammation, colorectal cancer and irritable bowel syndrome. It will be fascinating to elucidate the underlying mechanisms for xenobiotic resistance and metabolism in the active human gut microbiota in order to provide indications for unexplained patient-to-patient variations in drug efficacy and toxicity. Conclusions Overall, the GI tract is a complex and dynamic network with interplay between various gut mucosal cells and their defence molecules, the immune system, food particles, and the resident microbiota. An intricate and mutualistic symbiosis modulates the relationship between the host and the gut microbiota. Since commensal microbiota and the host are a unique entity in a continuum along the GI tract,
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every change in one of these players is able to modify the whole homeostasis. In this scenario, H. pylori infection is associated with changes in the gastric microenvironment, which in turn affects the gastric microbiota composition, but also might trigger large intestinal microbiota changes. It is able to influence all the vital pathways of human system and also to influence microbiota composition along the GI tract. This can cause a change in the normal functions exerted by intestinal commensal microorganisms (i.e., Clostridia) leading to a new gastrointestinal physiological balance. Furthermore, increasing evidences are focussing on its role also in pathological aspects not immediately related to the GI tract, such as metabolic syndrome and gynaecological diseases. This new approach in studying gut microbiota has obvious therapeutic implications and could lead to perform detailed mechanistic studies to improve the development of microbial therapies that may modulate the composition of the gut microflora with the end goal of promoting gut health.
Practice Points The GI tract is a complex and dynamic network with interplay between host cells and commensal microbiota. H. pylori infection is associated with changes in the gastric microenvironment, but also might trigger large intestinal microbiota changes leading to a new gastrointestinal physiological balance. Clostridia, contributing to a significant portion of indigenous bacteria in the large intestine, are strongly involved in the maintenance of overall gut function and could be influenced by H. pylori colonization.
Research agenda Detailed studies are necessary to understand if H. pylori colonization is associated to a functional modulation of the intestinal microbiota. Design of additional mechanistic studies to evaluate the overall impact of H. pylori eradication on the human health is required. It will be fascinating to elucidate the underlying mechanisms for xenobiotic resistance and metabolism in the active human gut microbiota. Detailed mechanistic studies are needed to improve the development of microbial therapies that may modulate the whole composition and function of the gut microflora.
Conflict of interest statement None. References [1] Walker WA, Wu M, Isselbacher KJ, Bloch KJ. Intestinal uptake of macromolecules. III. Studies on the mechanism by which immunization interferes with antigen uptake. J Immunol 1975;115:854e61. [2] Walker WA, Wu M, Isselbacher KJ, Bloch KJ. Intestinal uptake of macromolecules. IV e The effect of pancreatic duct ligation on the breakdown of antigen and antigen-antibody complexes on the intestinal surface. Gastroenterology 1975;69: 1223e9. [3] Leser TD, Molbak L. Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host. Environ Microbiol 2009;11:2194e206. [4] Neish AS. Microbes in gastrointestinal health and disease. Gastroenterology 2009;136:65e80.
L.R. Lopetuso et al. / Best Practice & Research Clinical Gastroenterology 28 (2014) 995e1002
1001
[5] Eckburg PB, Bik EM, Bernstein CN, Purdom E, Dethlefsen L, Sargent M, et al. Diversity of the human intestinal microbial flora. Science 2005;308:1635e8. [6] Gill SR, Pop M, Deboy RT, Eckburg PB, Turnbaugh PJ, Samuel BS, et al. Metagenomic analysis of the human distal gut microbiome. Science 2006;312:1355e9. [7] Scanlan PD, Marchesi JR. Micro-eukaryotic diversity of the human distal gut microbiota: qualitative assessment using culture-dependent and -independent analysis of faeces. ISME J 2008;2:1183e93. [8] Zhang T, Breitbart M, Lee WH, Run JQ, Wei CL, Soh SW, et al. RNA viral community in human feces: prevalence of plant pathogenic viruses. PLoS Biol 2006;4:e3. [9] Breitbart M, Haynes M, Kelley S, Angly F, Edwards RA, Felts B, et al. Viral diversity and dynamics in an infant gut. Res Microbiol 2008;159:367e73. [10] Hold GL, Pryde SE, Russell VJ, Furrie E, Flint HJ. Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis. FEMS Microbiol Ecol 2002;39:33e9. [11] Backhed F, Ley RE, Sonnenburg JL, Peterson DA, Gordon JI. Host-bacterial mutualism in the human intestine. Science 2005; 307:1915e20. [12] Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci U S A 2005;102:11070e5. [13] Ley RE, Peterson DA, Gordon JI. Ecological and evolutionary forces shaping microbial diversity in the human intestine. Cell 2006;124:837e48. [14] Frank DN, St Amand AL, Feldman RA, Boedeker EC, Harpaz N, Pace NR. Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases. Proc Natl Acad Sci U S A 2007;104:13780e5. [15] Rajilic-Stojanovic M, Smidt H, de Vos WM. Diversity of the human gastrointestinal tract microbiota revisited. Environ Microbiol 2007;9:2125e36. [16] Tap J, Mondot S, Levenez F, Pelletier E, Caron C, Furet JP, et al. Towards the human intestinal microbiota phylogenetic core. Environ Microbiol 2009;11:2574e84. [17] Manson JM, Rauch M, Gilmore MS. The commensal microbiology of the gastrointestinal tract. Adv Exp Med Biol 2008;635: 15e28. [18] McCracken VJ, Lorenz RG. The gastrointestinal ecosystem: a precarious alliance among epithelium, immunity and microbiota. Cell Microbiol 2001;3:1e11. [19] Lievin-Le Moal V, Servin AL. The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota. Clin Microbiol Rev 2006;19:315e37. [20] Scaldaferri F, Pizzoferrato M, Gerardi V, Lopetuso L, Gasbarrini A. The gut barrier: new acquisitions and therapeutic approaches. J Clin Gastroenterol 2012;46(Suppl.):S12e7. [21] Sekirov I, Russell SL, Antunes LC, Finlay BB. Gut mircobiota in health and disease. Physiol Rev 2010;90:859e904. [22] Silva AM, Barbosa FH, Duarte R, Vieira LQ, Arantes RM, Nicoli JR. Effect of Bifidobacterium longum ingestion on experimental salmonellosis in mice. J Appl Microbiol 2004;97. [23] Truusalu K, Rea M. Eradication of Salmonella typhimurium infection in a murine model of typhoid fever with the cimbination of probiotic Lactobacillus fermentum ME-3 and ofloxacin. BMC Microbiol 2008;8. [24] Searle LE, Best A, Nunez A, Salguero FJ, Johnson L, Weyer U, et al. A mixture containing galactooligosaccharide, produced by the enzymic activity of Bifidobacterium bifidum, reduces Salmonella enterica serovar Typhimurium infection in mice. J Med Microbiol 2009;58:37e48. [25] Martens EC, R Rea. Coordinate regulation of glycan degradation and polysaccharide capsule biosynthesis by a prominent gut symbiont. J Biol Chem 2009;284. [26] Burger van Paassen N, V Aea. The regulation of intestinal mucin MUC2 expression by short chain fatty acid: implications for epithelial protection. Biochem J 2009;420. [27] Dharmani P, S Vea. Role of intestinal mucins in annate host defense mechanisms against pathogens. J Innate Immun 2009;1. [28] Galdeano CM, Perdigon G. The probiotic bacterium Lactobacillus casei induces activation of the gut mucosal immune system through innate immunity. Clin Vaccine Immunol 2006;13:219e26. [29] Leblanc J, Fliss I, Matar C. Induction of a humoral immune response following an Escherichia coli O157:H7 infection with an immunomodulatory peptidic fraction derived from Lactobacillus helveticus-fermented milk. Clin Diagn Lab Immunol 2004;11:1171e81. [30] Allen CA, Torres AG. Host-microbe communication within the GI tract. Adv Exp Med Biol 2008;635:93e101. [31] Parashar UD, Gibson CJ, Bresee JS, Glass RI. Rotavirus and severe childhood diarrhea. Emerg Infect Dis 2006;12:304e6. [32] Swidsinski A, Ladhoff A, Pernthaler A, Swidsinski S, Loening-Baucke V, Ortner M, et al. Mucosal flora in inflammatory bowel disease. Gastroenterology 2002;122:44e54. [33] Hill DA, Artis D. Intestinal bacteria and the regulation of immune cell homeostasis. Annu Rev Immunol 2010;28:623e67. [34] Sartor RB. Microbial influences in inflammatory bowel diseases. Gastroenterology 2008;134:577e94. [35] Lozupone CA, Stombaugh JI, Gordon JI, Jansson JK, Knight R. Diversity, stability and resilience of the human gut microbiota. Nature 2012;489:220e30. [36] Lopetuso LR, Scaldaferri F, Petito V, Gasbarrini A. Commensal Clostridia: leading players in the maintenance of gut homeostasis. Gut Pathog 2013;5:23. [37] Camilleri M, Madsen K, Spiller R, Greenwood-Van Meerveld B, Verne GN. Intestinal barrier function in health and gastrointestinal disease. Neurogastroenterol Motil 2012;24:503e12. [38] Fasano A. Leaky gut and autoimmune diseases. Clin Rev Allergy Immunol 2012;42:71e8. [39] Fasano A. Zonulin and its regulation of intestinal barrier function: the biological door to inflammation, autoimmunity, and cancer. Physiol Rev 2011;91:151e75. [40] Kelly D, Conway S, Aminov R. Commensal gut bacteria: mechanisms of immune modulation. Trends Immunol 2005;26: 326e33. [41] Dzierzanowska-Fangrat K, Dzierzanowska D. Helicobacter pylori: microbiology and interactions with gastrointestinal microflora. J Physiol Pharmacol e Off J Pol Physiol Soc 2006;57(Suppl. 3):5e14. [42] Yamaoka Y. Mechanisms of disease: Helicobacter pylori virulence factors. Nat Rev Gastroenterol Hepatol 2010;7:629e41.
1002
L.R. Lopetuso et al. / Best Practice & Research Clinical Gastroenterology 28 (2014) 995e1002
[43] Pandey R, Misra V, Misra SP, Dwivedi M, Kumar A, Tiwari BK. Helicobacter pylori and gastric cancer. Asian Pac J Cancer Prev e APJCP 2010;11:583e8. [44] Gasbarrini A, Franceschi F, Armuzzi A, Ojetti V, Candelli M, Torre ES, et al. Extradigestive manifestations of Helicobacter pylori gastric infection. Gut 1999;45(Suppl. 1):I9e12. [45] Solnick JV, Franceschi F, Roccarina D, Gasbarrini A. Extragastric manifestations of Helicobacter pylori infectioneother Helicobacter species. Helicobacter 2006;11(Suppl. 1):46e51. [46] Capurso G, Marignani M, Delle Fave G, Annibale B. Iron-deficiency anemia in premenopausal women: why not consider atrophic body gastritis and Helicobacter pylori role? Am J Gastroenterol 1999;94:3084e5. [47] Akcam M, Ozdem S, Yilmaz A, Gultekin M, Artan R. Serum ferritin, vitamin B(12), folate, and zinc levels in children infected with Helicobacter pylori. Dig Dis Sci 2007;52:405e10. [48] Aebischer T, Fischer A, Walduck A, Schlotelburg C, Lindig M, Schreiber S, et al. Vaccination prevents Helicobacter pyloriinduced alterations of the gastric flora in mice. FEMS Immunol Med Microbiol 2006;46:221e9. [49] Yin YN, Wang CL, Liu XW, Cui Y, Xie N, Yu QF, et al. Gastric and duodenum microflora analysis after long-term Helicobacter pylori infection in Mongolian Gerbils. Helicobacter 2011;16:389e97. [50] Heimesaat MM, Fischer A, Plickert R, Wiedemann T, Loddenkemper C, Gobel UB, et al. Helicobacter pylori induced gastric immunopathology is associated with distinct microbiota changes in the large intestines of long-term infected Mongolian gerbils. PloS One 2014;9:e100362. [51] Merli M, Lucidi C, Di Gregorio V, Giannelli V, Giusto M, Ceccarelli G, et al. The chronic use of beta-blockers and proton pump inhibitors may affect the rate of bacterial infections in cirrhosis. Liver Int 2014 May 17. http://dx.doi.org/10.1111/liv. 12593 [Epub ahead of print]. [52] Maurice CF, Haiser HJ, Turnbaugh PJ. Xenobiotics shape the physiology and gene expression of the active human gut microbiome. Cell 2013;152:39e50.
