Gut-associated bacterial microbiota in paediatric patients with inflammatory bowel disease

Rectal administration of Lactobacillus casei DG modifies flora composition and Toll-like receptor expression in colonic mucosa of patients with mild ulcerative colitis

BACKGROUND

An imbalance in gut microbiota seems to contribute to the development of chronic inflammatory disorders of the gastrointestinal tract, such as ulcerative colitis (UC). Although it has been suggested that probiotic supplementation is an effective approach to colitis, its effects on intestinal flora and on mucosal cytokine balance have never been explored.

AIM

To evaluate the effect of Lactobacillus casei (L. casei) DG, a probiotic strain, on colonic-associated microbiota, mucosal cytokine balance, and toll-like receptor (TLR) expression.

METHODS

Twenty-six patients with mild left-sided UC were randomly allocated to one of three groups for an 8-week treatment period: the first group of 7 patients received oral 5-aminosalicylic acid (5-ASA) alone, the second group of 8 patients received oral 5-ASA plus oral L. casei DG, and the third group of 11 patients received oral 5-ASA and rectal L. casei DG. Biopsies were collected from the sigmoid region to culture mucosal-associated microbes and to assess cytokine and TLR messenger RNA (mRNA) levels by quantitative real-time polymerase chain reaction (RT-PCR).

RESULTS

5-ASA alone or together with oral L. casei DG failed to affect colonic flora and TLR expression in a significant manner, but when coupled with rectally administered L. casei DG, it modified colonic microbiota by increasing Lactobacillus spp. and reducing Enterobacteriaceae. It also significantly reduced TLR-4 and interleukin (IL)-1β mRNA levels and significantly increased mucosal IL-10.

CONCLUSIONS

Manipulation of mucosal microbiota by L. casei DG and its effects on the mucosal immune system seem to be required to mediate the beneficial activities of probiotics in UC patients.

The role of bacteria and pattern-recognition receptors in Crohn's disease

Crohn's disease is widely regarded as a multifactorial disease, and evidence from human and animal studies suggests that bacteria have an instrumental role in its pathogenesis. Comparison of the intestinal microbiota of patients with Crohn's disease to that of healthy controls has revealed compositional changes. In most studies these changes are characterized by an increase in the abundance of Bacteroidetes and Proteobacteria and a decrease in that of Firmicutes. In addition, a number of specific mucosa-associated bacteria have been postulated to have a role in Crohn's disease, including Mycobacterium avium subspecies paratuberculosis, adherent and invasive Escherichia coli, Campylobacter and Helicobacter species. The association between mutations in pattern-recognition receptors (Toll-like receptors and Nod-like receptors) and autophagy proteins and Crohn's disease provides further evidence to suggest that defective sensing and killing of bacteria may drive the onset of disease. In this Review, we present recent advances in understanding the role of bacteria and the contribution of pattern-recognition receptors and autophagy in the pathogenesis of Crohn's disease.

[Gut microbiota and IBD]

Gut microbiota contains about 10(14) bacterial cells classified within 4 bacterial phyla, namely Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria. Much of the information has been generated through the application of nucleic acid-based methodologies (16S rRNA) which provide a cornerstone of microbial taxonomy. Inflammatory bowel disease (IBD) involves a dysregulated immune response to the gut microbiota in genetically predisposed hosts. Experimental animal models of colitis provide the best evidence that bacteria present in the bowel of the animals have an essential role in the pathogenesis of colitis since in most models, germ-free animals do not develop disease. Moreover, in the immunodeficient mouse model of colitis called TRUC (T-bet-/- x RAG2-/-), a colitogenic gut microbiota is selected and can be transmitted to mice with intact immunity and induce colitis. Current interest therefore focuses on the bacterial community as the source of antigens that fuel the chronic inflammation seen in IBD. Dysbiosis, an imbalance between harmful and protective bacteria, has been evoked and investigated in IBD. Thus, besides the classical pathogens, gut microbiota can drive pathogenicity via two mechanisms: an expansion of 'pro-inflammatory' species or a restriction in the protective compounds of the microbiota. Complexity of the microbiota suggests that both mechanisms may contribute to chronic gut inflammation in IBD.

A role for the RNA chaperone Hfq in controlling adherent-invasive Escherichia coli colonization and virulence

Adherent-invasive Escherichia coli (AIEC) has been linked with the onset and perpetuation of inflammatory bowel diseases. The AIEC strain LF82 was originally isolated from an ileal biopsy from a patient with Crohn's disease. The pathogenesis of LF82 results from its abnormal adherence to and subsequent invasion of the intestinal epithelium coupled with its ability to survive phagocytosis by macrophages once it has crossed the intestinal barrier. To gain further insight into AIEC pathogenesis we employed the nematode Caenorhabditis elegans as an in vivo infection model. We demonstrate that AIEC strain LF82 forms a persistent infection in C. elegans, thereby reducing the host lifespan significantly. This host killing phenotype was associated with massive bacterial colonization of the nematode intestine and damage to the intestinal epithelial surface. C. elegans killing was independent of known LF82 virulence determinants but was abolished by deletion of the LF82 hfq gene, which encodes an RNA chaperone involved in mediating posttranscriptional gene regulation by small non-coding RNAs. This finding reveals that important aspects of LF82 pathogenesis are controlled at the posttranscriptional level by riboregulation. The role of Hfq in LF82 virulence was independent of its function in regulating RpoS and RpoE activity. Further, LF82Δhfq mutants were non-motile, impaired in cell invasion and highly sensitive to various chemical stress conditions, reinforcing the multifaceted function of Hfq in mediating bacterial adaptation. This study highlights the usefulness of simple non-mammalian infection systems for the identification and analysis of bacterial virulence factors.

Ulcerative colitis and irritable bowel patients exhibit distinct abnormalities of the gut microbiota

BACKGROUND

Previous studies suggest a link between gut microbiota and the development of ulcerative colitis (UC) and irritable bowel syndrome (IBS). Our aim was to investigate any quantitative differences in faecal bacterial compositions in UC and IBS patients compared to healthy controls, and to identify individual bacterial species that contribute to these differences.

METHODS

Faecal microbiota of 13 UC patients, 11 IBS patients and 22 healthy volunteers were analysed by PCR-Denaturing Gradient Gel Electrophoresis (DGGE) using universal and Bacteroides specific primers. The data obtained were normalized using in-house developed statistical method and interrogated by multivariate approaches. The differentiated bands were excised and identified by sequencing the V3 region of the 16S rRNA genes.

RESULTS

Band profiles revealed that number of predominant faecal bacteria were significantly different between UC, IBS and control group (p < 10-4). By assessing the mean band numbers in UC (37 ± 5) and IBS (39 ± 6), compared to the controls (45 ± 3), a significant decrease in bacterial species is suggested (p = 0.01). There were no significant differences between IBS and UC. Biodiversity of the bacterial species was significantly lower in UC (μ = 2.94, σ = 0.29) and IBS patients (μ = 2.90, σ = 0.38) than controls (μ = 3.25, σ = 0.16; p = 0.01). Moreover, similarity indices revealed greater biological variability of predominant bacteria in UC and IBS compared to the controls (median Dice coefficients 76.1% (IQR 70.9 - 83.1), 73.8% (IQR 67.0 - 77.5) and 82.9% (IQR 79.1 - 86.7) respectively). DNA sequencing of discriminating bands suggest that the presence of Bacteroides vulgatus, B. ovatus, B. uniformis, and Parabacteroides sp. in healthy volunteers distinguishes them from IBS and UC patients. DGGE profiles of Bacteroides species revealed a decrease of Bacteroides community in UC relative to IBS and controls.

CONCLUSION

Molecular profiling of faecal bacteria revealed abnormalities of intestinal microbiota in UC and IBS patients, while different patterns of Bacteroides species loss in particular, were associated with UC and IBS.

In vitro anaerobic biofilms of human colonic microbiota

The human gastrointestinal tract hosts a complex community of microorganisms that grow as biofilms on the intestinal mucosa. These bacterial communities are not well characterized, although they are known to play an important role in human health. This study aimed to develop a model for culturing biofilms (surface-adherent communities) of intestinal microbiota. The model utilizes adherent mucosal bacteria recovered from colonic biopsies to create multi-species biofilms. Culture on selective media and confocal microscopy indicated the biofilms were composed of a diverse community of bacteria. Molecular analyses confirmed that several phyla were represented in the model, and demonstrated stability of the community over 96 h when cultured in the device. This model is novel in its use of a multi-species community of mucosal bacteria grown in a biofilm mode of growth.

Abnormally expressed ER stress response chaperone Gp96 in CD favours adherent-invasive Escherichia coli invasion

BACKGROUND AND AIMS

Crohn's disease (CD) ileal lesions are colonised by pathogenic adherent-invasive Escherichia coli (AIEC) producing outer membrane vesicles (OMVs) that contribute to the bacterial invasion process. In addition, increased expression of endoplasmic reticulum (ER)-localised stress response proteins, due to ER stress, is observed in patients with CD. The expression of the ER-localised stress response protein Gp96 in patients with CD and its biological role with regards to the ability of AIEC to invade intestinal epithelial cells were analysed.

METHODS AND RESULTS

Immunohistochemistry on tissue arrays showed that, together with CEACAM6 (carcinoembryonic antigen-related cell adhesion molecule 6) or the ER stress protein Grp78, Gp96 is also strongly expressed at the apical plasma membrane of the ileal epithelial cells of 50% of patients with CD. Invasion experiments in the presence of antibodies raised against Gp96, or after transfection of Intestine-407 cells with gp96 small interfering RNA (siRNA), indicated that Gp96 is essential to promote AIEC LF82 invasion, allowing, via the recognition of the outer membrane protein OmpA, OMVs to fuse with intestinal epithelial cells.

CONCLUSIONS

Gp96 is overexpressed on the apical surface of ileal epithelial cells in patients with CD and acts as a host cell receptor for OMVs, promoting AIEC invasion. From the results shown here, it is speculated that AIEC could take advantage of the abnormal expression of Gp96 in patients with CD to invade the ileal mucosa.

Intestinal Host-Microbe Interactions under Physiological and Pathological Conditions

The intestinal mucosa is unique in that it can be tolerant to the resident, symbiotic microbiota but remaining, at the same time, responsive to and able to fight pathogens. The close interaction between host-symbiotic microbiota at the mucosal level poses important challenges since microbial breaches through the gut barrier can result in the breakdown of gut homeostasis. In this paper, hosts-integrated components that help to preserve intestinal homeostasis including barrier and immune function are discussed. In addition global alterations of the microbiota that can play a role in the initiation of an exaggerated inflammatory response through an abnormal signaling of the innate and adaptive immune response are briefly described.

Real-time analysis of mucosal flora in patients with inflammatory bowel disease in India

Mucosa-associated bacterial flora from control individuals and inflammatory bowel disease (IBD) patients were evaluated by real-time analysis using 16S rRNA-based genus-specific primers. Our data show a clear delineation in concentration of bacteria between the predominating and subdominating genera under disease conditions, indicating that the subsets of bacteria participating in the pathogenesis of ulcerative colitis (UC) and Crohn's disease (CD) are likely to be different.

Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82

BACKGROUND

Ileal lesions of Crohn's disease (CD) patients are abnormally colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells and macrophages.

PRINCIPAL FINDINGS

We report here the complete genome sequence of E. coli LF82, the reference strain of adherent-invasive E. coli associated with ileal Crohn's disease. The LF82 genome of 4,881,487 bp total size contains a circular chromosome with a size of 4,773,108 bp and a plasmid of 108,379 bp. The analysis of predicted coding sequences (CDSs) within the LF82 flexible genome indicated that this genome is close to the avian pathogenic strain APEC_01, meningitis-associated strain S88 and urinary-isolated strain UTI89 with regards to flexible genome and single nucleotide polymorphisms in various virulence factors. Interestingly, we observed that strains LF82 and UTI89 adhered at a similar level to Intestine-407 cells and that like LF82, APEC_01 and UTI89 were highly invasive. However, A1EC strain LF82 had an intermediate killer phenotype compared to APEC-01 and UTI89 and the LF82 genome does not harbour most of specific virulence genes from ExPEC. LF82 genome has evolved from those of ExPEC B2 strains by the acquisition of Salmonella and Yersinia isolated or clustered genes or CDSs located on pLF82 plasmid and at various loci on the chromosome.

CONCLUSION

LF82 genome analysis indicated that a number of genes, gene clusters and pathoadaptative mutations which have been acquired may play a role in virulence of AIEC strain LF82.

Lactobacillus plantarum prevents the upregulation of adhesion molecule expression in an experimental colitis model

BACKGROUND

Lactobacillus consumption has been shown to attenuate the severity of experimental colitis. Whether the effects of Lactobacillus on colitis are related to modulation of leukocyte recruitment into the inflamed intestine is unclear.

AIMS

To investigate the effect of Lactobacillus plantarum daily intragastric administration on lymphocyte homing and intestinal inflammation in interleukin 10 (IL-10) knockout mice, an experimental model of colitis.

METHODS

Two groups of ten IL-10 knockout mice were fed phosphate buffered saline containing Lactobacillus plantarum 1258 or unmodified vehicle for 4 weeks. Two groups of ten wild-type mice were used as controls. At killing, the bowels were histologically scored and evaluated by transmission electron microscopy. Mucosal addressin cell adhesion molecule 1 (MAdCAM-1) and intercellular adhesion molecule 1 (ICAM-1) expression were determined by immunohistochemistry. The levels of proinflammatory cytokines, tumor necrosis factor alpha (TNF-alpha), and interferon gamma (IFN-gamma) were determined by ELISA. In addition, levels of CD3, alpha4beta7, ICAM-1, and MAdCAM-1 were determined by reverse-transcription polymerase chain reaction and Western blot.

RESULTS

L. plantarum treatment improved the histological damage score in KO mice compared to untreated KO mice. L. plantarum significantly attenuated the expression of MAdCAM-1, ICAM-1, CD3, and alpha4beta7, but did not affect the levels of TNF-alpha and IFN-gamma when treated KO mice were compared to untreated KO mice.

CONCLUSIONS

L. plantarum interfered with the upregulation of adhesion molecules observed in IL-10 knockout mice compared to wild-type mice, attenuating the symptoms of colitis.

Abnormalities in the handling of intracellular bacteria in Crohn's disease

Ileal lesions in Crohn's disease (CD) patients are colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells. Recent advances have highlighted the importance of the innate immune system and the critical relationship between the gut flora and the intestinal mucosa. Several combinations of genetic predisposing factors to CD have been described, with the most significant replicable associations including genes for intracellular receptor of bacterial cell walls (NOD2/CARD15), and for bacterial clearance and antigen processing through autophagy (ATG16L1 and IRGM). We recently reported that in IRGM and ATG16L1 deficient cells, intracellular AIEC LF82 bacteria have enhanced replication and that autophagy deficiency surprisingly did not interfere with the ability of intracellular bacteria to survive and/or replicate for any other E. coli strains tested, including nonpathogenic, environmental, commensal, or pathogenic strains involved in gastroenteritis. As autophagy is an innate defense mechanism acting as a cell-autonomous system for elimination of intracellular pathogens, these findings lead weight to the notion that intracellular bacteria including AIEC might play a role in CD pathogenesis.

Probiotics and the gut microbiota in intestinal health and disease

The use of probiotics is increasing in popularity for both the prevention and treatment of a variety of diseases. While a growing number of well-conducted, prospective, randomized, controlled, clinical trials are emerging and investigations of underlying mechanisms of action are being undertaken, questions remain with respect to the specific immune and physiological effects of probiotics in health and disease. This Review considers recent advances in clinical trials of probiotics for intestinal disorders in both adult and pediatric populations. An overview of recent in vitro and in vivo research related to potential mechanisms of action of various probiotic formulations is also considered.

Microbiota in pediatric inflammatory bowel disease

OBJECTIVE

To test the hypothesis that compared with controls, children with inflammatory bowel disease (IBD) exhibit differences in the relationships between gut microbiota and disease activity.

STUDY DESIGN

Children and adolescents (n = 69; median age, 14 years) with IBD and 25 healthy controls (median age, 14 years) were recruited for the study. The disease activity was determined according to the Pediatric Ulcerative Colitis Activity Index or the Pediatric Crohn Disease Activity Index. Cell counts of 9 bacterial groups and species in the fecal microbiota were monitored by real-time polymerase chain reaction analysis.

RESULTS

Although no major changes were observed in patients with ulcerative colitis, except for a decrease in bifidobacteria in the active state of IBD, children with active and inactive Crohn's disease (CD) had lower numbers of Faecalibacterium prausnitzii and bifidobacteria (P <.05), and patients with active CD had higher numbers of Escherichia coli (P <.05).

CONCLUSIONS

The microbiota in children with CD is characterized by decreased numbers of F praunsitzii and increased numbers of E coli.

Role of the gut microbiota in defining human health

The human superorganism is a conglomerate of mammalian and microbial cells, with the latter estimated to outnumber the former by ten to one and the microbial genetic repertoire (microbiome) to be approximately 100-times greater than that of the human host. Given the ability of the immune response to rapidly counter infectious agents, it is striking that such a large density of microbes can exist in a state of synergy within the human host. This is particularly true of the distal gastrointestinal (GI) tract, which houses up to 1000 distinct bacterial species and an estimated excess of 1 x 10(14) microorganisms. An ever-increasing body of evidence implicates the GI microbiota in defining states of health and disease. Here, we review the literature in adult and pediatric GI microbiome studies, the emerging links between microbial community structure, function, infection and disease, and the approaches to manipulate this crucial ecosystem to improve host health.

A distinctive 'microbial signature' in celiac pediatric patients

BACKGROUND

Celiac Disease (CD) is an autoimmune disorder of the small intestine in which dietary gluten ingestion leads to a chronic enteropathy. Recently, scientific evidence suggested a potential role of gut microbiota in CD. To have a snapshot of dominant duodenal microbiota we analyzed the mucosa-associated microbiota of 20 children with CD, before and after a gluten-free diet (GFD) regimen, and of 10 controls. Total DNA was extracted from duodenal biopsies and amplification products of 16S ribosomal DNA were compared by temporal temperature gradient gel electrophoresis (TTGE). TTGE profiles were analyzed by statistical multivariate analysis.

RESULTS

The average number of bands in TTGE profiles was significantly higher (P < 0.0001) in active (n.b. 16.7 +/- 0.7) and inactive states (n.b. 13.2 +/- 0.8) than in controls (n.b. 3.7 +/- 1.3). Mean interindividual similarity index was 54.9% +/- 14.9% for active disease, 55.6% +/- 15.7% for remission state and 21.8% +/- 30.16% for controls. Similarity index between celiac children before and after GFD treatment was 63.9% +/- 15.8%. Differences in microbiota biodiversity were among active and remission state (P = 0.000224) and amid active CD and controls (P < 0.001). Bacteroides vulgatus and Escherichia coli were detected more often in CD patients than in controls (P < 0.0001).

CONCLUSIONS

Overall, the results highlighted a peculiar microbial TTGE profile and a significant higher biodiversity in CD pediatric patients' duodenal mucosa. The possible pathophysiological role of these microbial differences needs further characterization.

Cesarean delivery is associated with celiac disease but not inflammatory bowel disease in children

OBJECTIVES

The aim of this study was to analyze a possible association between cesarean delivery and enteric inflammatory diseases in children.

METHODS

A retrospective, multicenter, case-control study that included 1950 children was performed in cooperation with 26 university and 16 nonacademic children's hospitals. Information on intestinal disease manifestation, together with mode of delivery and gestational age at birth, postnatal complications, and breastfeeding, was collected by the attending physician from children and their parents who were visiting a gastrointestinal outpatient clinic for Crohn disease (CD; 516 cases), ulcerative colitis (250 cases), celiac disease (157 cases), and other gastrointestinal diseases (165 cases) and control subjects who were visiting ophthalmologic, orthodontic, and dental outpatient clinics (862 cases).

RESULTS

Whereas the rate of cesarean delivery of children with Crohn disease or ulcerative colitis was similar to that of control subjects, a significantly enhanced likelihood of being born by cesarean delivery was found in children with celiac disease compared with control subjects (odds ratio: 1.8 [95% confidence interval: 1.13-2.88]; P = .014).

CONCLUSIONS

The mode of delivery and associated alterations in the development of the enteric homeostasis during the neonatal period might influence the incidence of celiac disease.

Campylobacter concisus and other Campylobacter species in children with newly diagnosed Crohn's disease

BACKGROUND

Campylobacter concisus and other members of the Campylobacter genus have recently been suggested as possible etiological agents of Crohn's disease (CD). To further investigate this issue we determined the prevalence of these organisms in pediatric patients newly diagnosed with CD.

METHODS

DNA was extracted from fecal specimens collected from 54 children with CD, 27 noninflammatory bowel disease (non-IBD), and 33 healthy controls and subjected to polymerase chain reaction (PCR) sequencing.

RESULTS

Detection of C. concisus DNA using a newly developed PCR assay targeting the 16S rRNA gene of C. concisus showed that 65% (35/54) of fecal samples from CD children were positive, a prevalence significantly higher than that in the healthy (33%, 11/33, P = 0.008) and non-IBD controls (37%, 10/27, P = 0.03). The prevalence of all Campylobacter DNA using genus-specific primers in children with CD was 72% (39/54), which was significantly higher than the 30% (10/33, P = 0.0002) and 30% (8/27, P = 0.0003) observed in healthy and non-IBD controls, respectively.

CONCLUSIONS

Given the strengthening evidence for a significantly higher prevalence of C. concisus and other non-jejuni Campylobacter species in pediatric CD, investigation into the role of these non-jejuni Campylobacter species in the initiation of human IBD is clearly a priority.

Metronidazole effects on microbiota and mucus layer thickness in the rat gut

Both mucus and mucosa-associated bacteria form a specific environment in the gut; their disruption may play a crucial role in the development of intestinal bowel disease (IBD). Metronidazole, an antibiotic used in the treatment of IBD, alters gut microbiota and reduces basal oxidative stress to proteins in colonic tissue of healthy rats. The aim of this study was to evaluate the impact of the altered microbiota due to the metronidazole on the thickness of the mucus layer. This study was performed in healthy untreated rats (control group) or rats treated by metronidazole (metronidazole-treated rats, 1 mg mL(-1) in drinking water for 7 days). Both PCR-temporal temperature gradient gel electrophoresis and quantitative PCR (qPCR) revealed an altered microbiota with an increase in bifidobacteria and enterobacteria in metronidazole-treated rats compared with control rats. Moreover, a dominant bifidobacterial species, Bifidobacterium pseudolongum, was detected. Using qPCR and FISH, we showed that bifidobacteria were also increased in the microbiota-associated mucosa. At the same time, the mucus layer thickness was increased approximately twofold. These results could explain the benefits of metronidazole treatment and warrant further investigations to define the role of bifidobacteria in the colonic mucosa.

Inflammatory bowel disease

Insights into inflammatory bowel disease (IBD) are advancing rapidly owing to immunologic investigations of a plethora of animal models of intestinal inflammation, ground-breaking advances in the interrogation of diseases that are inherited as complex genetic traits, and the development of culture-independent methods to define the composition of the intestinal microbiota. These advances are bringing a deeper understanding to the genetically determined interplay between the commensal microbiota, intestinal epithelial cells, and the immune system and the manner in which this interplay might be modified by relevant environmental factors in the pathogenesis of IBD. This review examines these interactions and, where possible, potential lessons from IBD-directed, biologic therapies that may allow for elucidation of pathways that are central to disease pathogenesis in humans.

Inflammatory bowel disease

Insights into inflammatory bowel disease (IBD) are advancing rapidly owing to immunologic investigations of a plethora of animal models of intestinal inflammation, ground-breaking advances in the interrogation of diseases that are inherited as complex genetic traits, and the development of culture-independent methods to define the composition of the intestinal microbiota. These advances are bringing a deeper understanding to the genetically determined interplay between the commensal microbiota, intestinal epithelial cells, and the immune system and the manner in which this interplay might be modified by relevant environmental factors in the pathogenesis of IBD. This review examines these interactions and, where possible, potential lessons from IBD-directed, biologic therapies that may allow for elucidation of pathways that are central to disease pathogenesis in humans.

99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: induction and control of regulatory T cells in the gastrointestinal tract: consequences for local and peripheral immune responses

Regulatory T cells play a crucial role in normal gut homeostasis, as well as during infection with microbial or parasitic pathogens. Prior to infection, interactions with the commensal microflora are essential to differentiation of a healthy steady-state level of immunoregulation, mediated through both Toll-like receptor-dependent and -independent pathways. The ingress of pathogenic organisms may, according to the context, promote or reverse the regulatory environment, with onward consequences for inflammation in both the intestinal and extra-intestinal settings. Appropriate regulation of gut immunity thus depends upon a complex three-way interplay between host cells, commensals and pathogens, and can exert a major impact on systemic responses including allergy and autoimmunity.

Relationships between inflammatory bowel disease and perinatal factors: both maternal and paternal disease are related to preterm birth of offspring

BACKGROUND

The aims of this study were to explore the influences of familial, maternal, and paternal inflammatory disease (IBD) on perinatal outcomes in the offspring and the risk for development of IBD related to perinatal factors.

METHODS

Eighty-five patients with Crohn's disease (CD) and 86 with ulcerative colitis (UC) were included from a population-based incidence study enrolled 1990-1994. Family and birth records of these patients, as well as of their 207 infants, were drawn from the Norwegian Medical Birth Registry, established in 1967, and compared with the national birth cohort from the same period.

RESULTS

Maternal (odds ratio [OR] = 2.15, 95% confidence interval [CI]: 1.36, 3.39) and paternal IBD (OR = 3.02, 95% CI: 1.82, 5.01) influenced the risk of preterm birth (<37 weeks), which further increased if the affected parents had a first-degree relative with IBD (OR = 4.29, 95% CI: 1.59, 11.63). Maternal CD was associated with lower birth weight in the offspring (crude difference: 271.79 g, 95% CI: 87.83, 455.77, versus controls). Maternal UC increased the risk of perinatal bacterial infection in the offspring (OR = 6.03, 95% CI: 2.03, 17.91). IBD patients (2.3%) were less likely to be delivered by cesarean section than controls (8.1%) (OR = 0.27, CI: 95%: 0.10, 0.73).

CONCLUSIONS

Familial, maternal, and paternal IBD were linked to preterm birth, which might be explained by genetic mechanisms. The present protective effect of cesarean sections needs further clarification in future studies.

Novel Burkholderiales 23S rRNA genes identified in ileal biopsy samples from children: preliminary evidence that a subtype is associated with perianal Crohn's disease

A novel family of Burkholderiales bacteria was identified in ileal biopsy specimens from children presenting with symptoms of inflammatory bowel disease. A molecular subtyping approach based on sequencing of a variable region of the bacteria's 23S rRNA genes identified three variants. Pilot analysis identified one variant to be significantly associated with perianal Crohn's disease.

[Inflammatory bowel diseases and enteric microbiota]

Intestinal mucosal layers are colonized by a complex microbiota that provides beneficial effects under normal physiological conditions, but is capable of contributing to chronic inflammatory disease such as inflammatory bowel disease (IBD) in susceptible individuals. Studies have shown that the enteric microbiota may drive the development of the gut immune system and can induce immune homeostasis as well as contribute to the development of IBD although the precise etiology is still unknown. Therefore, intestinal microbes seem to play a key role in the disease pathogenesis. Especially, dysbiosis, which is a shift in the composition of enteric microbiota to a nonphysiologic composition, is associated with one or more defects in mucosal immune functions, including microbe recognition, barrier function, intercellular communication, and anti-microbial effector mechanisms. This review focuses on the impact of enteric microbiota on the development and perpetuation of IBD. In addition, interactions with enteric bacteria and mucosal cells, including intestinal epithelial cells, dendritic cells, and T cells, to induce immune responses at mucosal surfaces have been discussed in the point of IBD pathogenesis. Further extension of the knowledge of enteric microbiota may lead to insights on the pathogenesis and new therapeutic strategies for IBD.

Microbial control of regulatory and effector T cell responses in the gut

The human intestine harbors and is in constant contact with 1000 trillion microbes, composed of an estimated 15,000 strains. Recent studies have changed our perspective of commensal microbes from benign but inert passengers, to active participants in the processing of food into useful metabolic components, the postnatal development of mucosal and systemic immunity, and in its long-term steady state function. Although mucosal surfaces have to constitutively integrate a multitude of microbial derived signals, new evidence suggests that defined bacteria or microbial products can play a dominant role in the induction of distinct class of immune responses. In this review we will focus on recent findings associating microbes that colonize or invade the gut, specialized mucosal DCs, and induction of effector or regulatory response in the GI tract.

Mucosal bacterial microflora and mucus layer thickness in adolescents with inflammatory bowel disease

AIM: To assess the mucosa-associated bacterial microflora and mucus layer in adolescents with inflammatory bowel disease (IBD).

METHODS: Sixty-one adolescents (mean age 15 years, SD ± 4.13) were included in the study. Intestinal biopsies from inflamed and non-inflamed mucosa of IBD patients and from controls with functional abdominal pain were cultured under aerobic and anaerobic conditions. The number of microbes belonging to the same group was calculated per weight of collected tissue. The mucus thickness in frozen samples was measured under a fluorescent microscope.

RESULTS: The ratios of different bacterial groups in inflamed and non-inflamed mucosa of IBD patients and controls were specific for particular diseases. Streptococcus spp. were predominant in the inflamed mucosa of Crohn’s disease (CD) patients (80% of all bacteria), and Lactobacillus spp. were predominant in ulcerative colitis patients (90%). The differences were statistically significant (P = 0.01-0.001). Lower number of bifidobacteria was observed in the whole IBD group. A relation was also found between clinical and endoscopic severity and decreased numbers of Lactobacillus and, to a lesser extent, of Streptococcus in biopsies from CD patients. The mucus layer in the inflamed sites was significantly thinner as compared to controls (P = 0.0033) and to non-inflamed areas in IBD patients (P = 0.031).

CONCLUSION: The significantly thinner mucosa of IBD patients showed a predominance of some aerobes specific for particular diseases, their numbers decreased in relation to higher clinical and endoscopic activity of the disease.

Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly

Ileal lesions in Crohn's disease (CD) patients are colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells. Recent genome-wide association studies have highlighted the autophagy pathway as being associated with CD risk. In the present study we investigated whether defects in autophagy enhance replication of commensal and pathogenic Escherichia coli and CD-associated AIEC. We show that functional autophagy limits intracellular AIEC replication and that a subpopulation of the intracellular bacteria is located within LC3-positive autophagosomes. In IRGM and ATG16L1 deficient cells intracellular AIEC LF82 bacteria have enhanced replication. Surprisingly autophagy deficiency did not interfere with the ability of intracellular bacteria to survive and/or replicate for any other E. coli strains tested, including non-pathogenic, environmental, commensal, or pathogenic strains involved in gastro enteritis. Together these findings demonstrate a central role for autophagy restraining Adherent-Invasive E. coli strains associated with ileal CD. AIEC infection in patients with polymorphisms in autophagy genes may have a significant impact on the outcome of intestinal inflammation.

Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly

Ileal lesions in Crohn's disease (CD) patients are colonized by pathogenic adherent-invasive Escherichia coli (AIEC) able to invade and to replicate within intestinal epithelial cells. Recent genome-wide association studies have highlighted the autophagy pathway as being associated with CD risk. In the present study we investigated whether defects in autophagy enhance replication of commensal and pathogenic Escherichia coli and CD-associated AIEC. We show that functional autophagy limits intracellular AIEC replication and that a subpopulation of the intracellular bacteria is located within LC3-positive autophagosomes. In IRGM and ATG16L1 deficient cells intracellular AIEC LF82 bacteria have enhanced replication. Surprisingly autophagy deficiency did not interfere with the ability of intracellular bacteria to survive and/or replicate for any other E. coli strains tested, including non-pathogenic, environmental, commensal, or pathogenic strains involved in gastro enteritis. Together these findings demonstrate a central role for autophagy restraining Adherent-Invasive E. coli strains associated with ileal CD. AIEC infection in patients with polymorphisms in autophagy genes may have a significant impact on the outcome of intestinal inflammation.

Crohn's disease adherent-invasive Escherichia coli colonize and induce strong gut inflammation in transgenic mice expressing human CEACAM

Abnormal expression of CEACAM6 is observed at the apical surface of the ileal epithelium in Crohn's disease (CD) patients, and CD ileal lesions are colonized by pathogenic adherent-invasive Escherichia coli (AIEC). We investigated the ability of AIEC reference strain LF82 to colonize the intestinal mucosa and to induce inflammation in CEABAC10 transgenic mice expressing human CEACAMs. AIEC LF82 virulent bacteria, but not nonpathogenic E. coli K-12, were able to persist in the gut of CEABAC10 transgenic mice and to induce severe colitis with reduced survival rate, marked weight loss, increased rectal bleeding, presence of erosive lesions, mucosal inflammation, and increased proinflammatory cytokine expression. The colitis depended on type 1 pili expression by AIEC bacteria and on intestinal CEACAM expression because no sign of colitis was observed in transgenic mice infected with type 1 pili–negative LF82-ΔfimH isogenic mutant or in wild-type mice infected with AIEC LF82 bacteria. These findings strongly support the hypothesis that in CD patients having an abnormal intestinal expression of CEACAM6, AIEC bacteria via type 1 pili expression can colonize the intestinal mucosa and induce gut inflammation. Thus, targeting AIEC adhesion to gut mucosa represents a new strategy for clinicians to prevent and/or to treat ileal CD.

Clinical efficacy of Lactobacillus acidophilus against experimental murine colitis and its effects on the expression of STAT1, T-bet and GATA3

AIM: To investigate the therapeutic efficacy of Lactobacillus acidophilus against experimental murine colitis and its effects on the expression of STAT1, T-bet and GATA3.

METHODS: Experimental murine colitis was induced with 2.5% dextran sulfate sodium (DSS). A total of 70 mice were randomly and equally divided into seven groups: model control group, negative control group, mesalamine group, low-dose Lactobacillus acidophilus group, medium-dose Lactobacillus acidophilus group, high-dose Lactobacillus acidophilus group and normal control group. The expression of STAT1, T-bet and GATA3 mRNAs in colonic mucosa was measured by reverse transcription-polymerase chain reaction (RT-PCR). The expression of T-bet protein was measured by Western blot and immunohistochemistry (IHC). Colonic tissue damage was assessed using histopathologic score. The body weight and disease activity index (DAI) of all rats were evaluated daily.

RESULTS: Compared with the normal control group, the disease activity index and histopathologic scores were significantly increased (both P < 0.05) in the model control group. All doses of Lactobacillus acidophilus and mesalamine could significantly reduce disease activity index and histopathologic scores when compared to the model control group (6.20 ± 2.64, 5.00 ± 1.21, 5.72 ± 2.63 and 5.81 ± 1.32 vs 7.81 ± 1.02; 4.25 ± 2.05, 2.56 ± 1.81, 2.20 ± 1.12 and 3.10 ± 2.60 vs 5.80 ± 2.94; all P < 0.05). The expression levels of STAT1 and T-bet mRNAs in all Lactobacillus acidophilus groups (low-, medium- and high-dose) and mesalazine group were lower than that in the model control group (all P < 0.05). Moreover, the expression levels of T-bet protein in all Lactobacillus acidophilus groups and mesalazine group were also significantly lower than that in the model control group (0.27 ± 0.04, 0.23 ± 0.02, 0.18 ± 0.04 and 0.27 ± 0.11 vs 0.30 ± 0.04; 0.263 ± 0.045, 0.234 ± 0.015, 0.114 ± 0.025 and 0.252 ± 0.024 vs 0.322 ± 0.064; all P < 0.05). Optimum effects were achieved in the high-dose Lactobacillus acidophilus group.

CONCLUSION: Inhibition of transcriptional factors STAT1/T-bet activation maybe one mechanism contributing to the therapeutic effects of Lactobacillus acidophilus against ulcerative colitis.

Isolation of bacteria from the ileal mucosa of TNFdeltaARE mice and description of Enterorhabdus mucosicola gen. nov., sp. nov

The diversity of bacteria associated with inflamed mucosa was investigated by culturing ileal samples from TNF(deltaARE) mice on a selective medium containing mucin. Among eight isolates, two strains (Mt1B3 and Mt1B8(T)) belonged to bacterial groups not yet cultured from the mouse intestine. Whereas strain Mt1B3 was identified as a member of the family Planococcaceae and is closely related to Sporosarcina species and Filibacter limicola DSM 13886(T), strain Mt1B8(T) was a novel bacterium. Based on phylogenetic analysis, strain Mt1B8(T) is a member of the family Coriobacteriaceae. The closest relatives with validly published names were Asaccharobacter celatus, Adlercreutzia equolifaciens (<96 % similarity) and Eggerthella species (<92 %). With respect to Asaccharobacter celatus and Eggerthella, the phylogenetic position of strain Mt1B8(T) was confirmed at the chemotaxonomic level by Fourier-transform infrared spectroscopic analysis. The major fatty acid of strain Mt1B8(T) is C(16 : 0) (23.9 %). Menaquinones were monomethylated. DNA-DNA relatedness between strain Mt1B8(T) and Asaccharobacter celatus DSM 18785(T) was 28 %. Strain Mt1B8(T) is a Gram-positive-staining rod that does not form spores and has a high DNA G+C content (64.2 mol%). Cells are aerotolerant but grow only under strictly anoxic conditions. They are sensitive to cefotaxime, clarithromycin, erythromycin, metronidazole, tetracycline, tobramycin and vancomycin. API and VITEK analysis showed the ability of strain Mt1B8(T) to convert a variety of amino acid derivatives. According to these findings, it is proposed to create a novel genus and species, Enterorhabdus mucosicola gen. nov., sp. nov., to accommodate strain Mt1B8(T). The type strain of Enterorhabdus mucosicola is Mt1B8(T) (=DSM 19490(T) =CCUG 54980(T)).

Postinfectious irritable bowel syndrome

Approximately 1 in ten patients with irritable bowel syndrome (IBS) believe their IBS began with an infectious illness. Prospective studies have shown that 3% to 36% of enteric infections lead to persistent new IBS symptoms; the precise incidence depends on the infecting organism. Whereas viral gastroenteritis seems to have only short-term effects, bacterial enteritis and protozoan and helminth infections are followed by prolonged postinfective IBS (PI-IBS). Risk factors for developing PI-IBS include, in order of importance, prolonged duration of initial illness, toxicity of infecting bacterial strain, smoking, mucosal markers of inflammation, female gender, depression, hypochondriasis, and adverse life events in the preceding 3 months. Age older than 60 years might protect against PI-IBS, whereas treatment with antibiotics has been associated with increased risk. The mechanisms that cause PI-IBS are unknown but could include residual inflammation or persistent changes in mucosal immunocytes, enterochromaffin and mast cells, enteric nerves, and the gastrointestinal microbiota. Adverse psychological factors contribute to persistent low-grade inflammation. The prognosis for patients with PI-IBS is somewhat better than for those with unselected IBS, but PI-IBS can still take years to resolve. There are no specific treatments for PI-IBS; these should be tailored to the predominant bowel disturbance, which is most frequently diarrhea.

Dominant genotypes in mucosa-associated Escherichia coli strains from pediatric patients with inflammatory bowel disease

BACKGROUND

Studies performed in adults with inflammatory bowel disease (IBD) have suggested that mucosa-associated Escherichia coli strains may be involved in its pathogenesis. The aim of this study was to characterize E. coli strains from the intestinal mucosa of pediatric IBD patients to investigate whether a particular subset of strains could be associated with the disease.

METHODS

We analyzed the genomic and phenotypic traits of 60 E. coli strains isolated from biopsies of pediatric patients with Crohn's disease (CD), ulcerative colitis (UC), and from age-matched controls.

RESULTS

No noteworthy differences were found in the distribution of phylogroups. The percentage of adhesive E. coli strains was similar in biopsies from patients and controls. However, the adhesion ability of E. coli strains differed between ileal and colonic or rectal areas, only in the strains from CD and UC patients. The percentage of E. coli possessing more than 1 of the adhesive/virulence determinants was significantly higher in strains from UC than from CD and controls. Interestingly, the genetic profile examination revealed 2 large clusters of genetically linked E. coli strains from IBD patients. Ninety-two percent of the strains isolated from CD patients were in the first cluster (A) and were distributed between 2 genetic subclusters (A1 and A2), while a second cluster (B) contained most of the strains isolated from UC (78%; subcluster B1), and control strains (77%; subcluster B2).

CONCLUSIONS

Genomic analysis of mucosa-associated E. coli strains found a close genetic association between strains isolated from CD and UC patients.

Lactobacillus plantarum attenuates up-regulation of adhesion molecules expression in IL-10 gene knockout mice with colitis

AIM: To investigate the effect of lactobacillus plantarum (LP) daily intragastric administration on lymphocyte homing and intestinal inflammation in IL-10 gene knockout mice colitis.

METHODS: Both two groups of 10 IL-10 KO mice and two groups of normal background controls were consecutively fed on phosphate buffered saline containing LP 1258 at 10¹² CFU/L, and unmodified phosphate buffered saline, respectively, from 4 to 8 wk. At sacrifice, the bowels were histologically scored under light microscope and observed under transmission electron microscope. Expression of CD3 and intestinal homing-related molecules MAdCAM-1, ICAM-1, α4β7 were detected by reverse-transcription polymerase chain reaction and Western blot.

RESULTS: At 8 wk, 100% of the IL-10 gene-deficient mice showed histological inflammation. CD3, adhesion molecules α4β7, ICAM-1 and MAdCAM-1 had a significantly higher expression of both mRNA and protein levels in KO than WT group (mRNA: t = 39.42, 8.83, 25.53, 45.78, all P < 0.01; CD3, ICAM-1, MAdCAM-1 protein: t = 19.04, 29.57, 12.29, all P < 0.01). After LP treatment, the expression of both mRNA and protein was significantly reduced in KO+LP, compared with KO mice (mRNA: t = 20.34, 4.95, 14.21, 22.31, all P < 0.01; CD3, ICAM-1, MAdCAM-1 protein: t = 6.82, 14.10, 7.03, all P < 0.01). The expression of mRNA was significantly reduced in WT+LP, compared with WT mice (t = 9.33, 10.55, 7.75, 6.69, all P < 0.01), however, protein expression was not significantly reduced.

CONCLUSION: LP can interfere with upregulation of adhesion molecules, attenuating colitis of IL-10 gene knockout mice.

Pattern extraction of structural responses of gut microbiota to rotavirus infection via multivariate statistical analysis of clone library data

This study developed a new statistical strategy for analyzing clone library data to observe whether there is a defined pattern in structural responses of gut microbiota to environmental perturbations. A large clone library of genus Bacteroides was constructed with fecal samples for each subject in rotavirus-infected (Group R) and healthy children (Group H). In all, 665 clones of the 12 Group H subjects and 284 clones of the nine Group R subjects were sequenced and classified into 34 operational taxonomic units (OTUs) with a similarity cutoff at 98%. Partial least squares-discriminant analysis was used to observe the change of the Bacteroides spp. composition caused by rotavirus infection and to identify the most relevant species contributing to this shift. It was revealed that H subjects and R subjects were well separated. Bacteroides vulgatus, Bacteroides stercoris and Bacteroides fragilis were identified as the most important discriminating OTUs between two groups. The increased abundance of B. fragilis and the decreased populations of B. vulgatus and B. stercoris in infected guts observed in this study were in agreement with previous culture-based studies. The strategy developed in this work can be used to reveal patterns in structural responses of gut microbiota to environmental perturbations from large-scale 16S rRNA gene-based sequencing data.

16S rRNA gene-based analysis of fecal microbiota from preterm infants with and without necrotizing enterocolitis

Neonatal necrotizing enterocolitis (NEC) is an inflammatory intestinal disorder affecting preterm infants. Intestinal bacteria play a key role; however no causative pathogen has been identified. The purpose of this study was to determine if there are differences in microbial patterns which may be critical to the development of this disease. Fecal samples from twenty preterm infants, ten with NEC and ten matched controls (including four twin pairs) were obtained from patients in a single site Level III neonatal intensive care unit. Bacterial DNA from individual fecal samples were PCR amplified and subjected to terminal restriction fragment length polymorphism analysis and library sequencing of the 16S rRNA gene to characterize diversity and structure of the enteric microbiota. The distribution of samples from NEC patients distinctly clustered separately from controls. Intestinal bacterial colonization in all preterm infants was notable for low diversity. Patients with NEC had even less diversity, an increase in abundance of Gammaproteobacteria, a decrease in other bacteria species, and had received a higher mean number of previous days of antibiotics. Our results suggest that NEC is associated with severe lack of microbiota diversity which may accentuate the impact of single dominant microorganisms favored by empiric and wide-spread use of antibiotics.

Cytokine association with bacterial DNA in serum of patients with inflammatory bowel disease

BACKGROUND

The pathogenesis of inflammatory bowel disease (IBD) involves the interaction between genetic susceptibility, mucosal immunity, and intestinal bacteria. Bacterial translocation is a common event in these patients and plays an important role in the perpetuation of chronic intestinal inflammation. Blood microbiological cultures, however, are frequently negative. The aim was to evaluate the presence of bacterial DNA (bactDNA) and the associated cytokine response in patients with IBD.

METHODS

Fifteen healthy donors, 29 patients with ulcerative colitis (UC), and 33 patients with Crohn's disease (CD) were studied. The presence of bactDNA was pursued by PCR followed by nucleotide sequencing analysis. Microbiological cultures were carried out among all controls and patients. Cytokine serum levels were measured by enzyme-linked immunosorbent assay (ELISA).

RESULTS

BactDNA was detected in 14 out of 33 patients with CD (42.4%) and in 15 out of 29 patients with UC (51.7%). BactDNA translocation was present in 7 out of 21 (33%) and in 10 out of 15 (34%) patients with CD and UC in remission, respectively. None of healthy controls showed bactDNA in serum. A statistically significant increase in all Th1-derived cytokines in CD but not in UC patients with the presence of bactDNA was observed in comparison with patients without bactDNA and controls.

CONCLUSIONS

BactDNA is present in IBD patients, irrespective of their disease activity. This fact is associated with a marked Th1-driven immune reaction in CD patients, even in those in remission. Whether bactDNA is inducing or is favored by an increased inflammatory scenario in these patients remains under discussion.

Enterovirulent E. coli in inflammatory and noninflammatory bowel diseases

We determined the incidence of enterovirulent E. coli (EVEC; which can to cause gastrointestinal infections) in strains isolated from patients with both of the major inflammatory bowel diseases (IBD), Crohn's disease (CD) and ulcerative colitis (UC) and from patients with noninflammatory bowel diseases (nonIBD). Cell detachment E. coli (CDEC) were detected in 14 % of all strains. A significant difference in the presence of CDEC was found between the groups of strains isolated from UC (24.1 %), nonIBD (11.9 %) and CD (4.7 %). Enteroaggregative E. coli (EAggEC) were detected in 2.5 %, typical enteropathogenic strains (EPEC) in 1.3 % and enterotoxigenic ones (ETEC) in 1.5 %. Enteroinvasive (EIEC) and shigatoxin producing E. coli (STEC) were not detected. Some strains showed a high invasion level in gentamicin-protection assay. These strains could therefore belong to adherent-invasive E. coli (AIEC) because they are free of genes encoding invasins (ipaH, ial) and are equipped with fimA gene. However, complete characterization of these strains and their classification as AIEC will require further tests.

Intestinal bacteria and inflammatory bowel disease

Crohn's disease (CD) and ulcerative colitis (UC) are the two principal forms of inflammatory bowel disease (IBD). Animal studies show that bacteria are involved in the etiology of IBD, and much is now known about the inflammatory processes associated with CD and UC, as well as the underlying genetic, environmental, and lifestyle issues that can affect an individual's predisposition to these diseases. However, while a number of candidate microorganisms have been put forward as causative factors in IBD, the primary etiologic agents are unknown. This review discusses the potential role of luminal and mucosal microbial communities in the etiology of IBD, and outlines studies that have been made using a variety of biotherapeutic therapies, involving the use of antibiotics, probiotics, prebiotics, and synbiotics.

Intestinal dendritic cells and epithelial barrier dysfunction in Crohn's disease

Crohn's disease (CD) is a chronic gastrointestinal inflammatory disorder considered to be the result of an inappropriate and exaggerated mucosal immune reaction to yet undefined triggers from the gut flora in genetically predisposed individuals. This inflammatory phenomenon has been characterized by an adaptive T-cell response in addition to an abnormal function of the innate immune system. Dendritic cells (DCs) are constituents of this innate system, inducing T-cell activation via antigen presentation. In the gut, mucosal DCs are separated from the luminal milieu by a monolayer of cylindrical epithelial cells that forms an anatomical and physiological barrier that controls the normal traffic of antigens between both compartments. An imbalance of colonic and ileal DC distribution in tissues from CD patients as well as functional differences between DCs isolated from normal and diseased intestinal samples have been demonstrated. Moreover, a gut barrier defect in the para- and transepithelial routes in addition to a significant reduction in the intestinal secretion of epithelial products involved in barrier function has been well documented in CD. Therefore, this may expose the diseased mucosa to overwhelming amounts of antigens, resulting in abnormal DC activation and a subsequent imbalance in their distribution. In conclusion, this review provides a summary of relevant progress in CD, intestinal epithelial permeability, and DCs highlighting a potential relationship between increased epithelial permeability and abnormal DC distribution during the pathogenesis of intestinal inflammation.

Reduced microbial diversity and high numbers of one single Escherichia coli strain in the intestine of colitic mice

Commensal bacteria play a role in the aetiology of inflammatory bowel diseases (IBD). High intestinal numbers of Escherichia coli in IBD patients suggest a role of this organism in the initiation or progression of chronic gut inflammation. In addition, some E. coli genotypes are more frequently detected in IBD patients than others. We aimed to find out whether gut inflammation in an IBD mouse model is associated with a particular E. coli strain. Intestinal contents and tissue material were taken from 1-, 8-, 16- and 24-week-old interleukin 10-deficient (IL-10(-/-)) mice and the respective wild-type animals. Caecal and colonic inflammation was observed in IL-10(-/-) animals from the 8 weeks of life on accompanied by a lower intestinal microbial diversity than in the respective wild-type animals. Culture- based and molecular approaches revealed that animals with gut inflammation harboured significantly higher numbers of E. coli than healthy controls. Phylogenetic grouping according to the E. coli Reference Collection (ECOR) system and strain typing by random-amplified polymorphic DNA and pulsed-field gel electrophoresis revealed that all mice were colonized by one single E. coli strain. The strain was shown to have the O7:H7:K1 serotype and to belong to the virulence-associated phylogenetic group B2. In a co-association experiment with gnotobiotic mice, the strain outnumbered E. coli ECOR strains belonging to the phylogenetic group A and B2 respectively. A high number of virulence- and fitness-associated genes were detected in the strain's genome possibly involved in the bacterial adaptation to the murine intestine.

Bacterial-mucosal interactions in inflammatory bowel disease: an alliance gone bad

The complex interaction of genetic, microbial, and environmental factors may result in continuous activation of the mucosal immune system leading to inflammatory bowel disease (IBD). Most present treatments for IBD involve altering or suppressing the aberrant immune response; however, the role of the intestinal microbiota in the pathophysiology of IBD is becoming more evident. The epithelial layer is essential for the proper functioning of the gastrointestinal tract, and its increased permeability to the luminal antigens may lead to the inflammatory processes and mucosal damage observed in IBD. Factors affecting the efficacy of the epithelial barrier include presence of pathogenic bacteria (e.g., Helicobacter spp.), presence of probiotic bacteria, availability of selected nutrients, and others. Defective function of the mucosal barrier might facilitate the contact of bacterial antigens and adjuvants with innate and adaptive immune cells to generate prolonged inflammatory responses. This review will briefly describe the complex structure of the epithelial barrier in the context of bacterial-mucosal interactions observed in human IBD and mouse models of colitis.

Differential effects of Bifidobacterium pseudolongum strain Patronus and metronidazole in the rat gut

In the luminal contents of metronidazole-treated rats, there was a dominant Bifidobacterium species. A strain has been isolated, its 16S rRNA gene has been sequenced, and the strain has been named Bifidobacterium pseudolongum strain Patronus. In this study, using an experimental model of healthy rats, the effects of metronidazole treatment and B. pseudolongum strain Patronus administration on the luminal and mucosa-associated microbiota and on gut oxidation processes were investigated. Metronidazole treatment and the daily gavage of rats with B. pseudolongum strain Patronus increased the numbers of bifidobacteria in cecal contents and in cecal mucosa-associated microbiota compared with those in control rats. Metronidazole reduced the colonic oxidative damage to proteins. This is the first evidence that B. pseudolongum strain Patronus exerts an effect on a biomarker of oxidative damage by reducing the susceptibility to oxidation of proteins in the colon and the small bowel. Antioxidant effects of metronidazole could be linked to the bifidobacterial increase but also to other bacterial modifications.

Reduced diversity and increased virulence-gene carriage in intestinal enterobacteria of coeliac children

Background

Coeliac disease is an immune-mediated enteropathology triggered by the ingestion of cereal gluten proteins. This disorder is associated with imbalances in the composition of the gut microbiota that could be involved in its pathogenesis. The aim of the present study was to determine whether intestinal Enterobacteriaceae populations of active and non-active coeliac patients and healthy children differ in diversity and virulence-gene carriage, so as to establish a possible link between the pathogenic potential of enterobacteria and the disease.

Methods

Enterobacteriaceae clones were isolated on VRBD agar from faecal samples of 31 subjects (10 active coeliac patients, 10 symptom-free coeliac patients and 11 healthy controls) and identified at species level by the API 20E system. Escherichia coli clones were classified into four phylogenetic groups A, B1, B2 and D and the prevalence of eight virulence-associated genes (type-1 fimbriae [fimA], P fimbriae [papC], S fimbriae [sfaD/E], Dr haemagglutinin [draA], haemolysin [hlyA], capsule K1 [neuB], capsule K5 [KfiC] and aerobactin [iutA]) was determined by multiplex PCR.

Results

A total of 155 Enterobacteriaceae clones were isolated. Non-E. coli clones were more commonly isolated in healthy children than in coeliac patients. The four phylogenetic E. coli groups were equally distributed in healthy children, while in both coeliac patients most commensal isolates belonged to group A. Within the virulent groups, B2 was the most prevalent in active coeliac disease children, while D was the most prevalent in non-active coeliac patients. E coli clones of the virulent phylogenetic groups (B2+D) from active and non-active coeliac patients carried a higher number of virulence genes than those from healthy individuals. Prevalence of P fimbriae (papC), capsule K5 (sfaD/E) and haemolysin (hlyA) genes was higher in E. coli isolated from active and non-active coeliac children than in those from control subjects.

Conclusion

This study has demonstrated that virulence features of the enteric microbiota are linked to coeliac disease.

Mechanisms of probiotic action: Implications for therapeutic applications in inflammatory bowel diseases

Probiotics are defined as nonpathogenic living microorganisms, including some commensal bacterial flora, which have beneficial effects on host health and disease prevention and/or treatment. Clinical trials have shown beneficial effects of probiotics on several human diseases, such as inflammatory bowel diseases (IBDs), which are among the most-studied diseases testing probiotics as a potential therapy. However, a significant question regarding clinical use of probiotics is the mechanism underlying the wide range of actions. Studies discussed in this review suggest 3 distinct cellular and molecular mechanisms for probiotic regulation in IBD therapy: 1) Probiotics block pathogenic bacterial effects by producing bactericidal substances and competing with pathogens and toxins for adherence to the intestinal epithelium; 2) Probiotics regulate immune responses by enhancing the innate immunity and modulating pathogen-induced inflammation via toll-like receptor-regulated signaling pathways; and 3) Probiotics regulate intestinal epithelial homeostasis by promoting intestinal epithelial cell survival, enhancing barrier function, and stimulating protective responses. Probiotics modulate host cell signaling pathways, including Akt, mitogen-activated protein kinases, and nuclear factor-kappaB to mediate these intestinal epithelial functions. It is hoped that developing a mechanistic understanding of probiotic action will provide the rationale to support the development of new hypothesis-driven studies to define the clinical efficacy in preventive, adjunctive, or alternative treatments for IBD.

Molecular pathogenesis of inflammatory bowel disease: relevance for novel therapies

The immense load of microorganisms within the gastrointestinal tract is a great challenge for the mucosal immune system. Whereas the vast majority of commensal bacteria should be tolerated, pathogenic organisms have to be attacked. During inflammatory bowel disease, the balanced interaction between the mucosal flora and the intestinal immune system is disturbed. Various defective components of this complex interaction have been described, such as different susceptibility genes, impaired innate immune responses and environmental factors, suggesting that inflammatory bowel diseases are multifactorial diseases. Based on new insights into the pathogenesis of inflammatory bowel disease, various targets for future drugs have been identified and new substances are emerging. The following article will review the current understanding of inflammatory bowel disease pathogenesis in context with genetic risk factors, imbalanced innate and acquired immune responses, and altered barrier function. Clinical treatment of the diseases will be summarized and emerging therapies as well as individual management based on recent insights into pathogenesis will be discussed.

Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease

Molecular analysis of bacterial 16S rRNA genes has made a significant contribution to the identification and characterisation of bacterial flora in the human gut. In particular, this methodology has helped characterise bacterial families implicated in the aetiology of inflammatory bowel disease (IBD). In this study we have used a genus specific bacterial 16S PCR to investigate the prevalence and diversity of Pseudomonas species derived from the ileum of children with Crohn's disease (CD), and from control children with non-inflammatory bowel disease (non-IBD) undergoing their initial endoscopic examination. Fifty eight percent of CD patients (18/32) were positive using the Pseudomonas PCR, while significantly fewer children in the non-IBD group, 33% (12/36), were PCR positive for Pseudomonas (p<0.05, Fischer's exact test). Pseudomonas specific 16S PCR products from 13 CD and 12 non-IBD children were cloned and sequenced. Five hundred and eighty one sequences were generated and used for the comparative analysis of Pseudomonas diversity between CD and non-IBD patients. Pseudomonas species were less diverse in CD patients compared with non-IBD patients. In particular P.aeruginosa was only identified in non-IBD patients.