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OBJECTIVES: Wheat avoidance in the absence of celiac disease (CD) is common but occurrence of concurrent functional gastrointestinal disorders (FGIDs) in this group is uncertain. The aims of this study were to determine the prevalence of self-reported wheat or gluten sensitivity and doctor diagnosed CD in an Australian population, define the associated gastrointestinal (GI) symptoms and FGIDs, and determine the relationship between self-reported wheat sensitivity, demographic and medical factors.Methods: A total of 3542 people randomly selected from the Australian population returned a mail survey which contained questions on wheat avoidance, GI symptoms, demographic, medical, and lifestyle factors. We defined self-reported wheat sensitivity as people who reported gastrointestinal symptoms on ingestion of wheat based foods, but did not suffer from celiac disease, inflammatory bowel disease or colorectal cancer. Functional dyspepsia (FD) and irritable bowel syndrome (IBS) were diagnosed by Rome III criteria. CD status was self-reported.Results: The prevalence of self-reported wheat sensitivity in this cohort was 14.9% (95% CI 13.7-16.2). The prevalence of CD was 1.2% (95%CI 0.8-1.6). Doctor diagnosed CD was significantly associated with a diagnosis of FD (OR 3.35, 95%CI 1.72-6.52) and IBS (OR 2.28, 95%CI 1.08-4.81). Those with self-reported wheat sensitivity were more likely to report multiple abdominal symptoms (of the 18 assessed) than those without (3.9 symptoms with self-reported wheat sensitivity vs. 1.6 without, p = 0.0001). In a multivariate analysis, self-reported wheat sensitivity was independently associated with IBS (OR 3.55, 95%CI 2.71-4.65) and FD (1.48, 95%CI 1.13-1.94).Conclusions: Self-reported wheat sensitivity is common, with a prevalence of 14.9% in this cohort. There is a strong association between both celiac disease and self-reported wheat sensitivity, and chronic gastrointestinal symptoms, as well as a diagnosis of FD and IBS. [ABSTRACT FROM AUTHOR]

Introduction: The diagnosis of eosinophilic gastrointestinal diseases is largely based on mucosal eosinophil counts, but thresholds and normal ranges beyond the esophagus are debated, calling for much-needed methodological standardization. We aimed to develop a standardized workflow for duodenal cell quantification and estimate duodenal eosinophil and mast cell numbers in healthy controls., Methods: Software-based histological cell quantification using free-sized or fixed-sized regions was developed and applied to digitized hematoxylin and eosin (H&E)-stained slides from 58 individuals (healthy controls [HCs] and patients with functional dyspepsia). Intraclass correlation coefficients (ICCs) compared inter-rater reliability between software-based and microscopic quantification. Reproducibility of the software-based method was validated in an independent cohort of 37 control and functional dyspepsia subjects. Eosinophil identification on H&E staining was compared to immunohistochemistry (IHC). Normal eosinophil (H&E) and mast cell (cKit) ranges were determined in 70 adult HCs., Results: Eosinophil quantification on digitized slides demonstrated excellent (ICC = 0.909) and significantly improved reproducibility over microscopic evaluation (ICC = 0.796, P = 0.0014), validated in an independent cohort (ICC = 0.910). Duodenal eosinophils were more abundant around crypts than in villi ( P < 0.0001), while counts were similar on matched H&E- and IHC-stained slides ( P = 0.55). Mean ± SD (95th percentile) duodenal eosinophils and mast cells in HC were 228.8/mm 2 ± 94.7 (402.8/mm 2 ) and 419.5/mm 2 ± 132.2 (707.6/mm 2 ), respectively., Discussion: We developed and validated a standardized approach to duodenal histological cell quantification, generalizable to various mucosal cell types. Implementation of software-based quantification identified 400 eosinophils/mm 2 and 700 mast cells/mm 2 as thresholds for abnormal duodenal infiltration., (Copyright © 2024 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of The American College of Gastroenterology.)

Background and Aims: Diet plays an integral role in the modulation of the intestinal environment, with the potential to be modified for management of individuals with inflammatory bowel disease [IBD]. It has been hypothesised that poor 'Western-style' dietary patterns select for a microbiota that drives IBD inflammation and, that through dietary intervention, a healthy microbiota may be restored. This study aimed to systematically review the literature and assess current available evidence regarding the influence of diet on the intestinal microbiota composition in IBD patients, and how this may affect disease activity., Methods: MEDLINE, EMBASE, Scopus, Web of Science, and Cochrane Library were searched from January 2013 to June 2023, to identify studies investigating diet and microbiota in IBD., Results: Thirteen primary studies met the inclusion criteria and were selected for narrative synthesis. Reported associations between diet and microbiota in IBD were conflicting due to the considerable degree of heterogeneity between studies. Nine intervention studies trialled specific diets and did not demonstrate significant shifts in the diversity and abundance of intestinal microbial communities or improvement in disease outcomes. The remaining four cross-sectional studies did not find a specific microbial signature associated with habitual dietary patterns in IBD patients., Conclusions: Diet modulates the gut microbiota, and this may have implications for IBD; however, the body of evidence does not currently support clear dietary patterns or food constituents that are associated with a specific microbiota profile or disease marker in IBD patients. Further research is required with a focus on robust and consistent methodology to achieve improved identification of associations., (© The Author(s) 2023. Published by Oxford University Press on behalf of European Crohn’s and Colitis Organisation.)

Background: Gastro-oesophageal reflux disease (GORD) mechanisms are well described, but the aetiology is uncertain. Coeliac disease (CD), a gluten enteropathy with increased duodenal eosinophils overlaps with GORD. Functional dyspepsia is a condition where duodenal eosinophilia is featured, and a 6-fold increased risk of incident GORD has been observed. Perturbations of the duodenum can alter proximal gastric and oesophageal motor function. We performed a systematic review and meta-analysis assessing the association between CD and GORD., Methods: A systematic search of studies reporting the association of GORD and CD was conducted. CD was defined by combined serological and histological parameters. GORD was defined based on classical symptoms, oesophagitis (endoscopic or histologic) or abnormal 24-h pH monitoring; studies reporting oesophageal motility abnormalities linked with GORD were also included. Pooled odds ratios (OR) and 95% confidence intervals (CI) were calculated using a random-effects model., Findings: 31 papers were included. Individuals with CD on a gluten containing diet were 3 times more likely to have GORD than controls (OR: 3.37, 95% CI: 2.09-5.44), and over 10 times more likely when compared to those on a gluten free diet (GFD) (OR: 10.20, 95% CI: 6.49-16.04). Endoscopic oesophagitis was significantly associated with CD (OR: 4.96; 95% CI: 2.22-11.06). One year of a GFD in CD and GORD was more efficacious in preventing GORD symptom relapse than treatment with 8 weeks of PPI in non-CD GORD patients (OR: 0.18, 95% CI: 0.08-0.36). Paediatric CD patients were more likely to develop GORD (OR: 3.29, 95% CI: 1.46-7.43), compared to adult CD patients (OR: 2.55, 95% CI: 1.65-3.93)., Interpretation: CD is strongly associated with GORD but there was high heterogeneity. More convincingly, a GFD substantially improves GORD symptoms, suggesting a role for duodenal inflammation and dietary antigens in the aetiology of a subset with GORD. Ruling out CD in patients with GORD may be beneficial., Funding: The study was supported by an Investigator Grant from the NHMRC to Dr. Talley., Competing Interests: The study was supported by an Investigator Grant from the NHMRC to Dr. Talley., (© 2024 The Authors.)

Objective: Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke. The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies. The gastrointestinal microbiome has been implicated in chronic lung diseases via the gut-lung axis, but its role is unclear., Design: Using an in vivo mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT), we characterised the faecal microbiota using metagenomics, proteomics and metabolomics. Findings were correlated with airway and systemic inflammation, lung and gut histopathology and lung function. Complex carbohydrates were assessed in mice using a high resistant starch diet, and in 16 patients with COPD using a randomised, double-blind, placebo-controlled pilot study of inulin supplementation., Results: FMT alleviated hallmark features of COPD (inflammation, alveolar destruction, impaired lung function), gastrointestinal pathology and systemic immune changes. Protective effects were additive to smoking cessation, and transfer of CS-associated microbiota after antibiotic-induced microbiome depletion was sufficient to increase lung inflammation while suppressing colonic immunity in the absence of CS exposure. Disease features correlated with the relative abundance of Muribaculaceae, Desulfovibrionaceae and Lachnospiraceae family members. Proteomics and metabolomics identified downregulation of glucose and starch metabolism in CS-associated microbiota, and supplementation of mice or human patients with complex carbohydrates improved disease outcomes., Conclusion: The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. No commercial re-use. See rights and permissions. Published by BMJ.)

The uterus is a unique mucosal site where immune responses are balanced to be permissive of a fetus, yet protective against infections. Regulation of natural killer (NK) cell responses in the uterus during infection is critical, yet no studies have identified uterine-specific factors that control NK cell responses in this immune-privileged site. We show that the constitutive expression of IFNε in the uterus plays a crucial role in promoting the accumulation, activation, and IFNγ production of NK cells in uterine tissue during Chlamydia infection. Uterine epithelial IFNε primes NK cell responses indirectly by increasing IL-15 production by local immune cells and directly by promoting the accumulation of a pre-pro-like NK cell progenitor population and activation of NK cells in the uterus. These findings demonstrate the unique features of this uterine-specific type I IFN and the mechanisms that underpin its major role in orchestrating innate immune cell protection against uterine infection., (© 2024. Crown.)

Interactions between diet and gastrointestinal microbiota influence health status and outcomes. Evaluating these relationships requires accurate quantification of dietary variables relevant to microbial metabolism, however current dietary assessment methods focus on dietary components relevant to human digestion only. The aim of this study was to synthesize research on foods and nutrients that influence human gut microbiota and thereby identify knowledge gaps to inform dietary assessment advancements toward better understanding of diet-microbiota interactions. Thirty-eight systematic reviews and 106 primary studies reported on human diet-microbiota associations. Dietary factors altering colonic microbiota included dietary patterns, macronutrients, micronutrients, bioactive compounds, and food additives. Reported diet-microbiota associations were dominated by routinely analyzed nutrients, which are absorbed from the small intestine but analyzed for correlation to stool microbiota. Dietary derived microbiota-relevant nutrients are more challenging to quantify and underrepresented in included studies. This evidence synthesis highlights advancements needed, including opportunities for expansion of food composition databases to include microbiota-relevant data, particularly for human intervention studies. These advances in dietary assessment methodology will facilitate translation of microbiota-specific nutrition therapy to practice.

Introduction: An association between functional dyspepsia (FD) and wheat-containing foods has been reported in observational studies; however, an adaptive response has not been demonstrated. We examined whether antigens present in wheat could provoke a response from FD duodenal lymphocytes., Methods: Lamina propria mononuclear cells (LPMCs) were isolated from duodenal biopsies from 50 patients with FD and 23 controls. LPMCs were exposed to gluten (0.2 mg/mL) or gliadin (0.2 mg/mL) for 24 hours. Flow cytometry was performed to phenotype lymphocytes. Quantitative PCR was used to measure the expression of gliadin-associated T-cell receptor alpha variant ( TRAV ) 26-2., Results: In response to gliadin (but not gluten) stimulation, the effector Th2-like population was increased in FD LPMCs compared with that in controls and unstimulated FD LPMCs. Duodenal gene expression of TRAV26- 2 was decreased in patients with FD compared with that in controls. We identified a positive association between gene expression of this T-cell receptor variant and LPMC effector Th17-like cell populations in patients with FD, but not controls after exposure to gluten, but not gliadin., Discussion: Our findings suggest that gliadin exposure provokes a duodenal effector Th2-like response in patients with FD, supporting the notion that food antigens drive responses in some patients. Furthermore, these findings suggest that altered lymphocyte responses to wheat proteins play a role in FD pathogenesis., (Copyright © 2023 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of The American College of Gastroenterology.)

Functional dyspepsia (FD) is a highly prevalent disorder. Upper endoscopy is normal, and according to the Rome IV criteria, there is no established pathology. Data accumulated over the last 15 years has challenged the notion FD is free of relevant pathology, and in particular, increased duodenal eosinophils have been observed. Intestinal eosinophils play important roles in microbial defence, immune regulation, tissue regeneration and remodelling, and maintaining tissue homeostasis and metabolism; degranulation of eosinophils releases toxic granule products (e.g., major basic protein, eosinophil-derived neurotoxin) which can damage nerves. Normal cut-offs for eosinophil infiltration into the duodenum histologically are less than five eosinophils per high power field (<25 per five high power fields). In clinical practice there is evidence that pathologically increased intestinal eosinophils may often be overlooked. In a meta-analysis duodenal eosinophils were significantly increased in FD although there was substantial heterogeneity; degranulation of duodenal eosinophils was also significantly higher in FD without significant heterogeneity. In addition, increased duodenal permeability, systemic immune activation, and an altered mucosa-associated duodenal microbiome have been identified that may help explain why symptoms arise, often occur after food with exposure to food antigens, and typically fluctuate. Several potentially reversible risk factors for FD have now been identified. We evaluate the current evidence linking duodenal microinflammation and immune activation with FD and disorders of gut-brain interactions that overlap with FD. We propose a two-hit disease model for eosinophilic functional dyspepsia (EoFD) with management implications., Competing Interests: Nicholas J. Talley delivered the RD McKenna Memorial Lecture in 2023. He reports non-financial support from: Norgine (2021) (IBS interest group), personal fees from Allakos (gastroduodenal eosinophilic disease) (2021), Bayer (IBS) (2020), Planet Innovation (Gas capsule IBS) (2020), twoXAR Viscera Labs, (USA 2021) (IBS-diarrhoea), Dr Falk Pharma (2020) (EoE), Sanofi-aventis, Glutagen (2020) (celiac disease), IsoThrive (2021) (esophageal microbiome), BluMaiden (microbiome advisory board) (2021), Rose Pharma (IBS) (2021), Intrinsic Medicine (2022) (human milk oligosaccharide), Comvita Mānuka Honey (2021) (digestive health), Astra Zeneca (2022), outside the submitted work. In addition, Dr. Talley has a patent Nepean Dyspepsia Index (NDI) 1998, Biomarkers of IBS licensed, a patent Licensing Questionnaires Talley Bowel Disease Questionnaire licensed to Mayo/Talley, a patent Nestec European Patent licensed, and a patent Singapore Provisional Patent “Microbiota Modulation of BDNF Tissue Repair Pathway” issued, “Diagnostic marker for functional gastrointestinal disorders” Australian Provisional Patent Application 2021901692. Committees: OzSage; NHMRC Principal Committee (Research Committee) Asia Pacific Association of Medical Journal Editors, Rome V Working Team Member (Gastroduodenal Committee), International Plausibility Project Co-Chair (Rome Foundation funded), COVID-19 vaccine forum member (by invitation only). Community group: Advisory Board, IFFGD (International Foundation for Functional GI Disorders), AusEE. Editorial: Medical Journal of Australia (Emeritus Editor in Chief), Mayo Clinic Proceedings (Assoc Ed), Up to Date (Section Editor), Precision and Future Medicine, Sungkyunkwan University School of Medicine, South Korea, Med (Journal of Cell Press), Gastroenterology (Advisory Board). Simon Keely reports personal fees from Gossamer Bio, Anatara Lifescience, Immuron Ltd, Microba Life Science. He has received research support funding from Viscera Labs, Microba Life Science, Anatara Lifesciences and Gossamer Bio. He is currently funded by National Health and Medical Research Council (NHMRC) and Australian Department of Defence grants. He is listed as inventor on Diagnostic marker for functional gastrointestinal disorders” Australian Provisional Patent Application 2021901692., (© The Author(s) 2023. Published by Oxford University Press on behalf of the Canadian Association of Gastroenterology.)

Competing Interests: SK reports grants from the Australian National Health and Medical Research Council (via the Ideas Grant scheme and Centres of Research Excellence), Viscera Labs (research contract), and Microba Life Science (research contract), personal fees from Immuron and Microba Life Science, and participation on scientific advisory boards for Gossamer Bio and Anatara Lifesciences, outside the submitted work. GLB declares no competing interests.

Objective: Functional dyspepsia (FD) is a complex disorder, with debilitating epigastric symptoms. Evidence suggests alterations in gastrointestinal (GI) motility, visceral hypersensitivity, permeability and low-level immune activation in the duodenum may play a role. However, we still have a relatively poor understanding of how these factors interact to precipitate the onset of FD symptoms which are frequently meal related. The duodenal microbiota, in combination with specific dietary substrates, may be important mediators in disease pathophysiology; however, these interlinked factors have not been thoroughly investigated in FD., Design: Eighty-six individuals (56 FD, 30 controls) undergoing endoscopy were consecutively recruited and underwent detailed clinical assessment, including upper GI symptoms, gastric emptying and dietary assessment. Duodenal biopsies were obtained aseptically, and the mucosa-associated microbiota (MAM) analysed via 16S rRNA gene amplicon sequencing., Results: The relative abundances of predominant members of the Firmicutes, Bacteroidota and Fusobacteriota phyla were linked to symptom burden in FD. Inverse relationships between the relative abundances of Streptococcus and Prevotella, and the relative abundance of Veillonella spp with gastric emptying time, were also observed. No significant differences in long-term nutrient intake or diet quality were found between FD and controls, and there appeared to be limited association between habitual diet and duodenal MAM profiles., Conclusion: This study suggests a link between the duodenal MAM, gastric emptying and FD symptoms, and this is largely independent of long-term dietary intake., Competing Interests: Competing interests: These authors disclose the following: NJT reports personal fees from Allakos, Aviro Health, from Antara Life Sciences, Arlyx, Bayer, Danone, Planet Innovation, Takeda, Viscera Labs, twoXAR, Viscera Labs, Dr Falk Pharma, Censa, Cadila Pharmaceuticals, Progenity Inc, Sanofi-aventis, Glutagen, ARENA Pharmaceuticals, IsoThrive, BluMaiden, HVN National Science Challenge, non-financial support from HVN National Science Challenge NZ, outside the submitted work; In addition, NJT has a patent Biomarkers of IBS licensed (#12735358.9 -1405/2710383 and (#12735358.9 -1405/2710384), a patent Licensing Questionnaires Talley Bowel Disease Questionnaire licensed to Mayo/Talley, a patent Nestec European Patent licensed, and a patent Singapore Provisional Patent NTU Ref: TD/129/17 “Microbiota Modulation Of BDNF Tissue Repair Pathway” issued and copyright Nepean Dyspepsia Index (NDI) 1998 and Editorial: Medical Journal of Australia (Editor in Chief), Up to Date (Section Editor), Precision and Future Medicine, Sungkyunkwan University School of Medicine, South Korea, Med (Journal of Cell Press). NJT participates on committees for: Australian Medical Council (AMC) Council Member (2016-2019), MBS Review Taskforce (2016-2020), NHMRC Principal Committee, Research Committee (2016-2021), Asia Pacific Association of Medical Journal Editors (APAME) (current), GESA Board Member (2017-2019). NJT Misc: Avant Foundation (judging of research grants) (2019). NJT community and patient advocacy groups: Advisory Board, IFFGD (International Foundation for Functional GI Disorders). NJT acknowledges funding from the National Health and Medical Research Council (NHMRC) for the Centre for Research Excellence in Digestive Health. NJT holds an NHMRC Investigator grant. SK reports Grant/Research Support: National Health and Medical Research Council (Ideas Grant and Centre for Research Excellence) Viscera Labs (Research contract), Microba Life Science (Research contract). Consultant/Advisory Boards: Gossamer Bio (Scientific Advisory Board), Anatara Lifescience (Scientific Advisory Board), Microba Life Science (Consultancy). SK, MM, GLB, and NJT are co-inventors of “Diagnostic marker for functional gastrointestinal disorders” Australian Provisional Patent Application 2021901692, submitted 07/06/2021, via the University of Newcastle and UniQuest (University of Queensland) with PCT application 07/06/2022 (PCT/AU2022/050556). MM has received research grants from Soho Flordis International (SFI) Australia Research, Bayer Steigerwald Arzneimittelwerk and Yakult-Nature Global Grant for Gut Health; speaker’s honoraria, and travel sponsorship from Janssen Australia; consultancy fees from Sanofi Australia and Danone-Nutricia Australia; speaker honoraria and travel sponsorship from Perfect Company (China), and travel sponsorship from Yakult Inc (Japan). MM also acknowledges funding from NHMRC Australia, Australian Research Council, Princess Alexandra Hospital Research Foundation, Medical Research Futures Fund of Australia, Helmsley Charitable Trust via the Australasian Gastrointestinal Research Foundation, and United States Department of Defense. MM serves on the science advisory board (non-remunerated) for GenieBiome, Hong Kong. GJH reports to be on the advisory boards Australian Biotherapeutics, Glutagen, Bayer and received research support from Bayer, Abbott, Pfizer, Janssen, Takeda, Allergan. He serves on the Boards of the West Moreton Hospital and Health Service, Queensland, UQ Healthcare, Brisbane and the Gastro-Liga, Germany. He has a patent for the Brisbane aseptic biopsy device and serves as Editor of the Gastro-Liga Newsletter., (© Author(s) (or their employer(s)) 2023. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: Functional dyspepsia is characterised by chronic symptoms of post-prandial distress or epigastric pain not associated with defined structural pathology. Increased peripheral gut-homing T cells have been previously identified in patients. To date, it is unknown if these T cells were antigen-experienced, or if a specific phenotype was associated with FD., Objective: This study aimed to characterise T cell populations in the blood and duodenal mucosa of FD patients that may be implicated in disease pathophysiology., Methods: We identified duodenal T cell populations from 23 controls and 49 Rome III FD patients by flow cytometry using a surface marker antibody panel. We also analysed T cell populations in peripheral blood from 37 controls and 61 patients. Where available, we examined the number of duodenal eosinophils in patients and controls., Results: There was a shift in the duodenal T helper cell balance in FD patients compared to controls. For example, patients had increased duodenal mucosal Th2 populations in the effector (13.03 ± 16.11, 19.84 ± 15.51, p =0.038), central memory (23.75 ± 18.97, 37.52 ± 17.51, p =0.007) and effector memory (9.80±10.50 vs 20.53±14.15, p =0.001) populations. Th17 populations were also increased in the effector (31.74±24.73 vs 45.57±23.75, p =0.03) and effector memory (11.95±8.42 vs 18.44±15.63, p =0.027) subsets. Peripheral T cell populations were unchanged between FD and control., Conclusion: Our findings identify an association between lymphocyte populations and FD, specifically a Th2 and Th17 signature in the duodenal mucosa. The presence of effector and memory cells suggest that the microinflammation in FD is antigen driven., Competing Interests: Author GH received unrestricted educational support from Bayer Ptd, Ltd and the Falk Foundation. Research support was provided via the Princess Alexandra Hospital, Brisbane by GI Therapies Pty Limited, Takeda Development Center Asia, Pty Ltd, Eli Lilly Australia Pty Limited, F. Hoffmann-La Roche Limited, MedImmune Ltd Celgene Pty Limited, Celgene International II Sarl, Gilead Sciences Pty Limited, Quintiles Pty Limited, Vital Food Processors Ltd, Datapharm Australia Pty Ltd Commonwealth Laboratories, Pty Limited, Prometheus Laboratories, Falk GmbH and Co Kg, Nestle Pty Ltd, Mylan. Patent Holder: A biopsy device to take aseptic biopsies US 20150320407 A1. Author MV received grant/research Support: NIHR IBD clinical, LIVErNORTH Hepatology clinical. Author NP received advisory board fees from Abbvie, Allergan, Debiopharm International, Ferring, and Vifor Pharma and lecture fees from Allergan and Falk Pharma. Author MW received grant/research support: Prometheus Laboratories Inc Irritable bowel syndrome IBS Diagnostic, Commonwealth Diagnostics International biomarkers for FGIDs. Author NT received grant/research support: Rome Foundation; Abbott Pharmaceuticals; Datapharm; Pfizer; Salix irritable bowel syndrome; Prometheus Laboratories Inc irritable bowel syndrome IBS Diagnostic; Janssen constipation. Consultant/Advisory Boards: Allakos IBS, Adelphi Values functional dyspepsia patient reported outcome measures; Budesonide; GI therapies chronic constipation Rhythm IC; Allergens PLC; Napo Pharmaceutical; Outpost Medicine; Samsung Bioepis; Yuhan IBS; Synergy IBS; Theravance gastroparesis. Patent holder: Biomarkers of irritable bowel syndrome; Licensing Questionnaires Mayo Clinic Talley Bowel Disease Questionnaire—Mayo Dysphagia Questionnaire; Nestec European Patent Application No. 12735358.9; Singapore “Provisional” Patent NTU Ref: TD/129/17 “Microbiota Modulation of BDNF Tissue Repair Pathway. Author SK received grant/research support: Cancer Institute NSW Career Development Fellowship, National Health and Medical Research Council Project Grant, Commonwealth Diagnostics International biomarkers for FGIDs, Syntrix Biosystems contract research—drug delivery. Anatara Lifesciences Advisory Board/Funded research. Gossamer Bio Advisory Board/Funded research. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Burns, Bruce, Minahan, Mathe, Fairlie, Cameron, Naudin, Nair, Potter, Irani, Bollipo, Foster, Gan, Shah, Koloski, Foster, Horvat, Veysey, Holtmann, Powell, Walker, Talley and Keely.)

Background & Aims: This study explored the link between duodenal eosinophils and mast cells in patients with functional dyspepsia (FD)., Methods: MEDLINE (PubMed) and Embase electronic databases were searched until June 2021 for case-control studies reporting duodenal eosinophils and mast cells in FD. Pooled standardized mean difference (SMD), odds ratio, and 95% CIs of duodenal eosinophils and mast cells in FD patients and controls were calculated, using a random-effects model., Results: Twenty-two case-control studies with 1108 FD patients and 893 controls were identified. Duodenal eosinophils (SMD, 1.29; 95% CI, 0.85-1.73; P = .0001) and mast cells (SMD, 2.11; 95% CI, 1.14-3.07; P = .0001) were increased in FD patients compared with controls. Substantial heterogeneity was found (I 2  = 93.61, P = .0001; and I 2  = 96.69, P = .0001, respectively) and visual inspection of funnel plots confirmed publication bias. Degranulation of duodenal eosinophils was significantly higher in FD patients compared with controls (odds ratio, 3.78; 95% CI, 6.76-4.48; P = .0001), without statistically significant heterogeneity. We conducted a sensitivity analysis for duodenal eosinophils, by including only high-quality studies, and the results remained unchanged (SMD, 1.73; 95% CI, 1.06-2.40; P = .0001), with substantial heterogeneity. Postinfectious FD patients had increased duodenal eosinophils compared with controls (SMD, 3.91; 95% CI, 1.32-6.51; P = .001) and FD patients without any history of infection (SMD, 1.42; 95% CI, 0.88-1.96; P = .001). Helicobacter pylori-negative FD patients had significantly higher duodenal eosinophils compared with controls (SMD, 3.98; 95% CI, 2.13-5.84; P = .0001), with substantial heterogeneity. No significant difference in duodenal eosinophils was seen according to FD subtypes., Conclusions: This meta-analysis suggests a link between duodenal microinflammation and FD. However, the quality of evidence is very low, largely owing to the unexplained heterogeneity and serious risk of publication bias in all comparative analyses. Thus, causality remains uncertain and further studies are required., (Copyright © 2022. Published by Elsevier Inc.)

The gut-brain axis describes a bidirectional interplay within the enteric environment between the intestinal epithelium, the mucosal immune system, and the microbiota with the enteric nervous system. This interplay provides a link between exogenous environmental stimuli such as nutrient sensing, and nervous system function, as well as a mechanism of feedback from cortical and sensory centers of the brain to enteric activities. The intestinal epithelium is one of the human body's largest sources of hormones and neurotransmitters, which have critical effects on neuronal function. The influence of the gut microbiota on these processes appears to be profound; yet to date, it has been insufficiently explored. Disruption of the intestinal microbiota is linked not only to diseases in the gut but also to brain symptomatology, including neurodegenerative and behavioral disorders (Parkinson disease, Alzheimer disease, autism, and anxiety and/or depression). In this review we discuss the cellular wiring of the gut-brain axis, with a particular focus on the epithelial and neuronal interaction, the evidence that has led to our current understanding of the intestinal role in neurologic function, and future directions of research to unravel this important interaction in both health and allergic disease., (Copyright © 2022 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.)

Functional dyspepsia (FD) is a highly prevalent disorder of gut-brain interaction (DGBI), previously known as a functional gastrointestinal disorder. Characterized by early satiety, postprandial fullness, and/or epigastric pain or burning, diagnosis depends on positive symptomatology and exclusion of obvious structural diseases. A subtle inflammatory phenotype has been identified in FD patients, involving an increase in duodenal mucosal eosinophils, and imbalances in the duodenal gut microbiota. A dysregulated epithelial barrier has also been well described in FD and is thought to be a contributing factor to the low-grade duodenal inflammation observed, however the mechanisms underpinning this are poorly understood. One possible explanation is that alterations in the microbiota and increased immune cells can result in the activation of cellular stress response pathways to perpetuate epithelial barrier dysregulation. One such cellular response pathway involves the stabilization of hypoxia-inducible factors (HIF). HIF, a transcriptional protein involved in the cellular recognition and adaptation to hypoxia, has been identified as a critical component of various pathologies, from cancer to inflammatory bowel disease (IBD). While the contribution of HIF to subtle inflammation, such as that seen in FD, is unknown, HIF has been shown to have roles in regulating the inflammatory response, particularly the recruitment of eosinophils, as well as maintaining epithelial barrier structure and function. As such, we aim to review our present understanding of the involvement of eosinophils, barrier dysfunction, and the changes to the gut microbiota including the potential pathways and mechanisms of HIF in FD. A combination of PubMed searches using the Mesh terms functional dyspepsia, functional gastrointestinal disorders, disorders of gut-brain interaction, duodenal eosinophilia, barrier dysfunction, gut microbiota, gut dysbiosis, low-grade duodenal inflammation, hypoxia-inducible factors (or HIF), and/or intestinal inflammation were undertaken in the writing of this narrative review to ensure relevant literature was included. Given the findings from various sources of literature, we propose a novel hypothesis involving a potential role for HIF in the pathophysiological mechanisms underlying FD., Competing Interests: SH declares no conflicts of interest. GB declares no conflicts of interest. EH declares no conflicts of interest. SK declares grant/research support from Cancer Institute NSW (Career Development Fellowship), National Health and Medical Research Council (Center of Research Excellence, Project and Ideas Grant), Viscera Labs, Gossamer Bio, Anatara Lifesciences, Microba (Funded research and consultancy). NT reports, non-financial support from HVN National Science Challenge NZ, personal fees from Aviro Health (Digestive health) (2019), Anatara Life Sciences, Brisbane (2019), Allakos (gastric eosinophilic disease) (2021), Bayer (IBS) (2020), Danone (Probiotic) (2018), Planet Innovation (Gas capsule IBS) (2020), Takeda, Japan (gastroparesis) (2019), twoXAR (2019) (IBS drugs), Viscera Labs, (USA 2021) (IBS-diarrhea), Dr Falk Pharma (2020) (EoE), Censa, Wellesley MA USA (2019) (Diabetic gastroparesis), Cadila PharmIncaceuticals (CME) (2019), Progenity Inc. San Diego, (USA 2019) (Intestinal capsule), Sanofi-aventis, Sydney (2019) (Probiotic), Glutagen (2020) (Celiac disease), ARENA Pharmaceuticals (2019) (Abdominal pain), IsoThrive (2021) (esophageal microbiome), BluMaiden (2021), Rose Pharma (2021), Intrinsic Medicine (2021), Comvita Mānuka Honey (2021) outside the submitted work; In addition, NT has a patent Nepean Dyspepsia Index (NDI) 1998, Biomarkers of IBS licensed, a patent Licensing Questionnaires Talley Bowel Disease Questionnaire licensed to Mayo/Talley, a patent Nestec European Patent licensed, and a patent Singapore Provisional Patent “Microbiota Modulation Of BDNF Tissue Repair Pathway” issued, “Diagnostic marker for functional gastrointestinal disorders” Australian Provisional Patent Application 2021901692. Committees: OzSage, Australian Medical Council (AMC) [Council Member]; Australian Telehealth Integration Programme; MBS Review Taskforce; NHMRC Principal Committee (Research Committee) Asia Pacific Association of Medical Journal Editors. Boards: GESA Board Member, Sax Institute, Committees of the Presidents of Medical Colleges. Community group: Advisory Board, IFFGD (International Foundation for Functional GI Disorders), AusEE. Miscellaneous: Avant Foundation (judging of research grants). Editorial: Medical Journal of Australia (Editor in Chief), Up to Date (Section Editor), Precision and Future Medicine, Sungkyunkwan University School of Medicine, South Korea, Med (Journal of Cell Press). NT is supported by funding from the National Health and Medical Research Council (NHMRC) to the Center for Research Excellence in Digestive Health and he holds an NHMRC Investigator grant., (Copyright © 2022 Hari, Burns, Hoedt, Keely and Talley.)

Circadian rhythms are cyclic patterns of physiological, behavioural and molecular events that occur over a 24-h period. They are controlled by the suprachiasmatic nucleus (SCN), the brain's master pacemaker which governs peripheral clocks and melatonin release. While circadian systems are endogenous, there are external factors that synchronise the SCN to the ambient environment including light/dark cycles, fasting/fed state, temperature and physical activity. Circadian rhythms also provide internal temporal organisation which ensures that any internal changes that take place are centrally coordinated. Melatonin synchronises peripheral clocks to the external time and circadian rhythms are regulated by gene expression to control physiological function. Synchronisation of the circadian system with the external environment is vital for the health and survival of an organism and as circadian rhythms play a pivotal role in regulating GI physiology, disruption may lead to gastrointestinal (GI) dysfunction. Disorders of gut-brain interactions (DGBIs), also known as functional gastrointestinal disorders (FGIDs), are a group of diseases where patients experience reoccurring gastrointestinal symptoms which cannot be explained by obvious structural abnormalities and include functional dyspepsia (FD) and irritable bowel syndrome (IBS). Food timing impacts on the production of melatonin and given the correlation between food intake and symptom onset reported by patients with DGBIs, chronodisruption may be a feature of these conditions. Recent advances in immunology implicate circadian rhythms in the regulation of immune responses, and DGBI patients report fatigue and disordered sleep, suggesting circadian disruption. Further, melatonin treatment has been demonstrated to improve symptom burden in IBS patients, however, the mechanisms underlying this efficacy are unclear. Given the influence of circadian rhythms on gastrointestinal physiology and the immune system, modulation of these rhythms may be a potential therapeutic option for reducing symptom burden in these patients., Competing Interests: NT non-financial support from HVN National Science Challenge NZ, personal fees from Aviro Health (Digestive health) (2019), Anatara Lifesciences, Brisbane (2019), Allakos (gastric eosinophilic disease) (2021), Bayer (2020), Danone (Probiotic) (2018), Planet Innovation (Gas capsule IBS) (2020), Takeda, Japan (gastroparesis) (2019), twoXAR (2019) (IBS drugs), Viscera Labs, (United States 2021) (IBS-diarrhoea), Dr. Falk Pharma (2020) (EoE), Censa, Wellesley, MA, United States (2019) (Diabetic gastroparesis), Cadila Pharmaceuticals (CME) (2019), Progenity Inc., San Diego, (United States 2019) (Intestinal capsule), Sanofi-Aventis, Sydney (2019) (Probiotic), Glutagen (2020) (Celiac disease), ARENA Pharmaceuticals (2019) (Abdominal pain), IsoThrive (2021) (oesophageal microbiome), BluMaiden (2021), Rose Pharma (2021), Intrinsic Medicine (2021) outside the submitted work; In addition, NT has a patent Nepean Dyspepsia Index (NDI) 1998, Biomarkers of IBS licensed, a patent Licensing Questionnaires Talley Bowel Disease Questionnaire licensed to Mayo/Talley, a patent Nestec European Patent licensed, and a patent Singapore Provisional Patent “Microbiota Modulation Of BDNF Tissue Repair Pathway” issued. Committees: Australian Medical Council (AMC) Council Member; Australian Telehealth Integration Program; MBS Review Taskforce; NHMRC Principal Committee (Research Committee) Asia Pacific Association of Medical Journal Editors. Boards: GESA Board Member, Sax Institute, Committees of the Presidents of Medical Colleges. Community group: Advisory Board, IFFGD (International Foundation for Functional GI Disorders). Miscellaneous: Avant Foundation (judging of research grants). Editorial: Medical Journal of Australia (Editor in Chief), Up to Date (Section Editor), Precision and Future Medicine, Sungkyunkwan University School of Medicine, South Korea, Med (Journal of Cell Press). NT is supported by funding from the National Health and Medical Research Council (NHMRC) to the Centre for Research Excellence in Digestive Health and he holds an NHMRC Investigator grant. SK Grant/Research Support: National Health and Medical Research Council (Ideas Grant and Centre for Research Excellence) Viscera Labs (Research contract), Microba Life Science (Research contract). Consultant/Advisory Boards: Gossamer Bio (Scientific Advisory Board), Anatara Lifesciences (Scientific Advisory Board), Microba Life Science (Consultancy). The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2022 Fowler, Hoedt, Talley, Keely and Burns.)

Functional dyspepsia (FD) affects up to 15% of the population and is characterised by recurring upper gastrointestinal (GI) symptoms occurring in the absence of clinically identifiable pathology. Psychological stress is a key factor associated with the onset of FD and locally acting hypothalamic-pituitary-adrenal (HPA) axis hormones have been implicated in GI motility and barrier dysfunction. Recent pre-clinical work has identified mechanistic pathways linking corticotropin-releasing hormone (CRH) with the innate epithelial immune protein NLRP6, an inflammasome that has been shown to regulate GI mucus secretion. We recruited twelve FD patients and twelve healthy individuals to examine whether dysregulation of hypothalamic-pituitary adrenal (HPA) axis hormones and altered NLRP6 pathways were evident in the duodenal mucosa. Protein expression was assessed by immunoblot and immunohistochemistry in D2 duodenal biopsies. Plasma HPA axis hormones were assayed by ELISA and enteroid and colorectal cancer cell line cultures were used to verify function. FD patients exhibited reduced duodenal CRH-receptor 2, compared to non-GI disease controls, indicating a dysregulation of duodenal HPA signalling. The loss of CRH-receptor 2 correlated with reduced NLRP6 expression and autophagy function, processes critical for maintaining goblet cell homeostasis. In accordance, duodenal goblet cell numbers and mucin exocytosis was reduced in FD patients compared to controls. In vitro studies demonstrated that CRH could reduce NLRP6 in duodenal spheroids and promote mucus secretion in the HT29-MTX-E12 cell line. In conclusion, FD patients exhibit defects in the NLRP6-autophagy axis with decreased goblet cell function that may drive symptoms of disease. These features correlated with loss of CRH receptor 2 and may be driven by dysregulation of HPA signalling in the duodenum of FD patients., (Copyright © 2022 Elsevier Inc. All rights reserved.)

Background: Crohn's disease (CD), ulcerative colitis (UC), and indeterminate colitis are inflammatory bowel diseases (IBDs) that adversely affect the healthcare needs and quality of life (QoL) of people with IBD. The aim of this study was to explore the needs and perceptions of people with IBD in a primary care setting., Methods: This sequential explanatory mixed-methods study consisted of a cross-sectional survey (included validated tools), followed by semistructured interviews on participants' perceptions: IBD management, healthcare professionals, IBD care, flare management, and pharmacist's IBD roles., Results: Sixty-seven participants completed the survey, and 8 completed interviews. Quantitative findings : Age at diagnosis had significant association with medication nonadherence ( P = .04), QoL ( P = .04), and disease control ( P = .01) among the respondents. The odds of medication nonadherence were 8 times (adjusted odds ratio [AOR] = 8.04, 95% confidence interval [CI] = 1.08, 60.10) higher among younger participants aged <30 years. Those diagnosed with CD ( P = .02) reported more likely to have unfavorable perceptions of pharmacists' role in managing their IBD (AOR = 9.45, 95% CI = 1.57, 56.62) than those with UC and indeterminate colitis. Qualitative findings : General practitioners were considered the most important care provider and the first point of contact for patients in managing all aspects of IBD. Participants identified their key need to be timely access to specialized IBD care and found that other primary healthcare professionals lacked disease-specific knowledge for managing IBD., Conclusions: Primary healthcare professionals are well positioned but need targeted training to influence the needs of IBD patients. The specialty role of an IBD educator could complement existing services to deliver and address patient-specific care., (© The Author(s) 2022. Published by Oxford University Press on behalf of Crohn\'s & Colitis Foundation.)

Patients suffering functional dyspepsia symptoms have been shown to possess a greater relative abundance of Streptococcus compared to asymptomatic controls. Here, we describe the isolation and genomic features of a new Streptococcus isolate, from the duodenal tissue of a subject reporting dyspeptic symptoms, taxonomically assigned to Streptococcus salivarius and designated strain AGIRA0003.

Background: Inflammation results in significant shifts in tissue metabolism. Recent studies indicate that inflammation and hypoxia occur concomitantly. We examined whether circulating and tissue markers of hypoxia could serve as surrogate indicators of disease severity in adult and pediatric patients with inflammatory bowel disease (IBD)., Methods: Serum and colonic biopsies were obtained from pediatric subjects with active IBD colitis and adult subjects with active and inactive ulcerative colitis, along with healthy non-colitis controls of all ages. Disease activity was evaluated by endoscopy and histopathology. Levels of serum hypoxia markers (macrophage inflammatory protein-3α [MIP-3α], vascular endothelial growth factor [VEGF], and erythropoietin [EPO]) were measured., Results: Children with active IBD colitis had higher levels of serum MIP-3α and VEGF compared to non-colitis controls (p<0.01 and p<0.05, respectively). In adult subjects with endoscopically active ulcerative colitis, serum MIP-3α and EPO were significantly elevated compared to non-colitis controls (both p<0.01). In parallel, analysis of colon tissue MIP-3α mRNA and protein in pediatric subjects revealed increased expression in those with IBD colitis compared to controls (p<0.05 and p<0.01 for mRNA and protein, respectively). Serum MIP-3α and VEGF significantly increased with histology grade., Conclusion: Peripheral blood hypoxia markers may be useful indicators of disease activity for pediatric and adult IBD patients., Competing Interests: Dr Steven B. Colson reports T32 Training grants from NIH, during the conduct of the study. Dr Robert Isfort was a speaker for Takeda Pharmaceuticals, outside the submitted work. Dr Simon Keely reports grants from GossamBio, NHMRC, Cancer institute NSW, and Anatara Life Sciences, personal fees from Aerpio Therapeutics, Gossamer Bio, Anatara Life Sciences, outside the submitted work. The authors report no other conflicts of interest in this work., (© 2020 deZoeten et al.)

The composition of the lung microbiome is increasingly well characterised, with changes in microbial diversity or abundance observed in association with several chronic respiratory diseases such as asthma, cystic fibrosis, bronchiectasis, and chronic obstructive pulmonary disease. However, the precise effects of the microbiome on pulmonary health and the functional mechanisms by which it regulates host immunity are only now beginning to be elucidated. Bacteria, viruses, and fungi from both the upper and lower respiratory tract produce structural ligands and metabolites that interact with the host and alter the development and progression of chronic respiratory diseases. Here, we review recent advances in our understanding of the composition of the lung microbiome, including the virome and mycobiome, the mechanisms by which these microbes interact with host immunity, and their functional effects on the pathogenesis, exacerbations, and comorbidities of chronic respiratory diseases. We also describe the present understanding of how respiratory microbiota can influence the efficacy of common therapies for chronic respiratory disease, and the potential of manipulation of the microbiome as a therapeutic strategy. Finally, we highlight some of the limitations in the field and propose how these could be addressed in future research., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Background and Aim: Inflammatory bowel disease (IBD) refers to a group of complex and chronic conditions that requires long-term care delivered by a group of healthcare professionals through a multidisciplinary care model. We conducted a systematic review to examine and understand the role of healthcare professionals in the primary care management of IBD, and identify the gaps in IBD management that could be filled by primary care providers such as general practitioners (GPs) and pharmacists., Methods: The search strategy retrieved published studies from five databases, and eligible articles were assessed for quality. A gray literature search of the websites of organizations was also undertaken., Results: Twenty-one studies were included, of which 19 were peer-reviewed research articles and two reports were from organizational bodies. Although studies have shown the roles of GPs, pharmacists, dietitians, and psychologists in IBD management, nurses and gastroenterologists were the key drivers delivering specialized care to IBD patients. Many key services are accessible only for hospital inpatients (tertiary care) or through outpatient clinics (secondary care) with an absence of a multidisciplinary approach including GPs and pharmacists., Conclusion: Gastroenterologists and nurses have an important role in the delivery of care to patients with chronic gastrointestinal diseases including IBD, coeliac disease, irritable bowel syndrome, and functional dyspepsia. The role of nurses includes provision of specialized care to IBD patients, as well as supportive care such as education, monitoring of therapy, and ongoing assistance. The available evidence shows many opportunities for primary care providers to play a more active role in the management of IBD patients., (© 2019 The Authors. JGH Open: An open access journal of gastroenterology and hepatology published by Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.)

Objectives: Anti-cytolethal distending toxin B (CdtB) and anti-vinculin antibodies have been proposed as biomarkers that discriminate irritable bowel syndrome (IBS) diarrhea from inflammatory bowel disease; however, it is unknown whether they can also discriminate patients with IBS and IBS subtypes and functional dyspepsia (FD) from healthy individuals in the general population. We aimed to determine whether anti-CdtB and anti-vinculin can discriminate IBS and FD from health and from organic gastrointestinal (GI) disease., Methods: Adults were enrolled from 2 Australian studies: (i) a random, population-based study (n = 331) with subjects diagnosed with IBS (n = 63) or FD (n = 61) by modified Rome III criteria or healthy control subjects (n = 246) who did not meet criteria for IBS and/or FD and (ii) an outpatient-based study with subjects diagnosed with IBS (n = 256) and/or FD (n = 55) or organic GI disease (n = 182) by an independent clinician. Serum levels of anti-CdtB/anti-vinculin antibodies were determined by enzyme-linked immunosorbent assay., Results: There was a significantly higher mean value of anti-CdtB in FD vs healthy controls (mean = 2.46 [SD = 0.72] vs mean = 2.14 [SD = 0.77]; P = 0.005) and IBS/FD overlap vs healthy controls (mean = 2.47 [SD = 0.78] vs mean = 2.14 [SD = 0.77]; P = 0.02). There were no significant differences in anti-CdtB in IBS and FD outpatients or IBS/FD subgroups compared with patients with organic GI disease. In terms of anti-vinculin, there were no significant differences between IBS and FD and healthy controls or between IBS and FD and organic GI disease controls., Discussion: We did not confirm that anti-CdtB/anti-vinculin discriminated IBS diarrhea from organic GI disease in Australian subjects. However, we did find higher anti-CdtB in FD and IBS/FD overlap vs healthy controls. Postinfectious FD may be more common than currently recognized.

Background: Subtle histopathologic features such as eosinophilia and increased mast cells have been observed in functional gastrointestinal disorders (FGIDs), including functional dyspepsia (FD) and the irritable bowel syndrome (IBS). The mechanisms that drive recruitment of these cells to the gastrointestinal tract remain unexplained, largely due to the heterogeneity in phenotypes among patients diagnosed with such conditions. We aimed to systematically review the literature and collate the evidence for immune activation in FD and IBS, and where possible, detail the nature of activation., Methods: Seven literature databases were searched using the keywords: 'functional gastrointestinal disorder', FGID, 'functional dyspepsia', 'non-ulcer dyspepsia', 'idiopathic dyspepsia', 'irritable bowel syndrome', IBS and 'immun*'., Results: Fifty-one papers reporting discordant immune features met the selection criteria for this review. Changes in lymphocyte populations, including B and T lymphocyte numbers and activation status were reported in IBS and FD, in conjunction with duodenal eosinophilia in FD and increased colonic mast cells in IBS. Increases in circulating α4+β7+ gut-homing T cells appear to be linked to the pathophysiology of both FD and IBS. Studies in the area are complicated by poor phenotyping of patients into subgroups and the subtle nature of the immune activity involved in FD and IBS., Conclusions: Alterations in proportions of gut-homing T lymphocytes in both FD and IBS indicate that a loss of mucosal homeostasis may drive the symptoms of FD and IBS. There is indirect evidence that Th17 responses may play a role in FGIDs, however the evidence for a Th2 immune phenotype in FD and IBS is limited. Although immune involvement is evident, large, well-characterised patient cohorts are required to elucidate the immune mechanisms driving the development of FGIDs.

The gastrointestinal epithelium is a highly regenerative organ, where each cell is replaced in a cycle of 4-6 days, depending on the mammalian species. This highly proliferative state is driven by gastrointestinal stem and progenitor cells, located at the base of crypts. These cells give rise to at least six types of differentiated epithelial cells, each with a distinct function in maintaining homeostasis between the intestinal interface and the luminal environment. The isolation and culture of these cells from mammalian gastrointestinal tissue is a novel technique, which allows for the generation and maintenance of an in vitro culture system for adult epithelial cells. There are two predominant methods for isolation and propagation of gastrointestinal epithelial cells, the first is the organoid system developed in 2009, and the second is a later version known as the L-WRN spheroid system. In this chapter, we describe the method to isolate and culture human gastrointestinal stem and progenitor cells and culture them as three-dimensional spheroids using L-WRN cell conditioned media.

Background: Cell-free mitochondrial DNA (mtDNA) is proinflammatory and has been detected in high concentrations in trauma patients' plasma. Deoxyribonuclease (DNAse) is the free plasma enzyme responsible for the digestion of extracellular DNA. The relationship between mtDNA and DNAse after major trauma is unknown. We hypothesized that DNAse activity would be elevated after injury and trauma surgery and would be associated with high concentrations of extracellular DNA., Methods: Two-year prospective study was performed on 103 consecutive trauma patients (male, 81%; age, 38 years [interquartile range, 30-59 years]; injury severity score, 18 [interquartile range, 12-26 years]) who underwent standardized major orthopedic trauma surgical interventions. Blood was collected at five perioperative time points (preoperative, postoperative, 7 hours, 24 hours, and 3 days postoperatively). Healthy control subjects (n = 20) were also sampled. Cell-free mtDNA and nuclear DNA (nDNA) were measured using quantitative polymerase chain reaction. Deoxyribonuclease was also assayed in the same plasma samples., Results: Increased levels of mtDNA (from preoperative 163 ± 86 ng/mL to 3 days 282 ± 201 ng/mL, p < 0.0001) and nDNA (from preoperative 28 ± 20 ng/mL to 3 days 37 ± 27 ng/mL, p < 0.05) were present in trauma patients at all perioperative time points compared with healthy controls (mtDNA: 4 ± 2 ng/mL; nDNA: 10 ± 5 ng/mL). Deoxyribonuclease activity was lower in the trauma cohort (from preoperative 0.06 ± 0.04U/mL to 3 days 0.08 ± 0.04U/mL, p < 0.0001) compared with healthy controls (DNAse: 0.17 ± 0.03U/mL). There was no correlation between DNAse and perioperative DNA concentrations. Elevated mtDNA (but not nDNA) correlated with the development of systemic inflammatory response syndrome (SIRS) (p = 0.026) but not multiple organ failure., Conclusions: The significant perioperative elevation in plasma-free mtDNA concentration is associated with the development of SIRS. The fact that increased cell-free DNA concentrations present with significantly lower than healthy control DNAse activity suggests a potential therapeutic opportunity with DNAse administration to modulate postinjury severe SIRS., Level of Evidence: Prognostic/Epidemiological, level II.

Inflammatory bowel disease (IBD) is associated with several immune-mediated extraintestinal manifestations. More than half of all IBD patients have some form of respiratory pathology, most commonly neutrophil-mediated diseases, such as bronchiectasis and chronic bronchitis. Using murine models of colitis, we aimed to identify the immune mechanisms driving pulmonary manifestations of IBD. We found increased neutrophil numbers in lung tissue associated with the pulmonary vasculature in both trinitrobenzenesulfonic acid- and dextran sulfate sodium-induced models of colitis. Analysis of systemic inflammation identified that neutrophilia was associated with bacteremia and pyrexia in animal models of colitis. We further identified IL-6 as a systemic mediator of neutrophil recruitment from the bone marrow of dextran sulfate sodium animals. Functional inhibition of IL-6 led to reduced systemic and pulmonary neutrophilia, but it did not attenuate established colitis pathology. These data suggest that systemic bacteremia and pyrexia drive IL-6 secretion, which is a critical driver for pulmonary manifestation of IBD. Targeting IL-6 may reduce neutrophil-associated extraintestinal manifestations in IBD patients., (Copyright © 2018 American Society for Investigative Pathology. Published by Elsevier Inc. All rights reserved.)

Background: Severe steroid-insensitive asthma is a substantial clinical problem. Effective treatments are urgently required, however, their development is hampered by a lack of understanding of the mechanisms of disease pathogenesis. Steroid-insensitive asthma is associated with respiratory tract infections and noneosinophilic endotypes, including neutrophilic forms of disease. However, steroid-insensitive patients with eosinophil-enriched inflammation have also been described. The mechanisms that underpin infection-induced, severe steroid-insensitive asthma can be elucidated by using mouse models of disease., Objective: We sought to develop representative mouse models of severe, steroid-insensitive asthma and to use them to identify pathogenic mechanisms and investigate new treatment approaches., Methods: Novel mouse models of Chlamydia, Haemophilus influenzae, influenza, and respiratory syncytial virus respiratory tract infections and ovalbumin-induced, severe, steroid-insensitive allergic airway disease (SSIAAD) in BALB/c mice were developed and interrogated., Results: Infection induced increases in the levels of microRNA (miRNA)-21 (miR-21) expression in the lung during SSIAAD, whereas expression of the miR-21 target phosphatase and tensin homolog was reduced. This was associated with an increase in levels of phosphorylated Akt, an indicator of phosphoinositide 3-kinase (PI3K) activity, and decreased nuclear histone deacetylase (HDAC)2 levels. Treatment with an miR-21-specific antagomir (Ant-21) increased phosphatase and tensin homolog levels. Treatment with Ant-21, or the pan-PI3K inhibitor LY294002, reduced PI3K activity and restored HDAC2 levels. This led to suppression of airway hyperresponsiveness and restored steroid sensitivity to allergic airway disease. These observations were replicated with SSIAAD associated with 4 different pathogens., Conclusion: We identify a previously unrecognized role for an miR-21/PI3K/HDAC2 axis in SSIAAD. Our data highlight miR-21 as a novel therapeutic target for the treatment of this form of asthma., (Copyright © 2016 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.)

Crohn's disease (CD) is a chronic disease characterized by episodic and disabling inflammation of the gastrointestinal tract in genetically susceptible individuals. The incidence and prevalence of CD is rising rapidly across the world emphasising that disease risk is also influenced by environmental and lifestyle factors, as well as the microbial community resident in the gut. Childhood-onset CD is associated with an aggressive disease course that can adversely impact patient growth and development. There is no cure for CD however new onset and recurrent cases of paediatric CD are often responsive to exclusive enteral nutrition (EEN) treatment. EEN treatment involves the exclusive consumption of an elemental or polymeric formula for several weeks and it is well established as a primary intervention strategy. EEN treatments typically achieve remission rates of over 80% and importantly they are associated with a high rate of mucosal healing, far superior to steroids, which is prognostic of improved long-term health outcomes. Furthermore, they are safe, have few side effects, and improve nutritional status and linear growth. Surprisingly, despite the utility of EEN our understanding of the host-microbe-diet interactions that underpin clinical remission and mucosal healing are limited. Here, we review the current state of knowledge and propose that the induction of autophagy, in addition to modulation of the microbiota and coordinated effects on inflammation and epithelial cell biology, may be critical for the therapeutic effects associated with EEN. A better understanding of EEN treatment will provide new opportunities to restore gut homeostasis and prolong periods of remission, as well as provide new insights into the factors that trigger and perhaps prevent CD.

Gastrointestinal conditions may be broadly classified into two: organic and functional disease, with functional disorders accounting for the majority of patients with chronic gastrointestinal symptoms. Functional gastrointestinal disorders (FGIDs) present with no obvious pathology or well-accepted biochemical mechanism and, as such, treatment strategies are limited and focus on symptoms rather than cure. Irritable bowel syndrome and functional dyspepsia are the most widely recognised FGIDs, and there is a growing body of evidence to suggest an underlying inflammatory phenotype in subsets with these conditions. Here, we discuss the current knowledge of immune involvement in FGIDs and the commonalities between the different manifestations of FGIDs and propose a new hypothesis, potentially defining an underlying immunopathological basis of these conditions., (© 2015 Stichting European Society for Clinical Investigation Journal Foundation.)

Colon targeted drug delivery is an active area of research for local diseases affecting the colon, as it improves the efficacy of therapeutics and enables localized treatment, which reduces systemic toxicity. Targeted delivery of therapeutics to the colon is particularly advantageous for the treatment of inflammatory bowel disease (IBD), which includes ulcerative colitis and Crohn's disease. Advances in oral drug delivery design have significantly improved the bioavailability of drugs to the colon; however in order for a drug to have therapeutic efficacy during disease, considerations must be made for the altered physiology of the gastrointestinal (GI) tract that is associated with GI inflammation. Nanotechnology has been used in oral dosage formulation design as strategies to further enhance uptake into diseased tissue within the colon. This review will describe some of the physiological challenges faced by orally administered delivery systems in IBD, the important developments in orally administered nano-delivery systems for colon targeting, and the future advances of this research., From the Clinical Editor: Inflammatory Bowel Disease (IBD) poses a significant problem for a large number of patients worldwide. Current medical therapy mostly aims at suppressing the active inflammatory episodes. In this review article, the authors described and discussed the various approaches current nano-delivery systems can offer in overcoming the limitations of conventional drug formulations., (Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.)

Purpose: We examined the cytoprotective influences of the mucoadhesive polymer, poly(DMAEMA), on human mucus-producing intestinal epithelial monolayers against two bacterial exotoxins and S. typhimurium. Direct anti-bacterial effects were also assessed against S. typhimurium., Methods: In the presence and absence of mucus, untreated or poly(DMAEMA)-exposed monolayers were challenged with S. typhimurium or supernatants containing either cholera (CTx) or C. difficile toxins. Assays included LDH, cytokine secretion, cyclic AMP (cAMP) and microscopy to visualise bacterial adherence by monolayers. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of poly(DMAEMA) against S. typhimurium were established, along with a time-kill study., Results: CTx and C. difficile toxin induced LDH release from E12 monolayers. CTx also elevated intracellular epithelial cAMP, while S. typhimurium induced basolateral IL-8 secretion. Pre-treatment of E12 monolayers with poly(DMAEMA) reduced these effects, but only in the presence of mucus. The polymer co-localised with S. typhimurium in mucus and reduced bacteria-epithelia association. Poly(DMAEMA) was directly bactericidal against S. typhimurium at 1 mg/ml within 30 min., Conclusions: Poly(DMAEMA) may have potential as a non-absorbed polymer therapeutic against infection. These effects were mediated by a combination of physical interaction with mucus and by direct bacterial killing.