BackgroundInflammatory bowel disease (IBD) is characterized by marked clinical heterogeneity, reflecting complex interactions between host genetics, environmental exposures, and the gut microbiome. Although over 300 genetic risk loci have been identified, these account for only a fraction of disease variance, highlighting the importance of gene–environment interactions. ADAM-like Decysin-1 (ADAMDEC1) is a gastrointestinal-restricted metalloprotease implicated in mucosal repair and immune regulation, with reduced expression reported in IBD. While Adamdec1-deficient mice exhibit increased susceptibility to colitis, the mechanisms underlying phenotypic variability remain poorly understood.MethodsTo dissect genetic and environmental contributions to colitis severity, C57BL/6J wild-type (WT) and Adamdec1−/− mice were co-housed in two distinct environments and subjected to dextran sodium sulfate (DSS)-induced colitis. Disease severity was assessed by weight loss, immune cell infiltration, and transcriptional profiling of inflammatory and epithelial repair markers using flow cytometry and qPCR. Gut microbiome composition was analyzed from fecal samples collected following extended co-housing to evaluate environment-driven microbial differences.ResultsEnvironmental factors exerted a stronger influence than genotype on gut microbiome composition. WT mice displayed consistent inflammatory and transcriptional responses to DSS across environments, whereas Adamdec1−/− mice exhibited marked cage-dependent variability, ranging from severe colitis to a mild, WT-like phenotype. Severe disease in Adamdec1−/− mice was associated with enhanced neutrophil recruitment, increased CD11b expression, altered monocyte/macrophage activation, impaired epithelial proliferation, and disrupted stem cell–associated gene expression. These phenotypic differences correlated with distinct microbiome profiles indicating genotype-dependent microbial pathogenicity.ConclusionThese findings demonstrate that loss of Adamdec1 creates a state of heightened sensitivity to environmental and microbiome related factors, in which gut microbial composition correlates with differences in inflammatory and epithelial outcomes during colitis. This study identifies a gene–environment–microbiome axis associated with phenotypic variability in intestinal inflammation and provides mechanistic insight into the heterogeneity of IBD. Targeting environmentally driven microbial modifiers may represent a promising strategy for personalized intervention in genetically susceptible individuals.

A validated UV-HPLC method for the rapid detection of fluconazole and clobetasol propionate is presented. The method is proven to show excellent linearity for both drugs, alongside good robustness, specificity, precision, accuracy and selectivity.

While the use of antibiotics has been reported as extensive in the rearing of agricultural animals, insufficient information is available on the antibiotic residues in animal products and the adverse impact that consistent low-level exposure to antibiotics might have on the human body and its microbiome. The aim of this study was to estimate the antibiotic concentrations that humans are exposed to via their diet using the concentration of antibiotics in animal food products and water and an online survey on dietary intake. A total of 131 participants completed the dietary intake survey, with the majority belonging to the omnivorous diet group (76.3%). Distinct dietary trends were observed in the omnivorous and unknown groups eating animal products, with specific food types dominating each meal: pork (e.g., ham) and dairy products (e.g., milk, yoghurt) during breakfast, beef (e.g., burgers) and chicken (e.g., chicken breast) products during lunch, and fish (e.g., salmon fillet) during dinner. In total, 34 different animal-based food and drink products were tested for the presence of ten different antibiotics. Of all the products tested, over 35% exceeded the acceptable daily antibiotic intake for amoxicillin, ampicillin, and enrofloxacin.

Abstract Background As efforts to reduce antibiotic exposure through medical prescriptions have made significant progress, the potential consequences of residual antibiotics in animal-based food sources have been somewhat overlooked. The question of whether chronic exposure to antibiotic remnants in human diets could lead to the development of antimicrobial resistance (AMR) in human gut bacteria remains largely unanswered. This research aimed to address this gap by utilizing the hollow fibre infection model (HFIM) to investigate whether routine consumption of antibiotics from an omnivorous diet contributes to the emergence of resistance in a previously antibiotic-susceptible strain of E. coli isolated from the human gut. Methods To select the antibiotic mixtures for our study, we conducted a comprehensive diet survey involving 131 participants. Additionally, we employed LC-MS to quantify antibiotic concentrations in the most commonly consumed animal-based food products. We rigorously analysed triplicates of 34 food and beverage items, encompassing beef, chicken, pork, fish, and dairy, to detect and measure the concentrations of 10 specific antibiotics. Our findings revealed the presence of low levels of nine antibiotics across the samples, with amoxicillin and trimethoprim being the most frequently detected antibiotics. Alarmingly, 12 out of 34 products exceeded the acceptable daily intake levels for amoxicillin, ampicillin, and enrofloxacin. We further adapted the estimated daily intake formula to calculate antibiotic combinations and their intake from each meal. Subsequently, we subjected bacterial cells to the HFIM for 7 days, exposing them to three antibiotic ‘meals’ daily. We collected samples from the HFIM every 24 h to monitor changes in resistance phenotypes through MIC testing, as well as for subsequent transcriptomic analysis. Results Astonishingly, we observed the development of resistance to both individual antibiotics and combinations of antibiotics from the very first day, with resistance levels progressively increasing over the course of the week. Interestingly, the rate at which MICs increased was most rapid in the initial days, followed by a slower rate of increase while MICs continued to rise. This study provides compelling evidence that chronic exposure to low levels of antibiotics, akin to those found in animal-derived foods, can lead to rapid resistance development across multiple antibiotics within human gut bacteria. Further examination of samples from the HFIM through RT-PCR and WGS is warranted to elucidate the mechanisms underlying resistance development in the gut environment due to dietary factors. Conclusions Our research highlights the urgent need for greater scrutiny of antibiotic residues in the food chain and emphasizes the potential role of dietary habits in driving AMR development within human gut bacteria. Understanding the underlying mechanisms is crucial for devising effective strategies to mitigate this emerging public health concern.

While the use of a wide range of antibiotics has been reported as extensive in the rearing of agricultural animals, extremely limited information is available on the antibiotic residues in animal products and the adverse impact consistent low-level exposure to antibiotics might have on the human body as well as its microbiome. The aim of this study was to estimate the possible antibiotic concentrations humans are exposed to via their diet using the concentration of antibiotics in animal food products and water, and an online survey on dietary habits. A total of 131 participants completed the dietary habits survey, the majority belonging to the omnivorous diet habit. Distinct dietary trends were observed into omnivorous and unknown groups eating food-producing animal products, with specific food types dominating each meal: pork (e.g. ham) and dairy products (e.g. milk, yoghurt) during breakfast, beef (e.g. burger) and chicken (e.g. chicken breast) products during lunch, and fish (e.g. salmon fillet) during dinner. 34 different animal-based food and drink products were tested for the presence of ten different antibiotics. Low levels of nine of the ten antibiotics were detected across the samples tested with amoxicillin and trimethoprim being the most frequently detected antibiotics from all samples with concentrations ranging from 216.7-6866.9 μg/kg and 55.2-461.7 μg/kg, respectively. Of all products tested, over 35% exceeded the acceptable daily intake antibiotic concentration for amoxicillin, ampicillin, and enrofloxacin. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study did not receive any funding. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: Ethics Committee of the University College London gave ethical approval for this work, project number [19139/001]. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data produced in the present study are available upon reasonable request to the authors.

Background:Ustekinumab was approved in 2016 for the treatment of moderate–severe Crohn’s disease (CD). Clinical trials and real-world studies have suggested ustekinumab to be a safe and effective treatment; however, studies to date infrequently use imaging techniques to predict response to biologics in CD.Objectives:We assessed the 2-year real-world effectiveness and safety of ustekinumab in a tertiary CD cohort with the use of novel imaging techniques.Design:Retrospective cohort study.Methods:Retrospective data were collected between 2016 and 2021. Study end points included ustekinumab persistence, biological and/or clinical response and remission at 12, 18 and 24 months. Statistical analysis included demographic and inferential analyses.Results:In all, 131 CD patients [57.3% female, median age of 26.0 (21.0–37.0)] were included. Patients were non-bio naïve, and the majority received ustekinumab as third- or fourth-line treatment. At 24 months, 61.0% (80/131) persisted with ustekinumab [52.7% (69/131) steroid free]. Clinical response was reported in 55.2% (37/67), clinical remission in 85.7% (57/67), biological response in 46.8% (22/47) and biological remission in 31.9% (15/47) of patients at 24 months. The low outcome numbers were attributable to missing data. Improvements in routine disease markers, including C-reactive protein and Harvey–Bradshaw Index, were also reflected in magnetic resonance imaging-derived disease scores. The presence of penetrating CD, an -ostomy and sarcopenia were all predictors of poorer ustekinumab outcomes ( p < 0.05).Conclusion:Ustekinumab is effective in non-bio-naïve CD patients with non-stricturing, non-penetrating disease with an unremarkable safety profile but may be less effective in those with penetrating disease, -ostomies and sarcopenia.

Abstract Background Crohn’s disease (CD) is associated with a 3-4 fold increased risk of periodontitis compared to the general population1 though periodonitis is poorly recognised and diagnosed. Evidence from mouse models highlight an important link between oral and gut health. Periodontitis has been shown to lead to ectopic colonization of oral pathogens and oral Th17-T cells that activate lamina propria macrophages and exacerbate gut inflammation2. Very little is known about the patient demographics of those at risk of periodontitis. This study aimed to assess the risk factors for periodontitis in CD patients. Methods We conducted a cross-sectional study recruiting CD patients at UCLH through myCare, an online platform for patients linked to their clinical records. Patient data were obtained using EpicCare, a web-based electronic patient record database. Patient risk of periodontitis was determined using a previously validated oral health questionnaire3. Statistical tests were conducted using IBM SPSS Statistics 27. Results This single centre study included 89 CD patients; 54% female and median age of 40 (IQR 19-82). Patients predominantly identified as White British (56%). The majority had ileocolonic CD (51%) with non-stricturing/non-penetrating behaviour (70%) and were on biologic therapy (52%) (Tab 1). The oral health questionnaire identified 37% of CD patients at risk of periodontitis. There was no statistically significant association between periodontitis risk and age, gender, age at CD diagnosis, disease duration, CD phenotype, family history, body mass index (BMI) or smoking status. Current steroid, immunomodulator use and number of prior biologics also showed no association. Current use of adalimumab and ustekinumab were both independently correlated with risk of periodontitis (χ2 p=0.004 & χ2 p=0.044, respectively). 90% of patients receiving adalimumab were not at risk of periodontitis (Fig 1). In contrast, 60% of patients on ustekinumab were at risk of periodontitis. Logistic regression analysis showed that patients receiving adalimumab were 86% less likely to be at risk of periodontitis compared to patients not receiving adalimumab (OR 0.14 (CI 0.029 - 0.633, p=0.011)). 75% of the adalimumab group was anti-TNF naïve, but no association was seen between prior biologic use and periodontitis risk (p=0.91). Conclusion The questionnaire has identified a third of patients who are at risk of periodontitis in the CD cohort. Adalimumab shows benefit in mitigating this risk and may be a drug of choice in patients with oral disease. The questionnaire is a helpful tool to identify and refer at-risk patients.

Diet is an important lifestyle factor that is known to contribute in the development of human disease. It is well established that poor diet plays an active role in exacerbating metabolic diseases, such as obesity, diabetes and hypertension. Our understanding of how the immune system drives chronic inflammation and disease pathogenesis has evolved in recent years. However, the contribution of dietary factors to inflammatory conditions such as inflammatory bowel disease, multiple sclerosis and arthritis remain poorly defined. A western diet has been associated as pro-inflammatory, in contrast to traditional dietary patterns that are associated as being anti-inflammatory. This may be due to direct effects of nutrients on immune cell function. Diet may also affect the composition and function of gut microbiota, which consequently affects immunity. In animal models of inflammatory disease, diet may modulate inflammation in the gastrointestinal tract and in other peripheral sites. Despite limitations of animal models, there is now emerging evidence to show that anti-inflammatory effects of diet may translate to human gastrointestinal and inflammatory diseases. However, appropriately designed, larger clinical studies must be conducted to confirm the therapeutic benefit of dietary therapy.

OBJECTIVE To preliminary evaluate the clinical effects of probiotics in individuals with symptomatic oral lichen planus, and the possible mechanisms of action. SUBJECTS AND METHODS 30 individuals with symptomatic oral lichen planus were recruited in a double-blind parallel group randomised controlled (1:1) proof-of-concept pilot trial of probiotic VSL#3 vs placebo. Efficacy outcomes included changes in pain numeric rating scale, oral disease severity score and the chronic oral mucosal disease questionnaire. Adverse effects, home diary, and withdrawals were assessed as feasibility outcomes. Mechanistic outcomes included changes in salivary and serum levels of CXCL10 and IFN-γ and in oral microbial composition. RESULTS The probiotic VSL#3 was safe and well tolerated. We observed no statistically significant change in pain, disease activity, quality of life, serum/salivary CXCL10 or oral microbial composition with respect to placebo. Salivary IFN-γ levels demonstrate a trend for a reduced level in the active group (p=0.082) after 30 days of probiotic consumption. CONCLUSIONS The present proof-of-concept study provides some weak not convincing indication of biological and clinical effects of probiotic VSL#3 in individuals with painful oral lichen planus. Further research in this field is needed, with the current study providing useful information to the design of future clinical trials.

Background: Evidence suggests an important role for gut-microbiota dysbiosis in the development of rheumatoid arthritis (RA). The link between changes in gut bacteria and the development of joint inflammation is missing. Here, we address whether there are changes to the gut environment and how they contribute to arthritis pathogenesis. Methods: We analyzed changes in markers of gut permeability, damage, and inflammation in peripheral blood and serum of RA patients. Serum, intestines, and lymphoid organs isolated from K/BxN mice with spontaneous arthritis or from wild-type, genetically modified interleukin (IL) -10R(-/-) or claudin-8(-/-) mice with induced arthritis were analyzed by immunofluorescence/histology, ELISA, and flow cytometry. Findings: RA patients display increased levels of serum markers of gut permeability and damage and cellular gut-homing markers, both parameters positively correlating with disease severity. Arthritic mice display increased gut permeability from early stages of disease, as well as bacterial translocation, inflammatory gut damage, increases in interferon gamma (IFN gamma)(+) and decreases in IL-10(+) intestinal-infiltrating leukocyte frequency, and reduced intestinal epithelial IL-10R expression. Mechanistically, both arthritogenic bacteria and leukocytes are required to disrupt gut-barrier integrity. We show that exposing intestinal organoids to IFNg reduces IL-10R expression by epithelial cells and that mice lacking epithelial IL-10R display increased intestinal permeability and exacerbated arthritis. Claudin-8(-/-) mice with constitutively increased gut permeability also develop worse joint disease. Treatment of mice with AT-1001, a molecule that prevents development of gut permeability, ameliorates arthritis. Conclusions: We suggest that breakdown of gut-barrier integrity contributes to arthritis development and propose restoration of gut-barrier homeostasis as a new for RA.

The microbiome plays an important role in maintaining human health. Despite multiple factors being attributed to the shaping of the human microbiome, extrinsic factors such diet and use of medications including antibiotics appear to dominate. Mucosal surfaces, particularly in the gut, are highly adapted to be able to tolerate a large population of microorganisms whilst still being able to produce a rapid and effective immune response against infection. The intestinal microbiome is not functionally independent from the host mucosa and can, through presentation of microbe-associated molecular patterns (MAMPs) and generation of microbe-derived metabolites, fundamentally influence mucosal barrier integrity and modulate host immunity. In a healthy gut there is an abundance of beneficial bacteria that help to preserve intestinal homoeostasis, promote protective immune responses, and limit excessive inflammation. The importance of the microbiome is further highlighted during dysbiosis where a loss of this finely balanced microbial population can lead to mucosal barrier dysfunction, aberrant immune responses, and chronic inflammation that increases the risk of disease development. Improvements in our understanding of the microbiome are providing opportunities to harness members of a healthy microbiota to help reverse dysbiosis, reduce inflammation, and ultimately prevent disease progression.

Abstract Aims Following ERCP, NICE guidance suggests that surgically fit patients undergo cholecystectomy to prevent recurrence of choledocholithiasis and its complications. However, for many patients who are deemed unfit or who choose not to have surgery, ERCP is their definitive management. This study examines the clinical outcomes and costs of expectant management (EM) or cholecystectomy following ERCP. Methods All patients that underwent ERCP, sphincterotomy and common bile duct (CBD) clearance at St James’s University Hospital between January 2015 and December 2018 were identified from a prospectively maintained ERCP database. The clinical outcomes for patients that had undergone an ERCP, sphincterotomy and CBD clearance for gallstones were identified from their electronic patient record. A cost analysis for the complete patient pathway was performed. Results 820 patients underwent ERCP and CBD clearance for gallstones with a median 3.9 year follow up. 222 patients had undergone a cholecystectomy prior to ERCP and were excluded from analysis. 203 patients underwent planned cholecystectomy with 15% (31 patients) requiring complex surgery and 12% (24 patients) needing readmission. 395 patients received expectant management (EM). 9 (2.3%) patients returned with CBD stone symptoms, 6 (1.5%) went on to laparoscopic cholecystectomy (LC). The readmission rate in the EM group was 9%. The average cost per patient in the expectant management group was £7,487 and in the cholecystectomy group was £10,584. Conclusion The results from this study suggest that the need for cholecystectomy following ERCP is uncertain, with similar rates of biliary re-admissions in both groups.

Protein localisation and translocation between intracellular compartments underlie almost all physiological processes. The hyperLOPIT proteomics platform combines mass spectrometry with state-of-the-art machine learning to map the subcellular location of thousands of proteins simultaneously. We combine global proteome analysis with hyperLOPIT in a fully Bayesian framework to elucidate spatiotemporal proteomic changes during a lipopolysaccharide (LPS)-induced inflammatory response. We report a highly dynamic proteome in terms of both protein abundance and subcellular localisation, with alterations in the interferon response, endo-lysosomal system, plasma membrane reorganisation and cell migration. Proteins not previously associated with an LPS response were found to relocalise upon stimulation, the functional consequences of which are still unclear. By quantifying proteome-wide uncertainty through Bayesian modelling, a necessary role for protein relocalisation and the importance of taking a holistic overview of the LPS-driven immune response has been revealed. The data are showcased as an interactive application freely available for the scientific community.

Paneth cell defects in Crohn's disease (CD) patients (called the Type I phenotype) are associated with worse clinical outcomes. Recent studies have implicated mitochondrial dysfunction in Paneth cells as a mediator of ileitis in mice. We hypothesized that CD Paneth cells exhibit impaired mitochondrial health and that mitochondrial-targeted therapeutics may provide a novel strategy for ileal CD. Terminal ileal mucosal biopsies from adult CD and non-IBD patients were characterized for Paneth cell phenotyping and mitochondrial damage. To demonstrate the response of mitochondrial-targeted therapeutics in CD, biopsies were treated with vehicle or Mito-Tempo, a mitochondrial-targeted antioxidant, and RNA transcriptome was analyzed. During active CD inflammation, the epithelium exhibited mitochondrial damage evident in Paneth cells, goblet cells, and enterocytes. Independent of inflammation, Paneth cells in Type I CD patients exhibited mitochondrial damage. Mito-Tempo normalized the expression of interleukin (IL)-17/IL-23, lipid metabolism, and apoptotic gene signatures in CD patients to non-IBD levels. When stratified by Paneth cell phenotype, the global tissue response to Mito-Tempo in Type I patients was associated with innate immune, lipid metabolism, and G protein-coupled receptor (GPCR) gene signatures. Targeting impaired mitochondria as an underlying contributor to inflammation provides a novel treatment approach for CD.

From the earliest days of using natural remedies to modern applications of clinically tested medications, combining therapies for disease treatment has been standard practice. Combination treatments can exhibit synergistic effects, broadly defined as a greater-than-additive effect of two or more therapeutic agents. Indeed, clinicians often use their experience and expertise to tailor such combinations in the hopes of maximizing the therapeutic effect. Alongside these efforts, computational studies into understanding and predicting the biophysical underpinnings of how synergy is achieved have benefitted from high-throughput screening and computational biology. One challenge is how to best design and analyze the results of synergy studies performed at scale, especially because the number of possible combinations to test quickly becomes unmanageable, and the tools to analyze the resulting data are quite new. Nevertheless, the benefits of such studies are clear — by combining multiple drugs in the treatment of infectious disease and cancer, for instance, one can lessen host toxicity and simultaneously reduce the likelihood of resistance to treatment. In this study, we extend the widely validated chemogenomic HIPHOP assay to drug combinations. We identify a class of “combination-specific sensitive strains” that suggest mechanisms for the synergies we observe and further suggest focused follow-up studies.

Since the earliest days of using natural remedies, combining therapies for disease treatment has been standard practice. Combination treatments exhibit synergistic effects, broadly defined as a greater-than-additive effect of two or more therapeutic agents. Clinicians often use their experience and expertise to tailor such combinations to maximize the therapeutic effect. Although understanding and predicting biophysical underpinnings of synergy have benefitted from high-throughput screening and computational studies, one challenge is how to best design and analyze the results of synergy studies, especially because the number of possible combinations to test quickly becomes unmanageable. Nevertheless, the benefits of such studies are clear—by combining multiple drugs in the treatment of infectious disease and cancer, for instance, one can lessen host toxicity and simultaneously reduce the likelihood of resistance to treatment. This study introduces a new approach to characterize drug synergy, in which we extend the widely validated chemogenomic HIP–HOP assay to drug combinations; this assay involves parallel screening of comprehensive collections of barcoded deletion mutants. We identify a class of “combination-specific sensitive strains” that introduces mechanisms for the synergies we observe and further suggest focused follow-up studies.

From the earliest days of using natural remedies to modern applications of clinically tested medications, combining therapies for disease treatment has been standard practice. Combination treatments can exhibit synergistic effects, broadly defined as a greater-than-additive effect of two or more therapeutic agents. Indeed, clinicians often use their experience and expertise to tailor such combinations in the hopes of maximizing the therapeutic effect. Alongside these efforts, computational studies into understanding and predicting the biophysical underpinnings of how synergy is achieved have benefitted from high-throughput screening and computational biology. One challenge is how to best design and analyze the results of synergy studies performed at scale, especially because the number of possible combinations to test quickly becomes unmanageable, and the tools to analyze the resulting data are quite new. Nevertheless, the benefits of such studies are clear — by combining multiple drugs in the treatment of infectious disease and cancer, for instance, one can lessen host toxicity and simultaneously reduce the likelihood of resistance to treatment. In this study, we extend the widely validated chemogenomic HIPHOP assay to drug combinations. We identify a class of “combination-specific sensitive strains” that suggest mechanisms for the synergies we observe and further suggest focused follow-up studies. ### Competing Interest Statement The authors have declared no competing interest.