Search

Helicobacter pylori (H. pylori) infection causes chronic gastritis, peptic ulcers and gastric cancer. Although H. pylori prevalence is decreasing worldwide, regional variations exist in Europe, with the lowest infection prevalence in Northern Europe, and the highest in Eastern and Southern Europe (1). Changes in the treatment recommendations and the increasing available evidence have justified the implementation of new recommendations since last Belgian consensus in 1998 (2). Several non-H. pylori Helicobacter species (NH.PYLORI-H), colonizing the stomach of domestic animals, also have the ability to cause gastric disease in humans, although to a lesser extent. These zoonotic NH. PYLORIH are not the subject of the current recommendations.

Background and aims We aimed to identify mucin-microbiome signatures shaping the tumor microenvironment in gastric adenocarcinomas and clinical outcomes. Methods We performed high-throughput profiling of the mucin phenotypes present in 108 gastric adenocarcinomas and 20 functional dyspepsia cases using validated mucin-based RT-qPCRs with subsequent immunohistochemistry validation and correlated the data with clinical outcome parameters. The gastric microbiota was assessed by 16S rRNA gene sequencing, taxonomy, and community composition determined, microbial networks analyzed, and the metagenome inferred in association with mucin phenotypes and expression. Results Gastric adenocarcinomas with an intestinal mucin environment or high-level MUC13 expression are associated with poor survival. On the contrary, gastric MUC5AC or MUC6 abundance was associated with a more favorable outcome. The oral taxa Neisseria, Prevotella, and Veillonella had centralities in tumors with intestinal and mixed phenotypes and were associated with MUC13 overexpression, highlighting their role as potential drivers in MUC13 signaling in GC. Furthermore, dense bacterial networks were observed in intestinal and mixed mucin phenotype tumors whereas the lowest community complexity was shown in null mucin phenotype tumors due to higher Helicobacter abundance resulting in a more decreased diversity. Enrichment of oral or intestinal microbes was mucin phenotype dependent. More specifically, intestinal mucin phenotype tumors favored the establishment of pro-inflammatory oral taxa forming strong co-occurrence networks. Conclusions Our results emphasize key roles for mucins in gastric cancer prognosis and shaping microbial networks in the tumor microenvironment. Specifically, the enriched oral taxa associated with aberrant MUC13 expression can be potential biomarkers in predicting disease outcomes.

Additional file 10: Table S1. demographic information of the included patients. Table S2. overview of the used QuantiTect primers. Table S3. 90% confidence interval of the relative mucin mRNA expression levels of functional dyspepsia patients. Table S4. number of interactions within the bacterial communities of samples with different mucin phenotypes. Table S5. Analysis of interactions in bacterial communities associated with different mucin phenotypes. Table S6. Analysis of interactions in bacterial communities associated with different expression level of MUC13. Table S7. Differentially abundant metagenomic pathways.

Additional file 4. Unique protein-encoding genes in the highly virulent trout isolate genome. 374 genes were identified in the genome of the highly virulent F. columnare JIP P11/91 isolate while being absent in that of the non-virulent F. columnare ATCC 49512. Of these 374 genes, the 263 hypothetical genes were left out in the representation above. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database. *Gene locations are formatted as NODEn:s-e where n is a unique scaffold number, s and e are the gene’s start and end position respectively.

Additional file 2. Protein-encoding genes present only in the virulent F. columnare genomes. The latter 42 genes are only present in genomes of the highly virulent carp (04017018) and trout (JIPP11/91) and low virulent carp (CDI-A) F. columnare isolates that could cause tissue damage and mortality. These genes are not present in the genome of the non-virulent F. columnare trout isolate ATCC49512. Hypothetical genes (114) were not included here. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database.

Additional file 7. Characteristics of prophage regions in the four Flavobacterium columnare isolates. The prophage regions were identified in the genome of the reference isolate (ATCC49512) and the three newly assembled F. columnare isolates 04017018, CDI-A and JIP P11/91 via PHASTER. Prophage regions with scores less than 70 are incomplete.

Additional file 7. Characteristics of prophage regions in the four Flavobacterium columnare isolates. The prophage regions were identified in the genome of the reference isolate (ATCC49512) and the three newly assembled F. columnare isolates 04017018, CDI-A and JIP P11/91 via PHASTER. Prophage regions with scores less than 70 are incomplete.

Additional file 3. Unique protein-encoding genes in the highly virulent carp isolate genome. 80 genes were identified to be present in the genome of the highly virulent carp isolate 04017018 while absent in that of the low virulent carp isolate CDI-A. Of these 80 genes, the 62 hypothetical genes were left out in the representation above. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database. *Gene locations are formatted as NODEn:s-e where n is a unique scaffold number, s and e are the gene’s start and end position respectively.

Additional file 6. Unique single nucleotide variants (SNVs) present in gyrA of isolate CDI-A. The impact of the SNP (single nucleotide polymorphism) on protein activity/stability was predicted by comparison of amino acid characteristics, by using PredictSNP and I-Mutant Suite 3.0 tools, and by investigating which amino acids were present in the reference strain of F. columnare and of HV carp isolate 04017018, both of the latter not displaying acquired resistance towards fluoroquinolones, using BLAST and ConSurf.

Additional file 4. Unique protein-encoding genes in the highly virulent trout isolate genome. 374 genes were identified in the genome of the highly virulent F. columnare JIP P11/91 isolate while being absent in that of the non-virulent F. columnare ATCC 49512. Of these 374 genes, the 263 hypothetical genes were left out in the representation above. Genes marked in bold are also predicted to be involved in virulence when identifying them via Virulence Factor Database. *Gene locations are formatted as NODEn:s-e where n is a unique scaffold number, s and e are the gene’s start and end position respectively.

Additional file 5. Single nucleotide variants (SNVs) in gyrase genes of Flavobacterium columnare isolates. This table shows the SNVs present in the gyrase genes of F. columnare isolates CDI-A and 04017018 when compared to gyrase genes of the reference genome ATCC 49512. However, as only isolate CDI-A displayed phenotypic antimicrobial resistance towards both first- and second-generation quinolones, the unique SNVs in the gyrase genes of the latter isolate are highlighted in grey background. No SNVs were encountered in DNA gyrase subunit B (EC 5.99.1.3). Average read quality score of the bases supporting a variant was higher than 35 (which is considered very good quality).

In this review, we summarized the most important, accessible, and relevant literature published between April 2019 and March 2020 on the gut microbiota in child health. The first part of the review focuses on literature describing changes in microbiota composition in a wide spectrum of pathologies, while the subsequent section focuses on the impact of antimicrobial treatment and nutritional intervention on the pediatric microbiota during early infancy and development.

Currently, no curative treatments exist for most neurological disorders. Nevertheless, the involvement of the gut microbiota has gained increasing interest over the last years. In this review, we summarize the main findings published between April 2019 and March 2020 that are related to the use of microbiota-modulating agents to treat depression, Alzheimer’s disease (AD), and Parkinson’s disease (PD). These ‘psychobiotics’ were investigated individually or in combination and included probiotics (e.g., Bifidobacterium and Lactobacillus strains), prebiotics (e.g., polysaccharides and plant extracts), medicinal products (e.g., antidepressants and vitamins), as well as physical activity or infrared red-light treatment. All agents improved disease-related abnormalities to some extent. Their main effects involved the restoration of gut homeostasis by altering gut microbiota composition and suppressing intestinal inflammation. Disease symptoms improved associated with a reduction in cytokine levels, microglia activation, plaque deposition and neuronal cell death and with an increase in neurotrophic factors and glucose uptake in the brain. Furthermore, the 5-HT, TLR, NLRP3 and PPARʏ signaling pathways were highlighted as major bidirectional communication routes between the gut and the brain. In addition, whereas Bifidobacterium longum, Bifidobacterium lactis and Lactobacillus plantarum improved the symptom severity and affected pathophysiological pathways of both depression and AD, Lactobacillus rhamnosus and Lactobacillus acidophilus were shown to ameliorate PD as well as depression or AD. Although most studies have been performed in animal models and the exact underlying mechanisms and pathways need further investigation, influencing the microbiota-gut-brain communication has major potential for the future treatment of depression, AD and PD.

Background and Aims There is evidence for a disturbed intestinal barrier function in inflammatory bowel diseases [IBD] but the underlying mechanisms are unclear. Because mucins represent the major components of the mucus barrier and disturbed mucin expression is reported in the colon of IBD patients, we studied the association between mucin expression, inflammation and intestinal permeability in experimental colitis. Methods We quantified 4-kDa FITC-dextran intestinal permeability and the expression of cytokines, mucins, junctional and polarity proteins at dedicated time points in the adoptive T cell transfer and dextran sodium sulfate [DSS]-induced colitis models. Mucin expression was also validated in biopsies from IBD patients. Results In both animal models, the course of colitis was associated with increased interleukin-1β [IL-1β] and tumour necrosis factor-α [TNF-α] expression and increased Muc1 and Muc13 expression. In the T cell transfer model, a gradually increasing Muc1 expression coincided with gradually increasing 4-kDa FITC-dextran intestinal permeability and correlated with enhanced IL-1β expression. In the DSS model, Muc13 expression coincided with rapidly increased 4-kDa FITC-dextran intestinal permeability and correlated with TNF-α and Muc1 overexpression. Moreover, a significant association was observed between Muc1, Cldn1, Ocln, Par3 and aPKCζ expression in the T cell transfer model and between Muc13, Cldn1, Jam2, Tjp2, aPkcζ, Crb3 and Scrib expression in the DSS model. Additionally, MUC1 and MUC13 expression was upregulated in inflamed mucosa of IBD patients. Conclusions Aberrantly expressed MUC1 and MUC13 might be involved in intestinal barrier dysfunction upon inflammation by affecting junctional and cell polarity proteins, indicating their potential as therapeutic targets in IBD.

Additional file 13. Classification of down-regulated H. suis genes in cases compared to controls according to their function.

Additional file 6. Plots of the principal component analysis (PCA) of the restricted set of differentially expressed features. First 2 components (PC1 and PC2) of a PCA, with percentages of variance associated with each axis. These plots show the separation between samples based on the main sources of variation found in the rlog-transformed data sets (padj ≤ 0.01, fold change ≥ 2). (A) PCA-plot for H. suis (134 differentially expressed features) (B) PCA-plot for H. heilmannii (143 differentially expressed features). Blue dots indicate control samples (i.e. unbound Helicobacter); red dots indicate cases (i.e. Helicobacter bound to MKN7 cells). In both PCA plots, the sample groups (i.e. case and control) are well separated, indicating that the main variability within each experiment came from biological differences between cases and controls.

Additional file 7. H. suis up-regulated genes with (72) and without (11) H. heilmannii homologs according to BLASTp.

Additional file 11. Classification of up-regulated H. suis genes in cases compared to controls according to their function.

BACKGROUND: Guidelines give robust recommendations on which biopsies should be taken when there is endoscopic suggestion of gastric inflammation. Adherence to these guidelines often seems arbitrary. This study aimed to give an overview on current practice in tertiary referral centres across Europe. METHODS: Data was collected at ten tertiary referral centres. Demographic data, the indication for each procedure, endoscopic findings and the number and sampling site of biopsies were recorded. Findings were compared between centres and factors influencing the decision to take biopsies explored. RESULTS: Biopsies were taken in 56.6% of 9425 procedures, with significant variation between centres (p CONCLUSION: Adherence to guideline recommendations for biopsy sampling at gastroscopy was inconsistent across the participating centres. Our data suggest that instead centre-specific policies are applied.

Additional file 9. H. heilmannii up-regulated genes with (47) and without (13) H. suis homologs according to BLASTp.

Additional file 10. H. heilmannii down-regulated genes with (74) and without (9) H. suis homologs according to BLASTp.

Additional file 4. List of 83 significantly down-regulated H. heilmannii genes in cases compared to controls (with p adj ≤ 0.01; fold change ≤ -2).

Additional file 12. Classification of up-regulated H. heilmannii genes in cases compared to controls according to their function.

Additional file 5. Volcano plots of the comparisons (case versus control). Red dots represent significantly differentially expressed genes (padj ≤ 0.01, fold change ≥ 2) in MKN7-bound helicobacters (i.e. cases) compared to unbound helicobacters (i.e. controls). (A) Volcano plot of the comparison (case versus control) for H. suis. (B) Volcano plot of the comparison (case versus control) for H. heilmannii.

Additional file 1. List of 83 significantly up-regulated H. suis genes in cases compared to controls (with p adj ≤ 0.01; fold change ≥ 2).

Additional file 2. List of 51 significantly down-regulated H. suis genes in cases compared to controls (with p adj ≤ 0.01; fold change ≤ -2).

Additional file 8. H. suis down-regulated genes with (45) and without (6) H. heilmannii homologs according to BLASTp.

Additional file 14. Classification of down-regulated H. heilmannii genes in cases compared to controls according to their function.

Additional file 3. List of 60 significantly up-regulated H. heilmannii genes in cases compared to controls (with p adj ≤ 0.01; fold change ≥ 2).

Helicobacter suis is the most prevalent non-Helicobacter pylori Helicobacter species in the human stomach and is associated with chronic gastritis, peptic ulcer disease, and gastric mucosa-associated lymphoid tissue (MALT) lymphoma. H. suis colonizes the gastric mucosa of 60-95% of pigs at slaughter age, and is associated with chronic gastritis, decreased weight gain, and ulcers. Here, we show that experimental H. suis infection changes the mucin composition and glycosylation, decreasing the amount of H. suis-binding glycan structures in the pig gastric mucus niche. Similarly, the H. suis-binding ability of mucins from H. pylori-infected humans is lower than that of noninfected individuals. Furthermore, the H. suis growth-inhibiting effect of mucins from both noninfected humans and pigs is replaced by a growth-enhancing effect by mucins from infected individuals/pigs. Thus, Helicobacter spp. infections impair the mucus barrier by decreasing the H. suis-binding ability of the mucins and by decreasing the antiprolific activity that mucins can have on H. suis. Inhibition of these mucus-based defenses creates a more stable and inhabitable niche for H. suis. This is likely of importance for long-term colonization and outcome of infection, and reversing these impairments may have therapeutic benefits.

Chronic inflammation induced by Helicobacter pylori infection is a critical factor in the development of peptic ulcer disease and gastric cancer. Central to this inflammation is the initiation of pro-inflammatory signaling cascades within epithelial cells, in particular those mediated by two sensors of bacterial cell wall components, nucleotide-binding oligomerization domain-containing protein 1 (NOD1) and alpha-protein kinase 1 (ALPK1). H pylori is, however, also highly adept at mitigating inflammation in the host, thereby restricting tissue damage and favoring bacterial persistence. H pylori modulates host immune responses by altering cytokine signaling in epithelial and myeloid cells, which results in increased proliferation of regulatory T cells and downregulation of effector T-cell responses. H pylori vacuolating cytotoxin A (VacA) has been shown to play an important role in the dampening of immune responses and induction of immune tolerance capable of protecting against asthma. It is also possible to generate protective immune responses by immunization with various H pylori antigens or their epitopes, in combination with an adjuvant, though this for now has only been shown in mouse models. Novel non-toxic adjuvants, consisting of modified bacterial enterotoxins or nanoparticles, have recently been developed that may not only enhance vaccine efficacy, but also help translate candidate vaccines to the clinic. This review will summarize the main discoveries in the past year regarding host immune responses to H pylori infection, as well as the design of new vaccine approaches against this infection.

Aims: The aim of this study was to investigate the effect of subtherapeutic intestinal doxycycline (DOX) concentrations (4 and 1mgl(-1)), caused by cross-contamination of feed, on the enrichment of a DOX-resistant commensal Escherichia coli and its resistance plasmid in an exvivo model of the porcine caecum. Methods and Results: A DOX-resistant, tet(A)-carrying, porcine commensal E.coli strain (EC 682) was cultivated for 6days in the porcine caecum model under different conditions (0, 1 and 4mgl(-1) DOX). EC 682, other coliforms and anaerobic bacteria were enumerated daily. A selection of isolated DOX-resistant coliforms (n=454) was characterized by rep-PCR clustering, PCR assays (Inc1 and tet(A)) and micro broth dilution susceptibility tests (Sensititre). Both 1 and 4mgl(-1) DOX-enriched medium had a significantly higher selective effect on EC 682 and other resistant coliforms than medium without DOX. Transconjugants of EC 682 were isolated more frequently in the presence of 1 and 4mgl(-1) DOX compared to medium without DOX. Conclusions: Subtherapeutic intestinal DOX concentrations have the potential to select for DOX-resistant E.coli, and promote the selection of transconjugants in a porcine caecum model. Significance and Impact of the Study: Cross-contamination of feed with antimicrobials such as DOX likely promotes the spread of antimicrobial resistance. Therefore, it is important to develop or fine-tune guidelines for the safe use of antimicrobials in animal feed and its storage.

Background Helicobacter heilmannii is a zoonotic bacterium associated with gastric disease in humans. We recently showed that H. heilmannii binds to human gastric mucins and epithelial cells and highlighted a potential role for the murine Muc13 mucin in gastric Helicobacter colonization. The aims of this study were to investigate the role of the H. heilmannii hof gene locus encoding HofH/F/E/G/C/D in adhesion to the gastric mucosa and induction of increased gastric Muc13 expression. Methods Bacterial hof gene and host gene expression experiments, Helicobacter binding assays and experimental infection studies in mice were performed. H. pylori and its ΔhofF mutant were included for comparison. Results Helicobacter heilmannii strains lacking HofE or HofF showed a clear decrease in binding to gastric mucins and epithelial cells as well as a lower gastric colonization level in the stomach of Balb/c mice at 4 and 9 weeks post-infection compared to the H. heilmannii wildtype strain. Interestingly, H. heilmannii ΔhofE and ΔhofF and H. pylori ΔhofF did not induce an increased expression of MUC13 in human gastric epithelial cells and of Muc13 in the stomach of mice. Finally, we demonstrated that IL-1β is induced in the stomach as a response to Helicobacter colonization which on its turn is involved in the expression of MUC13/Muc13 in the gastric epithelium. Conclusion These novel results in Helicobacter research identified H. heilmannii HofE and HofF as adhesins and suggest an important role of H. heilmannii HofE and HofF and H. pylori HofF in IL-1β-induced gastric MUC13/Muc13 expression.

Validation parameters for quantification of chlortetracycline (CTC), doxycycline (DOX), sulfadiazine (SDZ) and trimethoprim (TRIM) in pig feed and feces. (DOCX 15 kb)

Aims: The behaviour of an E. coli isolate of broiler origin harbouring a blaTEM-52-carrying plasmid (lactose negative mutant of B1-54, IncII group) was studied in an in situ continuous flow culture system, simulating the human caecum and the ascending colon during cefotaxime administration. Methods and Results: Fresh faeces from a healthy volunteer, negative for cephalosporin-resistant E. coli, were selected to prepare inocula. The microbiota was monitored by plating on diverse selective media, and a shift in the populations of bacteria was examined by 16S rDNA PCR denaturing gradient gel electrophoresis. E. coli transconjugants were verified by plasmid and pulsed field gel electrophoresis profiles (PFGE). The avian extended-spectrum β-lactamase (ESBL) positive E. coli was able to proliferate without selective pressure of cefotaxime and E. coli transconjugants of human origin were detected 24 h after inoculation of the donor strain. Upon administration of cefotaxime to the fresh medium, an increase of the population size of E. coli B1-54 and the transconjugants was observed. PFGE and plasmid analysis revealed a limited number of human E. coli clones receptive for the blaTEM-52-carrying plasmid. Conclusions: These observations provide evidence of the maintenance of an E. coli strain of poultry origin and the horizontal gene transfer in the human commensal bowel microbiota even without antimicrobial treatment. Significance and Impact of Study: The fact that an E. coli strain of poultry origin might establish itself and transfer its bla gene to commensal human E. coli raises public health concerns.

The main Helicobacter species colonizing the stomach of pigs is H. suis which causes gastritis in experimentally and naturally infected pigs. This bacterium has also been associated with ulcers of the nonglandular part of the porcine stomach and is of zoonotic significance. The definite mode of transmission of H. suis between pigs and from pigs to humans remains to be investigated. This study was carried out to determine if the oral secretions of pigs might be a possible route of transmission. Oral swabs were taken from slaughtered pigs originating from 4 different herds (10 pigs/herd). DNA was extracted from these swabs with PrepMan sample preparation reagent from Applied Biosystems as described by the manufacturer. The presence of H. suis DNA was examined using a quantitative PCR based on the urease A gene. In each herd, 2-3 of the 10 swabs were positive for H. suis DNA. These positive samples contained 3000 to 60 000 bacteria. Further studies are required to determine viability of these bacteria.

Three Gram-negative, microaerophillic bacteria with a corkscrew-like morphology isolated from the gastric mucosa of cats and designated ASB1, ABS2 and ASB3, were subjected to a polyphasic taxonomic study. The isolates grew on biphasic culture plates in microaerobic conditions at 37°C and exhibited urease, oxidase and catalase activity. They were also able to grow in colonies on dry agar plates. Based on 16S rRNA gene sequence analysis, ASB1, ABS2 and ASB3 were identified as a member of the genus Helicobacter and showed 98 to 99% sequence similarity to H. felis, H. bizzozeronii, Candidatus H. heilmannii, H. cynogastricus and H. salomonis, five related Helicobacter species belonging to the “Helicobacter heilmannii” type 2 group and previously detected in the feline or canine gastric mucosa. Sequencing of the partial hsp60 gene demostrated that ASB1, ASB2 and ASB3 constitute a separate taxon in the “Helicobacter heilmannii” type 2 group. The urease gene sequences of ASB1, ASB2 and ASB3 showed approximately 92% homology to the urease gene sequences of “Candidatus Helicobacter heilmannii” described by O’Rourke et al. (2004). Protein profiling of the strains ASB1, ASB2 and ASB3 using SDS-PAGE also allowed to differentiate them from other Helicobacter species of feline or canine gastric origin. The results of this polyphasic taxonomic study indicate that the cultured isolates constitute a new taxon corresponding to “Candidatus Helicobacter heilmannii” from cats but further investigations are still needed.

Background: Serine proteases are believed to play a key role in the origin of abdominal pain in IBD and IBS. We previously demonstrated a reduction of visceral pain in a post-inflammatory IBS rat model after a single intraperitoneal or intracolonic administration of a serine protease inhibitor. The aim of this study was to investigate the efficacy of serine protease inhibition on visceral pain in two different animal models involving a colonic insult based either on acute inflammation or on neonatal irritation. Moreover, protease profiling was explored in the acute colitis model.Methods: An acute 2,4,6-trinitrobenzenesulphonic acid (TNBS) colitis rat model and a chronic neonatal acetic acid mouse model were used in this study. Visceral sensitivity was quantified by visceromotor responses (VMRs) to colorectal distension, 30 min after intraperitoneal administration of the serine protease inhibitors nafamostat, UAMC-00050 or their vehicles. Colonic samples from acute colitis rats were used to quantify the mRNA expression of a panel of serine proteases and mast cell tryptase by immunohistochemistry. Finally, proteolytic activities in colonic and fecal samples were characterized using fluorogenic substrates.Key Results: We showed a significant and pressure-dependent increase in visceral hypersensitivity in acute colitis and neonatal acetic acid models. UAMC-00050 and nafamostat significantly reduced VMRs in both animal models. In acute colitis rats, the administration of a serine protease inhibitor did not affect the inflammatory parameters. Protease profiling of these acute colitis animals revealed an increased tryptase immunoreactivity and a downregulation of matriptase at the mRNA level after inflammation. The administration of UAMC-00050 resulted in a decreased elastase-like activity in the colon associated with a significantly increased elastase-like activity in fecal samples of acute colitis animals.Conclusion: In conclusion, our results suggest that serine proteases play an important role in visceral hypersensitivity in an acute TNBS colitis model in rats and a neonatal acetic acid model in mice. Moreover, we hypothesize a potential mechanism of action of UAMC-00050 via the alteration of elastase-like proteolytic activity in acute inflammation. Taken together, we provided fundamental evidence for serine protease inhibitors as a promising new therapeutic strategy for abdominal pain in gastrointestinal diseases. This study was funded by the University Research Fund (BOFTOP) no. 35018, the Research Foundation Flanders (FWO) no. V438117N (grant for long stay abroad), no. 1244421N (junior postdoc) and the Research Foundation Flanders-Strategic Basic Research (FWO-SBO) no. S001017N. A special thanks to our laboratory technicians, P. Aerts, A. Jürgens, M. Vinckx, and L. Vits, for their assistance in the qPCR and MPO activity experiments and R. Van Den Bossche and M. Vermont for the microscopy