Host-microbe multi-omics and succinotype profiling have prognostic value for future relapse in patients with inflammatory bowel disease

Crohn's disease (CD) and ulcerative colitis (UC) are chronic relapsing inflammatory bowel disorders (IBD), the pathogenesis of which is uncertain but includes genetic susceptibility factors, immune-mediated tissue injury and environmental influences, most of which appear to act via the gut microbiome. We hypothesized that host-microbe alterations could be used to prognostically stratify patients experiencing relapses up to four years after endoscopy. We therefore examined multiple omics data, including published and new datasets, generated from paired inflamed and non-inflamed mucosal biopsies from 142 patients with IBD (54 CD; 88 UC) and from 34 control (non-diseased) biopsies. The relapse-predictive potential of 16S rRNA gene and transcript amplicons (standing and active microbiota) were investigated along with host transcriptomics, epigenomics and genetics. While standard single-omics analysis could not distinguish between patients who relapsed and those that remained in remission within four years of colonoscopy, we did find an association between the number of flares and a patient's succinotype. Our multi-omics machine learning approach was also able to predict relapse when combining features from the microbiome and human host. Therefore multi-omics, rather than single omics, better predicts relapse within 4 years of colonoscopy, while a patient's succinotype is associated with a higher frequency of relapses.

Microbiota transplant therapy in inflammatory bowel disease: advances and mechanistic insights

Microbiota transplant therapy is an emerging therapy for inflammatory bowel disease, but factors influencing its efficacy and mechanism remain poorly understood. In this narrative review, we outline key elements affecting therapeutic outcomes, including donor factors (such as age and patient relationship), recipient factors, control selection, and elements impacting engraftment and its correlation with clinical response. We also examine potential mechanisms through inflammatory bowel disease trials, focusing on the interplay between the microbiota, host, and immune system. Finally, we briefly explore potential future directions for microbiota transplant therapy and promising emerging treatments.

PMA1-containing extracellular vesicles of Candida albicans triggers immune responses and colitis progression

Candida albicans (C. albicans) exhibits aberrant changes in patients with colitis, and it has been reported to dominate the colonic mucosal immune response. Here, we found that PMA1 expression was significantly increased in C. albicans from patients with IBD compared to that in healthy controls. A Crispr-Cas9-based fungal strain editing system was then used to knock out PMA1 expression in C. albicans. Compared to WT-C.a, ΔPMA1-C.a could not aggravate colitis. Proteomic analysis showed that PMA1 was transported by extracellular vesicles (EVs) of C. albicans. PMA1-containing EVs aggravated colitis, modulated the migration of cDC2 from the lamina propria to mesenteric lymph nodes, and induced TH17 cell differentiation. Moreover, the adaptor protein CARD9 was critical in PMA1-containing EV-induced colitis, and CARD9-deficient DCs did not induce TH17 cell differentiation or IL-17A production. Mechanically, CARD9 combines with the glycolytic protein GAPDH (aa2-146 domain) through its CARD region. CARD9 deficiency led to decreased enzyme activity of GAPDH and decreased glycolysis of DCs. These findings indicate that PMA1 is a potential virulence factor responsible for the pathogenesis of C. albicans colitis.

The intestinal mucosa-associated microbiota in IBD-associated arthritis displays lower relative abundance of Roseburia intestinalis

The most common extra-intestinal manifestation (EIM) of inflammatory bowel disease (IBD), IBD-associated arthritis (IAA), occurs in 25-40% of patients and can be debilitating. In IBD, mucosal and stool microbiota richness is decreased, and compositional changes can precede or accompany disease onset. Likewise, spondyloarthritides are associated with altered gut microbiota, with overlapping bacterial signatures observed in IBD, suggesting key shared microbial factors are involved in both conditions. Much has been learned about the role of the intestinal microbiome in IBD, but less is known regarding its role in IAA. To address this knowledge gap, we analyzed the mucosa-associated intestinal microbiota of participants enrolled in the LOCATION-IBD cohort. Microbiota composition was established using 16S rRNA gene amplicon sequencing of intestinal biopsy samples taken from participants with IBD, with or without arthropathy. Microbiota samples clustered predominantly by participant, and similar taxa were present across the colon. The mucosal intestinal microbiota of females with IAA displayed a lower relative abundance of R. intestinalis, while males with IAA had a higher relative abundance of Corynebacterium, even when controlling for IBD-type, whether samples were taken from a site of inflammation and intestinal location. These findings indicate the mucosa-associated intestinal microbiota is associated with IAA in a sex-specific manner.

Predictive value of three nutritional indexes for disease activity in patients with inflammatory bowel disease

BACKGROUND

Malnutrition is prevalent in patients with inflammatory bowel disease (IBD); however, its ability to predict the disease activity in IBD remains unexplored. Therefore, this study aimed to explore the association between malnutrition and disease activity in IBD.

METHODS

In this retrospective study, we enrolled 1006 patients diagnosed with IBD from the First Affiliated Hospital of Wenzhou Medical University from 2011 to 2022. Malnutrition was assessed based on the prognostic nutritional index (PNI), geriatric nutritional risk index (GNRI), and controlling nutritional status (CONUT) scores. Logistic regression analyses were performed to identify predictors for disease activity. Restricted cubic spline analysis was performed to evaluate the possible nonlinear relations, and subgroup analysis was performed to explore potential interactions. Additionally, prediction performances were compared through receiver operating characteristic curves, net reclassification improvement, and integrated discrimination improvement.

RESULTS

The prevalence of malnutrition calculated by the PNI, GNRI, and CONUT scores in IBD was 16.9%, 72.1%, and 75.6%, respectively and significant correlations were observed among them. Multivariate logistic regression analysis showed that PNI, GNRI, and CONUT were independent risk factors for disease activity, and no significant nonlinear relationship was observed between disease activity and all three indexes. No statistically significant interactive effect was found in nearly all the subgroups. GNRI showed the highest predictive value compared with PNI and CONUT. Additionally, combining any of the three indexes improved the ability of C-reactive protein to predict IBD activity.

CONCLUSIONS

All three nutritional indexes evaluated malnutrition to be an independent risk factor for IBD activity.

Synergistic and off-target effects of bacteriocins in a simplified human intestinal microbiome: implications for Clostridioides difficile infection control

Clostridioides difficile is a major cause of nosocomial diarrhea. As current antibiotic treatment failures and recurrence of infections are highly frequent, alternative strategies are needed for the treatment of this disease. This study explores the use of bacteriocins, specifically lacticin 3147 and pediocin PA-1, which have reported inhibitory activity against C. difficile. We engineered Lactococcus lactis strains to produce these bacteriocins individually or in combination, aiming to enhance their activity against C. difficile. Our results show that lacticin 3147 and pediocin PA-1 display synergy, resulting in higher anti-C. difficile activity. We then evaluated the effects of these L. lactis strains in a Simplified Human Intestinal Microbiome (SIHUMI-C) model, a bacterial consortium of eight diverse human gut species that includes C. difficile. After introducing the bacteriocin-producing L. lactis strains into SIHUMI-C, samples were collected over 24 hours, and the genome copies of each species were assessed using qPCR. Contrary to expectations, the combined bacteriocins increased C. difficile levels in the consortium despite showing synergy against C. difficile in agar-based screening. This can be rationally explained by antagonistic inter-species interactions within SIHUMI-C, providing new insights into how broad-spectrum antimicrobials might fail to control targeted species in complex gut microbial communities. These findings highlight the need to mitigate off-target effects in complex gut microbiomes when developing bacteriocin-based therapies with potential clinical implications for infectious disease treatment.

Precision microbiota therapy for IBD: premise and promise

Inflammatory Bowel Disease (IBD) is a spectrum of chronic inflammatory diseases of the intestine that includes subtypes of ulcerative colitis (UC) and Crohn's Disease (CD) and currently has no cure. While IBD results from a complex interplay between genetic, environmental, and immunological factors, sequencing advances over the last 10-15 years revealed signature changes in gut microbiota that contribute to the pathogenesis of IBD. These findings highlight IBD as a disease target for microbiome-based therapies, with the potential to treat the underlying microbial pathogenesis and provide adjuvant therapy to the emerging spectrum of advanced therapies for IBD. Building on the success of fecal microbiota transplantation (FMT) for Clostridioides difficile infection, therapies targeting gut microbiota have emerged as promising approaches for treating IBD; however, unique aspects of IBD pathogenesis highlight the need for more precision in the approach to microbiome therapeutics that leverage aspects of recipient and donor selection, diet and xenobiotics, and strain-specific interactions to enhance the efficacy and safety of IBD therapy. This review focuses on both pre-clinical and clinical studies that support the premise for microbial therapeutics for IBD and aims to provide a framework for the development of precision microbiome therapeutics to optimize clinical outcomes for patients with IBD.

Gut microbiome shifts in adolescents after sleeve gastrectomy with increased oral-associated taxa and pro-inflammatory potential

Bariatric surgery is highly effective in achieving weight loss in children and adolescents with severe obesity, however the underlying mechanisms are incompletely understood, and gut microbiome changes are unknown. Here, we show that adolescents exhibit significant gut microbiome and metabolome shifts several months after laparoscopic vertical sleeve gastrectomy (VSG), with increased alpha diversity and notably with enrichment of oral-associated taxa. To assess causality of the microbiome/metabolome changes in phenotype, pre-VSG and post-VSG stool was transplanted into germ-free mice. Post-VSG stool was not associated with any beneficial outcomes such as adiposity reduction compared pre-VSG stool. However, post-VSG stool exhibited a potentially inflammatory phenotype with increased intestinal Th17 and decreased regulatory T cells. Concomitantly, we found elevated fecal calprotectin and an enrichment of proinflammatory pathways in a subset of adolescents post-VSG. We show that in some adolescents, microbiome changes post-VSG may have inflammatory potential, which may be of importance considering the increased incidence of inflammatory bowel disease post-VSG.

Integrating multi-omics data to reveal the host-microbiota interactome in inflammatory bowel disease

Numerous studies have accelerated the knowledge expansion on the role of gut microbiota in inflammatory bowel disease (IBD). However, the precise mechanisms behind host-microbe cross-talk remain largely undefined, due to the complexity of the human intestinal ecosystem and multiple external factors. In this review, we introduce the interactome concept to systematically summarize how intestinal dysbiosis is involved in IBD pathogenesis in terms of microbial composition, functionality, genomic structure, transcriptional activity, and downstream proteins and metabolites. Meanwhile, this review also aims to present an updated overview of the relevant mechanisms, high-throughput multi-omics methodologies, different types of multi-omics cohort resources, and computational methods used to understand host-microbiota interactions in the context of IBD. Finally, we discuss the challenges pertaining to the integration of multi-omics data in order to reveal host-microbiota cross-talk and offer insights into relevant future research directions.

Microbiota-derived IPA alleviates intestinal mucosal inflammation through upregulating Th1/Th17 cell apoptosis in inflammatory bowel disease

The gut microbiota-derived metabolite indole-3-propionic acid (IPA) plays an important role in maintaining intestinal mucosal homeostasis, while the molecular mechanisms underlying IPA regulation on mucosal CD4+ T cell functions in inflammatory bowel disease (IBD) remain elusive. Here we investigated the roles of IPA in modulating mucosal CD4+ T cells and its therapeutic potential in treatment of human IBD. Leveraging metabolomics and microbial community analyses, we observed that the levels of IPA-producing microbiota (e.g. Peptostreptococcus, Clostridium, and Fournierella) and IPA were decreased, while the IPA-consuming microbiota (e.g. Parabacteroides, Erysipelatoclostridium, and Lachnoclostridium) were increased in the feces of IBD patients than those in healthy donors. Dextran sulfate sodium (DSS)-induced acute colitis and CD45RBhighCD4+ T cell transfer-induced chronic colitis models were then established in mice and treated orally with IPA to study its role in intestinal mucosal inflammation in vivo. We found that oral administration of IPA attenuated mucosal inflammation in both acute and chronic colitis models in mice, as characterized by increased body weight, and reduced levels of pro-inflammatory cytokines (e.g. TNF-α, IFN-γ, and IL-17A) and histological scores in the colon. We further utilized RNA sequencing, molecular docking simulations, and surface plasmon resonance analyses and identified that IPA exerts its biological effects by interacting with heat shock protein 70 (HSP70), leading to inducing Th1/Th17 cell apoptosis. Consistently, ectopic expression of HSP70 in CD4+ T cells conferred resistance to IPA-induced Th1/Th17 cell apoptosis. Therefore, these findings identify a previously unrecognized pathway by which IPA modulates intestinal inflammation and provide a promising avenue for the treatment of IBD.

Serum regenerative islet-derived protein 1α: a novel and sensitive biomarker for endoscopic disease activity in ulcerative colitis

INTRODUCTION

Mucosal healing (MH) has established as a long-term therapeutic goal for inflammatory bowel disease (IBD). Regenerative Islet-derived Protein 1α (reg1α) was reported to be closely related to gastrointestinal mucosal injury; however, its potential in monitoring MH remains unexplored.

METHODS

Serum reg1α levels were quantified in 156 consecutive IBD patients (January 2021-December 2023) and stratified by endoscopic findings into MH (n = 136) and non-mucosal healing (NMH) groups. Diagnostic performance of reg1α was evaluated and compared to C-reactive protein (CRP) using receiver operating characteristic analysis.

RESULTS

A total of 136 patients (85 with CD and 51 with UC) were finally included. Serum reg1α levels were significantly correlated with endoscopic activity. Patients in NMH group demonstrating markedly higher reg1α levels than those in MH group (92.6 vs. 55.5 ng/ml, p < 0.001). In UC, reg1α outperformed CRP in sensitivity (82.4% vs. 55.9%, p = 0.012) and accuracy (80.4% vs. 70.6%, p = 0.001) for monitoring MH. This superiority persisted in UC subgroups with non-or mild clinical symptoms. Combined index (reg1α + CRP) and multivariate model (incorporating clinical indices, reg1α and CRP) also enhanced sensitivity and accuracy over CRP alone in UC (all p < 0.05). However, reg1α showed no significantly higher efficacy in monitoring NMH compared to CRP in CD. In CRP-normal patients, patients with NMH had higher reg1α levels than those with MH in UC (77.6 vs. 49.8 ng/ml, p = 0.018), but not in CD.

CONCLUSION

Reg1α represents as a novel and sensitive biomarker of endoscopic disease activity in patients with UC, even in patients with non- or mild clinical symptoms or normal CRP levels.

Gut microbiota and associated metabolites: key players in high-fat diet-induced chronic diseases

Excessive intake of dietary fats is strongly associated with an increased risk of various chronic diseases, such as obesity, diabetes, hepatic metabolic disorders, cardiovascular disease, chronic intestinal inflammation, and certain cancers. A significant portion of the adverse effects of high-fat diet on disease risk is mediated through modifications in the gut microbiota. Specifically, high-fat diets are linked to reduced microbial diversity, an overgrowth of gram-negative bacteria, an elevated Firmicutes-to-Bacteroidetes ratio, and alterations at various taxonomic levels. These microbial alterations influence the intestinal metabolism of small molecules, which subsequently increases intestinal permeability, exacerbates inflammatory responses, disrupts metabolic functions, and impairs signal transduction pathways in the host. Consequently, diet-induced changes in the gut microbiota play a crucial role in the initiation and progression of chronic diseases. This review explores the relationship between high-fat diets and gut microbiota, highlighting their roles and underlying mechanisms in the development of chronic metabolic diseases. Additionally, we propose probiotic interventions may serve as a promising adjunctive therapy to counteract the negative effects of high-fat diet-induced alterations in gut microbiota composition.

Faecalibacterium prausnitzii regulates carbohydrate metabolic functions of the gut microbiome in C57BL/6 mice

The probiotic impact of microbes on host metabolism and health depends on both host genetics and bacterial genomic variation. Faecalibacterium prausnitzii is the predominant human gut commensal emerging as a next-generation probiotic. Although this bacterium exhibits substantial intraspecies diversity, it is unclear whether genetically distinct F. prausnitzii strains might lead to functional differences in the gut microbiome. Here, we isolated and characterized a novel F. prausnitzii strain (UT1) that belongs to the most prevalent but underappreciated phylogenetic clade in the global human population. Genome analysis showed that this butyrate-producing isolate carries multiple putative mobile genetic elements, a clade-specific defense system, and a range of carbohydrate catabolic enzymes. Multiomic approaches were used to profile the impact of UT1 on the gut microbiome and associated metabolic activity of C57BL/6 mice at homeostasis. Both 16S rRNA and metagenomic sequencing demonstrated that oral administration of UT1 resulted in profound microbial compositional changes including a significant enrichment of Lactobacillus, Bifidobacterium, and Turicibacter. Functional profiling of the fecal metagenomes revealed a markedly higher abundance of carbohydrate-active enzymes (CAZymes) in UT1-gavaged mice. Accordingly, UT1-conditioned microbiota possessed the elevated capability of utilizing starch in vitro and exhibited a lower availability of microbiota-accessible carbohydrates in the gut. Further analysis uncovered a functional network wherein UT1 reduced the abundance of mucin-degrading CAZymes and microbes, which correlated with a concomitant reduction of fecal mucin glycans. Collectively, our results reveal a crucial role of UT1 in facilitating the carbohydrate metabolism of the gut microbiome and expand our understanding of the genetic and phenotypic diversity of F. prausnitzii.

Microbial micronutrient sharing, gut redox balance and keystone taxa as a basis for a new perspective to solutions targeting health from the gut

In health, the gut microbiome functions as a stable ecosystem maintaining overall balance and ensuring its own survival against environmental stressors through complex microbial interaction. This balance and protection from stressors is maintained through interactions both within the bacterial ecosystem as well as with its host. As a consequence, the gut microbiome plays a critical role in various physiological processes including maintaining the structure and function of the gut barrier, educating the gut immune system, and modulating the gut motor, digestive/absorptive, as well as neuroendocrine system all of which are crucial for human health and disease pathogenesis. Pre- and probiotics, widely available and clinically established, offer various health benefits primarily by beneficially modulating the gut microbiome. However, their clinical outcomes can vary significantly due to differences in host physiology, diets, individual microbiome compositions, and other environmental factors. This perspective paper highlights emerging scientific insights into the importance of microbial micronutrient sharing, gut redox balance, keystone species, and the gut barrier in maintaining a diverse and functional microbial ecosystem, and their relevance to human health. We propose a novel approach that targets microbial ecosystems and keystone taxa performance by supplying microbial micronutrients in the form of colon-delivered vitamins, and precision prebiotics [e.g. human milk oligosaccharides (HMOs) or synthetic glycans] as components of precisely tailored ingredient combinations to optimize human health. Such a strategy may effectively support and stabilize microbial ecosystems, providing a more robust and consistent approach across various individuals and environmental conditions, thus, overcoming the limitations of current single biotic solutions.

New insights in amino sugar metabolism by the gut microbiome

Gut microorganisms inhabiting the intestinal tract play key roles in host's health and disease. A properly functioning gut microbiome requires the availability of adequate carbon, nitrogen and energy sources. One of the main sources of energy for intestinal bacteria are glycans, of which amino sugars are important components. Amino sugars are a class of carbohydrates in which one or more hydroxyl groups are substituted with amino groups. However, bacterial utilization of amino sugars and their impact on the gut microbiome and host health have not been thoroughly assessed. In this review, we summarize the latest discoveries about amino sugar metabolism by gut microbes, paying particular attention to the metabolism of N-acetyl-galactosamine (GalNAc), one of the most abundant amino sugars in the intestine, and its potential implications for microbial functionality and host health.

Identification of S100A9 as a target for diagnosis and treatment of Crohn's Disease after Vedolizumab treatment failure

The vedolizumab medication is the treatment that precisely targets the gut for Crohn's Disease (CD). It can inhibit the migration of lymphocytes to the intestinal site despite the fact that a significant portion of the population continues to be ineffectively treated. In this study, peripheral blood leukocytes sampled from the CD patients who are nonresponsive or responsive to vedolizumab treatment were used for transcriptome sequencing. Intersected differentially expressed mRNA obtained from transcriptome sequencing and GSE191328 were utilized to predict key therapeutic targets. Bioinformatics analyses were used to explore potential biological mechanisms and to screen pivotal genes. Inhibitor of S100A9 increased the body weight and colon length of mice with colitis, and decreased the DAI score. Our study also demonstrated that the combination of anti-α4β7 integrin antibody with inhibitor of S100A9 further alleviates colitis. Through flow cytometry, changes in the composition of immune cell populations in colon tissues were found after intragastric administration of paquinimod, an inhibitor of S100A9. It is important that blocking S100A9 inhibited the recruitment of neutrophils in the mice's colon. Our findings lay a foundation for the further exploration of the new targets for non-responders to vedolizumab in CD patients.

A systematic review on the role of gut microbiome in inflammatory bowel disease: Spotlight on virome and plant metabolites

Inflammatory bowel diseases (IBD), including ulcerative colitis and Crohn's disease, arise from various factors such as dietary, genetic, immunological, and microbiological influences. The gut microbiota plays a crucial role in the development and treatment of IBD, though the exact mechanisms remain uncertain. Current research has yet to definitively establish the beneficial effects of the microbiome on IBD. Bacteria and viruses (both prokaryotic and eukaryotic) are key components of the microbiome uniquely related to IBD. Numerous studies suggest that dysbiosis of the microbiota, including bacteria, viruses, and bacteriophages, contributes to IBD pathogenesis. Conversely, some research indicates that bacteria and bacteriophages may positively impact IBD outcomes. Additionally, plant metabolites play a crucial role in alleviating IBD due to their anti-inflammatory and microbiome-modulating properties. This systematic review discusses the role of the microbiome in IBD pathogenesis and evaluates the potential connection between plant metabolites and the microbiome in the context of IBD pathophysiology.

Gut Microbiota in Patients with Tuberculosis Associated with Different Drug Exposures of Antituberculosis Drugs

Interindividual variability in drug exposure can significantly influence treatment outcomes and may lead to drug concentration-related side effects during tuberculosis (TB) treatment. Although the gut microbiota is known to affect drug metabolism, its impact on anti-TB drugs has not been thoroughly explored. This study sought to elucidate the relationship between pre-treatment gut microbiota and drug exposure levels among patients with pulmonary TB. Two cohorts were analyzed: a discovery cohort (N = 99) and a validation cohort (N = 32), both comprising patients undergoing anti-TB therapy with rifampicin, isoniazid, pyrazinamide, and ethambutol. The gut microbiota patterns of participants from the discovery cohort and the validation cohort were profiled by 16S rRNA gene sequencing and metagenomics, respectively. Analyses of both cohorts robustly established a positive association between pre-treatment microbial diversity and drug exposure, as well as significant differences in gut microbiota composition across various drug exposure groups. At the species level, Faecalibacterium prausnitzii was positively associated with drug exposure to rifampicin. Moreover, functional analysis revealed that starch and sucrose metabolism and secondary bile acid biosynthesis were more abundant in the high drug exposure group. To identify biomarkers capable of stratifying patients based on their drug exposure levels, 11 taxa, represented by Faecalibacterium, were selected in the discovery cohort (AUC = 0.992) and were confirmed in the validation cohort with high predictive accuracy (AUC = 0.894). This study demonstrated a correlation between microbial dysbiosis and reduced exposure to anti-TB medications. Optimizing treatment by regulating gut microbiota to improve drug exposure levels requires further validation through larger scale multicenter clinical trials.

Omega-3 polyunsaturated fatty acids attenuate cognitive impairment via the gut-brain axis in diabetes-associated cognitive dysfunction rats

Diabetes-related cognitive dysfunction (DACD) is a comorbidity of type 2 diabetes that has a negative effect on patients' quality of life. Research has indicated that disruption of the gut microbiota (GM) may be linked to dementia with altered cognitive performance. Conversely, omega-3 polyunsaturated fatty acids (n-3 PUFAs) may reverse DACD. The present study aimed to assess the effects of an n-3 PUFA intervention and fecal microbiota transplantation (FMT) on high-fat and streptozotocin-induced DACD model rats. In DACD rats, n-3 PUFA treatment restored fasting blood glucose (FBG) levels and cognitive function, increased the expression of anti-inflammatory cytokines and downregulated the expression of proinflammatory cytokines in the cortex and colon. Additionally, the expression of the postsynaptic density protein-95 mRNA and protein varied with n-3 PUFA treatment. Treatment with n-3 PUFAs also increased the expression of tight junction proteins. Beneficial and short-chain fatty acid-producing bacteria were more abundant when rats were exposed to n-3 PUFAs. After FMT from the rats with DACD symptoms that were improved by the n-3 PUFA dietary intervention into another batch of DACD rats, we observed recovery in recipient DACD rats. These results indicated that the alleviation of DACD symptoms by n-3 PUFAs was attributed to gut microbiota remodeling.

Gut virome: New key players in the pathogenesis of inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic inflammatory illness of the intestine. While the mechanism underlying the pathogenesis of IBD is not fully understood, it is believed that a complex combination of host immunological response, environmental exposure, particularly the gut microbiota, and genetic susceptibility represents the major determinants. The gut virome is a group of viruses found in great frequency in the gastrointestinal tract of humans. The gut virome varies greatly among individuals and is influenced by factors including lifestyle, diet, health and disease conditions, geography, and urbanization. The majority of research has focused on the significance of gut bacteria in the progression of IBD, although viral populations represent an important component of the microbiome. We conducted this review to highlight the viral communities in the gut and their expected roles in the etiopathogenesis of IBD regarding published research to date.

Reevaluating therapeutic strategies in Crohn’s disease: Comparing Modulen and budesonide

This article explores the significant implications of the study by Ovadia et al, which innovatively compares the efficacy of a nutritional intervention (Modulen) to conventional pharmaceutical therapy (budesonide) in promoting mucosal healing in Crohn’s disease. Highlighting the paradox of a well-established yet underutilized nutritional approach, the findings suggest that Modulen may offer comparable therapeutic benefits despite its high withdrawal rate due to adherence challenges. This advancement underscores the evolving paradigm in inflammatory bowel disease treatment, shifting focus toward non-pharmacologic alternatives that target both clinical remission and endoscopic healing. The article advocates for the development of integrative treatment strategies that balance efficacy, patient adherence, and long-term disease management, emphasizing the need for further research to refine and optimize the role of nutritional therapies in clinical practice.

IBD impact on quality of life and perception of disease activity in Italian patients and physicians: An IBD-PODCAST study sub analysis

BACKGROUND

IBD-PODCAST was a global real-world study to assess suboptimal disease control (SDC) in patients with Crohn's disease (CD) and ulcerative colitis (UC) using STRIDE-II criteria.

AIM

To evaluate quality of life (QoL), disease characteristics and control in patients with SDC, comparing perspectives of patients and healthcare providers (HCPs) in the Italian subpopulation.

METHODS

IBD-PODCAST-Italy enrolled adult outpatients from 17 centers. The study used a combination of retrospective chart reviews and cross-sectional assessments to gather data on treatment, patient-reported outcomes (QoL, fatigue, work productivity) and clinical activity. Patient and HCP perceptions of disease control based on STRIDE-II criteria, which included clinical, laboratory and endoscopic findings were also assessed.

RESULTS

SDC was identified in 53.4 % (95 % CI: 44-62.8 %) of CD and 49.0 % (95 % CI: 39.1-59.0 %) of UC patients. Those with SDC had lower short IBD questionnaire scores (45.9 ± 12.0) compared to optimal disease control (ODC) patients (57.4 ± 9.9). Extraintestinal manifestations and bowel urgency were more frequent in SDC patients. Physician-perceived SDC (14.5 %) was higher than patient-perceived SDC (8.8 %) and agreement between patient and HCP assessments was low.

CONCLUSIONS

Patients with SDC experienced impaired QoL. The discrepancy between patient and physician perceptions of disease control, alongside objective measures, highlights the need for further research to optimize care and improve outcomes.

A Review of Cutaneous Extraintestinal Manifestations of Inflammatory Bowel Disease in Skin of Color

The incidence of inflammatory bowel disease (IBD) is increasing in racial and ethnic minority groups. Cutaneous extraintestinal manifestations (EIMs) of IBD are well-known comorbid conditions that can occur in both active and quiescent IBD. Historically, cutaneous EIMs of IBD are described in White skin with a lack of literature describing these conditions in darker skin tones. This potentially creates a knowledge gap and awareness among providers in recognizing these conditions and offering therapy in a timely manner to non-White patients. This review aims to describe the cutaneous manifestations of IBD in a wide range of skin tones with several examples to improve awareness. With further awareness, this review will enable to provide equitable care to IBD patients with cutaneous EIMs.

Integration of Artificial Intelligence-Enhanced Capsule Endoscopy in Clinical Practice: A Review of Market-Available Tools for Clinical Practice

The integration of artificial intelligence (AI) into capsule endoscopy is transforming gastrointestinal diagnostics by enhancing lesion detection and optimizing reading efficiency. This review focuses on the clinical applications of commercially available AI-powered capsule endoscopy systems, particularly for small bowel evaluation. Recent clinical trials and observational studies are analyzed to assess the diagnostic performance, practical benefits, and limitations of these systems. Additionally, key challenges related to standardization, data quality, and clinical validation are discussed. Currently available AI systems significantly reduce reading times and demonstrate high detection capabilities, depending on the algorithm and device used. However, a substantial number of lesions remain undetected, preventing full reliance on these tools. Future advancements must focus on improving detection rates and validating the clinical relevance of missed lesions. Additionally, standardizing AI algorithms across different capsule systems is essential to ensure consistency, reliability, and broader clinical adoption. Establishing homologation frameworks will be key to achieving uniform performance and seamless integration into routine practice.

Lactobacillus plantarum-derived extracellular vesicles from dietary barley leaf supplementation attenuate Citrobacter rodentium infection and intestinal inflammation

BACKGROUND

Inflammatory bowel disease (IBD) is a gastrointestinal inflammatory disorder characterized by disturbed interactions between gut microbiota and host immune response. Barley leaf (BL) is a traditional Chinese herb recorded to have health-promoting effects. However, little is known about the beneficial role of BL against enteric infection-induced intestinal inflammation. Here, we uncover that BL protects against Citrobacter rodentium (C. rodentium)-induced infectious colitis by improving host-microbiota interactions.

METHODS

C3H/HeN mice were fed a diet with/without BL and infected with C. rodentium. Transcriptome sequencing, anti-CD4 antibody treatment, and flow cytometry were conducted to investigate the mechanisms of T cell immune modulation. The intervention involved administering anti-CD4 antibody at 500 µg each time for three times before and during C. rodentium infection. Analysis of gut microbiota composition was performed by 16S rRNA gene sequencing on fecal samples. Fecal microbiota transplantation was conducted by administering microbiota from donor group to recipient group via oral gavage to investigate the role of intestinal microbiota in immune modulation.

RESULTS

BL ameliorated the severity of C. rodentium-induced colitis, and this effect was linked to improved gut homeostasis and enhanced mucosal barrier function. BL enriched the pathways of T helper 1 (Th1)/Th2 and Th17 cell differentiation in the colon, suggesting the involvement of CD4+ T cells. Consistent with this, anti-CD4 antibody treatment abrogated the effect of BL and flow cytometry analysis revealed that BL mitigated C. rodentium-induced pro-inflammatory Th1 immune response. Moreover, the protective effect of BL was associated with alleviation of gut microbiota dysbiosis and increased abundance of Lactobacillus. Our in vivo studies further revealed that live Lactobacillus plantarum (L. plantarum) administration attenuated the pathogenic effects induced by C. rodentium infection, whereas heat-inactivated L. plantarum did not show the same results. Mechanistically, BL supplementation enriched L. plantarum, which subsequently released nanosized extracellular vesicles (EVs) that serve as a key mediator in alleviating C. rodentium-associated pathology and Th1 cell dysregulation.

CONCLUSIONS

Our work thus provides evidence for utilizing BL and L. plantarum-derived EVs to manage enteric infection-associated IBD.

Classification of pediatric video capsule endoscopy images for small bowel abnormalities using deep learning models

BACKGROUND

Video capsule endoscopy (VCE) is a noninvasive technique used to examine small bowel abnormalities in both adults and children. However, manual review of VCE images is time-consuming and labor-intensive, making it crucial to develop deep learning methods to assist in image analysis.

AIM

To employ deep learning models for the automatic classification of small bowel lesions using pediatric VCE images.

METHODS

We retrospectively analyzed VCE images from 162 pediatric patients who underwent VCE between January 2021 and December 2023 at the Children's Hospital of Nanjing Medical University. A total of 2298 high-resolution images were extracted, including normal mucosa and lesions (erosions/erythema, ulcers, and polyps). The images were split into training and test datasets in a 4:1 ratio. Four deep learning models: DenseNet121, Visual geometry group-16, ResNet50, and vision transformer were trained using 5-fold cross-validation, with hyperparameters adjusted for optimal classification performance. The models were evaluated based on accuracy, precision, recall, F1-score, and area under the receiver operating curve (AU-ROC). Lesion visualization was performed using gradient-weighted class activation mapping.

RESULTS

Abdominal pain was the most common indication for VCE, accounting for 62% of cases, followed by diarrhea, vomiting, and gastrointestinal bleeding. Abnormal lesions were detected in 93 children, with 38 diagnosed with inflammatory bowel disease. Among the deep learning models, DenseNet121 and ResNet50 demonstrated excellent classification performance, achieving accuracies of 90.6% [95% confidence interval (CI): 89.2-92.0] and 90.5% (95%CI: 89.9-91.2), respectively. The AU-ROC values for these models were 93.7% (95%CI: 92.9-94.5) for DenseNet121 and 93.4% (95%CI: 93.1-93.8) for ResNet50.

CONCLUSION

Our deep learning-based diagnostic tool developed in this study effectively classified lesions in pediatric VCE images, contributing to more accurate diagnoses and increased diagnostic efficiency.

ECCO Topical Review on Predictive Models on Inflammatory Bowel Disease Disease Course and Treatment Response

BACKGROUND AND AIMS

Inflammatory bowel disease (IBD) poses a clinical challenge due to its variable progression and treatment response. Despite the development of predictive models, their clinical application remains limited due to validation and methodological inconsistencies. The current topical review examines existing predictive models, assesses their relevance, and discusses the barriers to their clinical implementation.

METHODS

An expert panel formed by European Crohn's and Colitis Organisation, including gastroenterologists, surgeons, and clinical epidemiologists, reviewed predictive models on IBD disease course and treatment response. Delphi methodology was applied to develop practice position statements. A practice position was set when at least 80% of participants reached agreement on a recommendation.

RESULTS

Fourteen practice positions and 2 perspective points were developed, highlighting factors included in models predicting IBD disease course and treatment response identified in the literature and barriers to clinical implementation. The appropriate methodological approaches for model development and validation have been defined, while methodological barriers to tackle have been identified. Perspectives on the inclusion of relevant biomarkers, and flexible study design have been outlined.

CONCLUSIONS

This topical review offers practice recommendations and guidance for future predictive models on IBD disease course and treatment response including their implementation in clinical practice.

Positive nutritional selection of adults with healthy lifestyle and high daily fiber consumption for the isolation of beneficial intestinal bacteria: The iTARGET cohort study protocol

Recent advances in the study of the gut microbiota has pointed to its under-utilized source of potentially beneficial bacteria, known as next generation probiotics, offering a promising avenue to restore or compensate impaired gut microbiota toward a healthy state. Aside from the difficulties to achieve in-lab adequate culture conditions, the use of beneficial bacterial isolates is also limited by their bioavailability in the donor itself. In the iTARGET study, we positively selected donors based on their diet enriched in fiber, that has been shown to increase the prevalence of bacterial species associated with health. The iTARGET study is a monocenter, prospective, observational study of adults with healthy lifestyle and high daily fiber consumption. We aim to recruit individuals in two phases, the first one for all individuals that will permit the identification of carriers for bacteria of interest and the second phase for a subset of individuals to allow for culture and isolation of previously identified potentially beneficial bacteria. Our primary outcome is the isolation and culture of at least one potentially beneficial isolate. The secondary outcomes comprised the high throughput metagenomic profiles of the intestinal microbiota and the characterization of the cultured isolates. The study was approved by the French Research Ethics Committees (Comité de Protection des Personnes Sud-Est I) under the National reference ID 2023-A01677-38. Study findings and results will be published in peer-reviewed Open Access journals. (Trial registration number on ClinicalTrials.gov: NCT06166810).

Optimizing Therapeutic Potential of Fecal Transplant in Inflammatory Bowel Disease

Inflammatory bowel disease (IBD) is a chronic inflammatory condition of the gastrointestinal tract influenced by genetic, environmental, immune, and microbial factors. Reduced gut microbial diversity and elevated proinflammatory bacteria levels in IBD disrupt mucosal immunity, barrier function, and inflammatory pathways. Fecal microbiota transplantation (FMT) is a potential therapy to restore microbial balance. Studies suggest that FMT may induce remission in mild-to-moderate ulcerative colitis but show limited efficacy in Crohn's disease and pouchitis. Donor microbiota colonization correlates with remission, but varied study designs challenge findings. Further research is required to standardize FMT protocols, optimize donor selection, and ensure long-term safety.

Modulation of Intestinal Flora: a Novel Immunotherapeutic Approach for Enhancing Thyroid Cancer Treatment

Over the past 3 years, there has been a growing interest in clinical research regarding the potential involvement of intestinal flora in thyroid cancer (TC). This review delves into the intricate connection between intestinal flora and TC, focusing on the particular intestinal flora that is directly linked to the disease and identifying which may be able to predict potential microbial markers of TC. In order to shed light on the inflammatory pathways connected to the onset of TC, we investigated the impact of intestinal flora on immune modulation and the connection between chronic inflammation when investigating the role of intestinal flora in the pathogenesis of TC. Furthermore, the potential role of intestinal flora metabolites in the regulation of thyroid function was clarified by exploring the effects of short-chain fatty acids and lipopolysaccharide on thyroid hormone synthesis and metabolism. Based on these findings, we further explore the effects of probiotics, prebiotics, postbiotics, vitamins, and trace elements.

Beneficial effects of Akkermansia muciniphila on benign prostatic hyperplasia and metabolic syndrome

Benign prostatic hyperplasia (BPH) is a prevalent condition associated with male lower urinary tract symptoms (LUTS) and is influenced by metabolic syndrome (MetS) and gut microbiota. Akkermansia muciniphila (AKK) is a gut commensal that has emerged as a potential modulator of metabolic health and inflammatory conditions. This study investigated the correlation between Akkermansia abundance and BPH severity and metabolic indices in fecal and serum samples from BPH patients and healthy donors using 16S rRNA sequencing and metabolic profiling. A testosterone-induced BPH mouse model was used to evaluate the effects of AKK administration on BPH severity and metabolic indices. Altered gut microbiota diversity was observed in BPH patients, with a significant reduction in Akkermansia abundance. Akkermansia abundance was negatively correlated with BPH symptom score, serum lipopolysaccharides (LPS), body mass index (BMI), blood glucose, total cholesterol (TC), low-density lipoprotein cholesterol (LDL-C), and high-density lipoprotein cholesterol (HDL-C). AKK administration in BPH mice resulted in histopathological improvements, reduced prostate index, and amelioration of glandular hyperplasia. Although changes in blood glucose, TC, and LDL-C levels post-AKK supplementation were not statistically significant, a trend toward improvement was noted. Additionally, AKK administration led to a reduction in systemic inflammation markers and restoration of intestinal barrier integrity. In conclusion, AKK might modulate the gut microbiota-prostate axis and MetS. AKK's influence on systemic inflammation and gut barrier function suggests its therapeutic promise in managing BPH and associated metabolic disorders. These findings pave the way for novel microbiota-targeted therapies in the treatment of BPH and MetS.

Comparative Colonisation Ability of Human Faecal Microbiome Transplantation Strategies in Murine Models

The gut microbiome plays a crucial role in maintaining intestinal homeostasis and influencing immune-mediated diseases. Human faecal microbiota transplantation (FMT) is often employed in murine models to investigate the role of human microbes in disease regulation, but methods for effective colonisation require refinement. This study aimed to assess the colonisation efficiency of human microbiota in a murine model using FMT with human faeces, focusing particularly on the impact of gut microbiota depletion via polyethylene glycol (PEG) and comparing oral-gastric gavage with enema administration routes. Our findings revealed that PEG-induced depletion enhanced human microbiome colonisation in mice. Oral-gastric gavage prolonged colonisation, while enema administration facilitated quicker resolution of dysbiosis, both inducing selective human microbial colonisation in a time-dependent manner. Notably, genera such as Bacteroides, Blautia, Medicaternibacter and Bifidobacteria were successfully colonised, whereas Roseburia, Anaerostipes, Anaerobutyricum and Faecalibacterium failed to establish in the murine gut post-FMT. These findings highlight the challenges of replicating human gut microbiota in murine models and underscore the importance of selecting appropriate FMT methods based on desired outcomes. This study provides valuable insights into the colonisation dynamics of human microbiota in mice, contributing to the development of more effective FMT strategies for disease treatment.

Long-term efficacy and safety of upadacitinib in patients with moderately to severely active ulcerative colitis: an interim analysis of the phase 3 U-ACTIVATE long-term extension study

BACKGROUND

The U-ACTIVATE long-term extension study aims to evaluate the long-term efficacy and safety of upadacitinib in patients with moderately to severely active ulcerative colitis. Here, we report interim results after 3 years of total treatment.

METHODS

U-ACTIVATE is an ongoing, 288-week, phase 3, long-term extension study done at 307 centres across 43 countries (active sites on Dec 31, 2021, are presented as part of this interim analysis) and began on Jan 31, 2017. In brief, patients aged 16-75 years with a confirmed diagnosis of moderately to severely active ulcerative colitis for 90 days or more, an adapted Mayo score of 5-9, and an endoscopic subscore of 2 or 3 were eligible for the upadacitinib induction studies; patients who had a clinical response in the induction studies were eligible to enter the U-ACHIEVE maintenance study. Individuals who completed the U-ACHIEVE maintenance study were subsequently eligible for inclusion in the efficacy population of this long-term extension study. Patients in clinical remission per adapted Mayo score at week 52 of the maintenance study could continue their double-masked treatment upon entering the long-term extension study. Patients not in clinical remission originally randomly assigned to upadacitinib 15 mg were eligible to escalate to upadacitinib 30 mg, those originally randomly assigned to upadacitinib 30 mg continued on upadacitinib 30 mg, and those originally assigned to placebo were eligible to escalate to upadacitinib 15 mg in a masked way. We present data from weeks 48 and 96 of the long-term extension period. Key efficacy outcomes were clinical remission (per adapted Mayo score), endoscopic remission, maintenance of clinical remission, and maintenance of endoscopic remission, and are presented for those patients who had a clinical response after 8 weeks of upadacitinib 45 mg induction, completed 52 weeks of maintenance (U-ACHIEVE maintenance), and subsequently entered the long-term extension. Safety outcomes were treatment-emergent adverse events and adverse events of special interest, which were prespecified and were recorded in two populations: one comprising patients who received at least one dose of study drug in the long-term extension study and the other comprising all patients in the maintenance or long-term extension studies. Our primary approach for efficacy analysis was as-observed (ie, all observed data were used without imputation for missing data until patients switched to a different dose during the long-term extension study). This study is registered with ClinicalTrials.gov (NCT03006068).

FINDINGS

414 patients from the phase 3 upadacitinib U-ACHIEVE maintenance study were eligible to enter this long-term extension study for assessment of efficacy endpoints following treatment with upadacitinib. Of these individuals, 369 patients (231 [63%] male individuals and 138 [37%] female individuals) were treated with upadacitinib in the long-term extension study: 142 patients with upadacitinib 15 mg and 227 with upadacitinib 30 mg. In the as-observed population, 84 (71%) of 118 patients receiving upadacitinib 15 mg were in clinical remission at week 48, as were 130 (67%) of 193 receiving upadacitinib 30 mg; by week 96, 69 (76%) of 91 patients receiving upadacitinib 15 mg and 104 (74%) of 141 of those receiving upadacitinib 30 mg were in clinical remission. Most patients who entered the long-term extension in clinical remission maintained it in the as-observed analysis (week 48 upadacitinib 15 mg 62 [81%] of 77 and upadacitinib 30 mg 90 [81%] of 111; week 96 upadacitinib 15 mg 50 [78%] of 64 and upadacitinib 30 mg 69 [84%] of 82). In the as-observed population, 60 (49%) of 123 patients receiving upadacitinib 15 mg and 93 (46%) of 202 receiving upadacitinib 30 mg were in endoscopic remission at week 48; by week 96, 45 (47%) of 95 patients receiving upadacitinib 15 mg and 69 (45%) of 153 receiving upadacitinib 30 mg were in endoscopic remission. Most patients who entered the long-term extension in endoscopic remission maintained it in the as-observed analysis (week 48 upadacitinib 15 mg 28 [70%] of 40 and upadacitinib 30 mg 51 [76%] of 67; week 96 upadacitinib 15 mg 20 [65%] of 31 and upadacitinib 30 mg 37 [73%] of 51). In the long-term extension-only safety analysis, we assessed data from 467 patients, representing 1027·9 patient-years of continuous long-term extension exposure on a consistent upadacitinib dose. Treatment-emergent adverse events were recorded at 238·5 events per 100 patient-years for upadacitinib 15 mg and 233·4 events per 100 patient-years for upadacitinib 30 mg. Event rates of serious treatment-emergent adverse events were 11·7 events per 100 patient-years for upadacitinib 15 mg and 12·4 events per 100 patient-years for upadacitinib 30 mg. The most common adverse events of special interest were hepatic disorder, lymphopenia, creatine phosphokinase elevation, serious infection, neutropenia, and herpes zoster. Three treatment-emergent adverse events leading to death were reported in the long-term extension-only safety population.

INTERPRETATION

This interim analysis supports the positive long-term risk-benefit profile for upadacitinib 15 mg and 30 mg among patients with moderately to severely active ulcerative colitis.

FUNDING

AbbVie.

Fecal microbiota transplantation as a potential therapeutic approach to improve impaired glucose tolerance via gut microbiota modulation in rat model

Objectives

To investigate the impact of diet-induced gut microbiota alterations on type 2 diabetes and assess the therapeutic potential of Fecal Microbiota Transplantation (FMT) in restoring a balanced gut microenvironment.

Methods

To induce type 2 diabetes, rats were fed a high-sugar high-fat diet (HSFD) for 90 days. After diabetes induction, animals were divided into an HSFD control group, a metformin group (100 mg/kg), and an FMT group (100 mg/kg), receiving treatment for an additional 90 days. Fasting blood glucose levels, glucose tolerance, serum markers (HbA1C, free fatty acids, lipopolysaccharides, pro-inflammatory and anti-inflammatory cytokines), and gut microbiota profiles via cecal metagenome sequencing were analyzed post-treatment.

Results

FMT effectively restored gut microbiota composition to a profile similar to healthy controls, rebalancing the Firmicutes/Bacteroidetes ratio and increasing beneficial taxa, including Prevotella ruminicola, Akkermansia muciniphila, Roseburia, and Faecalibacterium prausnitzii. These microbial shifts corresponded with significant metabolic improvements: FMT reduced inflammatory markers (LPS and FFA), lowered HbA1c, and improved glucose tolerance. Enhanced gut barrier integrity observed in FMT-treated animals likely contributed to reduced endotoxemia and systemic inflammation, distinguishing FMT's metabolic effects from those of metformin. Notably, FMT addressed the dysbiosis associated with HSFD, promoting microbial resilience and mitigating the metabolic disruptions linked to type 2 diabetes.

Conclusion

These findings underscore the potential of FMT as a targeted therapeutic approach to modulate gut microbiota composition and mitigate metabolic dysregulation induced by high sugar high fat diet.

Development of a capsule endoscopy scoring system for the early diagnosis of small bowel Crohn's disease

BACKGROUND

Small bowel capsule endoscopy (SBCE) is a reliable method of evaluating small bowel mucosal lesions, and its use in Crohn's disease (CD) is increasing. We previously reported useful SBCE findings for early diagnosis of CD. In the present study, we developed a scoring model for early diagnosis of CD using SBCE findings.

METHODS

We collected clinical and SBCE data of 110 patients with small bowel mucosal lesions and randomly divided them into derivation and validation cohorts. After selecting variables for scoring models by univariate analysis, the adopted model was determined. The score of each variable was based on the odds ratio obtained by multivariate analysis, and the cut-off value for the diagnosis of CD was examined by receiver operating characteristic analysis. Its reliability was verified in the validation cohort.

RESULTS

The model containing age (≤ 30 vs. ≥ 31), linear erosion, and circumferential alignment had the best fit (odds ratios of 4.97, 7.56, and 5.34, respectively). The linear erosion score was defined as 4 points, circumferential alignment as 4, and age of ≤ 30 years as 3. When the cut-off value was defined as 7 points, the scoring model had 85.4% sensitivity, 80.0% specificity, 83.7% positive predictive value, and 82.1% negative predictive value for diagnosis of CD. The validation cohort demonstrated an area under the curve of 0.93, similar to the derivation cohort.

CONCLUSION

We developed a scoring model for early diagnosis of CD based on SBCE findings, possibly contributing to the improvement of the long-term outcome of CD.

Safety Assessment of Levilactobacillus brevis KU15006: A Comprehensive Analysis of its Phenotypic and Genotypic Properties

Levilactobacillus brevis KU15006, isolated from kimchi, exhibits pathogen-antagonistic and anti-diabetic activities; however, the safety of this strain has not been assessed. In the present study, L. brevis KU15006 was evaluated to elucidate its safety as a probiotic strain using phenotypic and genotypic analyses. Its safety was assessed using a minimum inhibitory concentration test comprising nine antibiotics, 26 antibiotic resistance genes, a single conjugative element, virulence gene analysis, hemolysis, cell cytotoxicity, mucin degradation, and toxic metabolite production. L. brevis KU15006 exhibited equal or lower minimum inhibitory concentration for the nine antibiotics than the cut-off value established by the European Food Safety Authority. It did not harbor antibiotic resistance and virulence genes. L. brevis KU15006 lacked β-hemolysis, mucin degradation, cytotoxicity against Caco-2 cells, gelatin liquefaction, bile salt deconjugation, and toxic metabolite production abilities. Based on the results, L. brevis KU15006, which has antagonistic and anti-diabetic effects, could be marketed as a probiotic in the future.

Bifidobacteria in Fermented Dairy Foods: A Health Beneficial Outlook

Bifidobacteria, frequently present in the human gastrointestinal tract, play a crucial role in preserving gut health and are mostly recognized as beneficial probiotic microorganisms. They are associated with fermenting complex carbohydrates, resulting in the production of short-chain fatty acids, bioactive peptides, exopolysaccharides, and vitamins, which provide energy and contribute to gut homeostasis. In light of these findings, research in food processing technologies has harnessed probiotic bacteria such as lactobacilli and bifidobacteria for the formulation of a wide range of fermented dairy products, ensuring their maximum survival and contributing to the development of distinctive quality characteristics and therapeutic benefits. Despite the increased interest in probiotic dairy products, introducing bifidobacteria into the dairy food chain has proved to be complicated. However, survival of Bifidobacterium species is conditioned by strain of bacteria used, metabolic interactions with lactic acid bacteria (LAB), fermentation parameters, and the temperature of storage and preservation of the dairy products. Furthermore, fortification of dairy foods and whey beverages with bifidobacteria have ability to change physicochemical and rheological properties beyond economic value of dairy products. In summary, this review underscores the significance of bifidobacteria as probiotics in diverse fermented dairy foods and accentuates their positive impact on human health. By enhancing our comprehension of the beneficial repercussions associated with the consumption of bifidobacteria-rich products, we aim to encourage individuals to embrace these probiotics as a means of promoting holistic health.

Lab-on-a chip electrochemical sensing platform for simultaneous, ultra-sensitive and on-spot detection of 4-aminosalicylic acid and 5-aminosalicylic acid based on synergistic potential of chitosan functionalized MWCNTs supported on Ni doped Bi2S3

Mesalamine or 5-aminosalicylic acid (5-ASA) and its isomer 4-aminosalicylic acid (4-ASA), well known key therapeutic agents used to treat inflammatory bowel diseases (IBDs) can pose toxicity risks upon unregulated consumption. However, their simultaneous real-time detection from physiological fluids like urine remains unexplored. This study presents an innovative electrochemical sensing platform using modified screen-printed electrodes capable of simultaneous detection of both the drugs by harnessing the synergistic potential of a novel nanocomposite comprising chitosan functionalized multi-walled carbon nanotubes and nickel doped bismuth sulphide. Comprehensive optical and microstructural characterization validate the modified sensor platform's morphological characteristics. The sensor was evaluated using CV and DPV, exhibiting notably low detection limits which is of the value 39.559 μM for 5-ASA and 85.21 μM for 4-ASA. Sensitivity was found to be 0.174 μA μM-1cm-2 for the linear dynamic range (LDR) of 50 μM-5750 μM for 5-ASA and 0.139 μA μM-1cm-2 for the linear dynamic range (LDR) of 100 μM-2200 μM for 4-ASA. Moreover, the adaptability of the sensor for integration into hand-held point-of-care devices for practical application has been demonstrated in this paper. Experimental validation using real urine samples underscores the sensor's impressive recovery rate of 98-99.6 % for 5-ASA and 95.12-99.24 % for 4-ASA and its capability of detecting target drugs even when present with typical urinary constituents as interferences. The real-world applicability of this sensing platform is further emphasized by conducting experiments on miniaturized hand-held device thus making it a promising tool for on-the-spot detection, offering substantial potential for future integration into point-of-care diagnostic devices to monitor patients requiring precise medical monitoring. Our approach offers unprecedented real-time identification capabilities of 4-ASA and 5-ASA which has not been explored before.

Calibration, Clinical Utility, and Specificity of Clinical Decision Support Tools in Inflammatory Bowel Disease

BACKGROUND & AIMS

Clinical decision support tools (CDSTs) have been developed to predict response to vedolizumab (VDZ) and ustekinumab (UST) in Crohn's disease (CD) and ulcerative colitis (UC). In addition to assessing their discrimination performance, our study aimed to evaluate their calibration, clinical utility, and specificity.

METHODS

We included 280 patients with CD and 218 patients with UC initiating VDZ, and 194 patients with CD initiating UST. We assessed discrimination by comparing rates of effectiveness outcomes between response probability groups forecasted by CDSTs. Calibration curves and decision curve analysis evaluated the calibration and clinical utility of VDZ-CDSTs. Additionally, we examined the agreement between UST-CDST and VDZ-CDST in assigning response probability groups among patients with CD starting UST.

RESULTS

In the overall cohort, CDSTs allocated 7.2%, 50.0%, and 42.8% of the patients to the low-, intermediate-, and high-response probability groups, respectively. VDZ-CDSTs groups demonstrated significant differences in the rates of clinical and endoscopic response and remission, whereas UST-CDST groups showed significant discrimination only for clinical remission. Although VDZ-CDSTs overestimated clinical remission rates, they more accurately predicted rates of VDZ persistence without need for surgery or dose escalation. Compared with empirically treating all patients with VDZ, VDZ-CDSTs yielded higher net benefits in selecting patients who would continue VDZ without need for surgery or dose escalation. Finally, the agreement between UST-CDST and VDZ-CDST in predicting response was 73.7%.

CONCLUSION

VDZ-CDSTs significantly discriminated response to VDZ and were more beneficial in identifying patients who would continue therapy without requiring surgery or dose escalation, compared with treating all patients empirically.

Lactobacilli-derived extracellular vesicles as synergistic biomolecules for colistin efficacy against Acinetobacter baumannii

Acinetobacter baumannii (A. baumannii), a gram-negative bacterium resistant to antibiotics, presents substantial medical challenges, causing nosocomial infections with high fatality rates. Colistin (COL) is frequently employed as a last-line defense against these pathogens. Nevertheless, its therapeutic efficacy has been significantly reduced due to the emergence of COL-resistant strains. With the slow development of novel antibiotics, researchers have explored materials to boost the effectiveness of COL against such pathogens. Postbiotics, comprising bioactive compounds derived from probiotic microorganisms, have shown potential antibacterial properties and may work synergistically with certain antibiotics. This study aimed to confirm the role of extracellular vesicles (EVs) as a collection of bioactive molecules that could potentially synergize with COL. EVs from various Lactobacilli strains (LEVs) were evaluated for their effect on COL susceptibility. The findings indicated that, compared to COL treatment alone, LEVs enhanced 4- to 8-fold bactericidal efficacy of COL against A. baumannii strains in the level of minimum inhibitory concentrations (MIC). Additional mechanistic investigations into the synergistic effects of LEVs on established COL mechanisms, including lipopolysaccharide binding, reactive oxygen species (ROS) generation, and biofilm formation, showed that LEVs act as either ROS enhancers or biofilm inhibitors, depending on the bacterial strains. Finally, we demonstrated that repeated use of LEVs did not induce COL resistance in A. baumannii. These results provide the first evidence that LEVs can serve as effective postbiotics, enhancing the susceptibility of A. baumannii strains to COL.

Small molecule drug absorption in inflammatory bowel disease and current implementation in physiologically- based pharmacokinetic models

Inflammatory bowel disease (IBD) is characterized by a chronic inflammation of the intestinal mucosa, with predominant localization in the colon in ulcerative colitis (UC) or affecting the entire length of the gastrointestinal tract in Crohn's disease (CD). Recent advances in the drug development space have been marked by a return to orally administered small molecules with novel mechanisms of action such as Janus kinase inhibitors. Additionally, the prevalence of certain chronic conditions is higher in IBD patients, many of which are treated with orally administered drugs. Given the pathophysiology and localization of IBD, altered drug absorption from the gastrointestinal tract can be expected. This review discusses several physiological differences between the small and large intestine with the potential to influence drug absorption including pathophysiology related alterations associated with IBD. The main physiological parameters which are identified include luminal fluid volume, luminal pH, transit time, bile salt concentration, microbiome, absorptive surface area, permeability and metabolizing enzymes and transporters. Literature regarding these factors in IBD patients is marked with high heterogeneity in reporting of disease severity and location leading to difficulties in interpreting data across different studies. While the influence of most of these factors has been directly assessed in healthy volunteers, this is rarely the case for IBD patients. Furthermore, studies which used PBPK modelling to describe the PK of an orally administered drug in an IBD population and were able to verify their findings using clinical data are critically examined. These models were able to incorporate the pathophysiological changes associated with IBD and partly succeeded in adequately predicting drug absorption in this population. Given the limited amount of PBPK studies performed on a limited number of drugs, the developed models are most likely not suitable to be used as a general PBPK model for the IBD population.

Fire in the belly: Stress and antibiotics induce dysbiosis and inflammation in the gut of common carp

Fish are exposed to numerous stressors which negatively affect their immune response and increase infection susceptibility. The risk of bacterial infections results in the excessive and preventive use of antibiotics. Therefore, we aimed to study how antibiotic treatment and restraint stress will affect the stress response, microbiota composition, gut morphology, and inflammatory reaction in common carp. Both restraint stress and antibiotic treatment increased cortisol level. Moreover, antibiotics induced dysbiosis in fish gut, manifested by a decrease in the total abundance of bacteria, and a shift in bacteria diversity, including a reduced number of Aeromonas, Bacteroides, Barnesiellaceae, Cetobacterium and Shewanella and an increased abundance of Flavobacterium. To a lesser extent, stress modified gut microbiota, as it decreased bacteria number and slightly changed the microbiota composition by decreasing Cetobacterium abundance and increasing Vibrio abundance. Microbiota of the antibiotic-treated and stressed fish shifted from the beneficial bacterial genera - Cetobacterium and Bacteroides, to the increased presence of unfavorable bacteria such as Brevinema, Flavobacterium and Desulfovibrionaceae. Stress and antibiotic-induced changes in the gut microbiota were related to the changes in the gut morphology when the higher abundance of goblet and rodlet cells and increased secretion activity of goblet cells were observed. Moreover, up-regulation of the expression of genes encoding pro-inflammatory mediators and cytokines involved in the Th17 immune response was present in the gut of the antibiotic-treated and stressed fish. We conclude that in carp antibiotics and stress alter the abundance and composition of the microbiota and induce Th17-dependent inflammatory reaction in the gut. Moreover, our results strongly suggest the interplay of the stress axis and the brain-gut-microbiota axis.

A case of pancreatic arteriovenous malformation diagnosed after the onset of abdominal symptoms

Pancreatic arteriovenous malformation (P-AVM) is an extremely rare vascular anomaly characterized by abnormal connections between arteries and veins bypassing the capillary network. Less than 200 cases have been reported worldwide, and standardized treatment guidelines have not yet been established. A 72-year-old man presented with abdominal distension, diarrhea, and appetite loss. Contrast-enhanced abdominal computed tomography revealed a 5 cm mass in the pancreatic tail with multiple feeding and draining vessels, a portosystemic shunt, and moderate ascites, suggesting a P-AVM. Endoscopic ultrasonography revealed a hypoechoic area in the pancreatic tail measuring 50 mm in diameter. Esophagogastroduodenoscopy revealed F2-type esophageal varices. Based on imaging findings and clinical history, the patient was diagnosed with P-AVM, and Osler-Weber-Rendu disease was excluded. Initial treatment with transarterial embolization was attempted, but proved insufficient due to high blood flow and multiple feeders. Surgical resection via distal pancreatectomy was subsequently performed to alleviate portal hypertension and resolve abdominal symptoms, although significant intraoperative bleeding occurred. This case highlights the diagnostic and therapeutic challenges of P-AVMs, particularly in high-flow lesions with complex vascular anatomy. Surgical resection remains the definitive treatment for symptomatic P-AVM and effectively resolves the associated complications. The insights gained from this case may contribute to the clinical management of this rare condition.

Bifidobacterium animalis subsp. lactis A6 alleviates perennial allergic rhinitis in adults by inhibiting serum total IgE and IL-13: A randomized, double-blind, placebo-controlled trial

OBJECTIVES

The evidence regarding the efficacy of probiotics in improving allergic rhinitis (AR) remains inconsistent. This study aimed to evaluate the potential effects of Bifidobacterium animalis subsp. lactis A6 (A6) on perennial AR.

METHODS

A randomized, double-blind, placebo-controlled trial was conducted involving 70 adults with perennial AR receiving either probiotic (A6, 5 × 1010 CFU/sachet per day) or placebo intervention for 8 weeks. Nasal symptoms and quality of life (QoL) were recorded using total nasal symptom scores (TNSS) and the rhinitis quality of life questionnaire (RQLQ). Blood eosinophil count, total immunoglobulin E (IgE), allergen-specific IgE, and immunological parameters were also assessed.

RESULTS

After 8 weeks of intervention, the probiotic group showed a statistically significant greater reduction in TNSS total score compared with the placebo group [-3.11 (3.53) vs. -1.29 (3.34), p = 0.029, Cohen's d = 0.68]. Similar results were noted for serum total IgE and interleukin-13 (IL-13). Comparable findings were seen for RQLQ score only at week 4 but not at week 8.

CONCLUSIONS

In conclusion, A6 could statistically significantly alleviate rhinitis symptoms and improve QoL in adults with perennial AR. The effect size, as measured by Cohen's d, suggests that A6 may provide clinically meaningful benefits for AR patients to a certain degree.

CLINICAL TRIAL REGISTRATION

Chictr.org.cn Identifier no. ChiCTR2200064158.

In Search of Healthy Ageing: A Microbiome-Based Precision Nutrition Approach for Type 2 Diabetes Prevention

Background/Objectives: Type 2 diabetes (T2D) is a leading cause of morbidity and mortality worldwide and in Spain, particularly in the elderly population, affecting healthy ageing. Nutritional strategies are key to its prevention. The gut microbiota is also implicated in T2D and can be modulated by nutrition. We hypothesize that precision nutrition through microbiota modulation may help prevent T2D. This article aims to (1) describe a gut microbiota bacterial profile associated with T2D prevention, (2) provide precision nutrition tools to optimize this profile, (3) analyze how overweight influences the microbiota composition and precision nutrition response, and (4) address the technical challenges of microbiome-based precision nutrition clinical implementation to prevent T2D. Methods: A review of gut microbiota associated with T2D prevention was conducted. 13 healthy Spanish participants over 62 with optimal blood glucose levels (7 normal weight and 6 overweight) underwent a 3-month precision nutrition intervention to optimize T2D-preventive gut microbiota using a bioinformatics food recommendation system, Phymofood (EP22382095). Fecal microbiota was analyzed pre- and post-intervention using full-length 16S rRNA gene amplification, MinION sequencing, and NCBI taxonomic classification. Results: 31 potentially preventive bacteria against T2D were selected. The intervention increased the relative abundance of beneficial genera (Butyrivibrio and Faecalibacterium) and species (Eshraghiella crossota, and Faecalibacterium prausnitzii). The overweight influenced microbiota composition and intervention response. Conclusions: A gut microbiota profile associated with T2D prevention was identified, and precision nutrition could increase the relative abundance of beneficial bacteria. Confounding factors such as overweight should be considered when designing microbiome-based precision nutrition interventions. These results contribute to a better understanding of the microbiota associated with T2D prevention and address technical challenges for clinical implementation in future healthy ageing strategies.

Changes in Medical Management of Inflammatory Bowel Disease and Reducing Surgical Risk: Investigating Causality Through the Bradford-Hill Criteria

Background: Inflammatory bowel diseases (IBDs) are chronic progressive conditions, and their management has evolved over time, not only in the number of available medications but also in therapeutic strategies, resulting in a paradigm shift from treat-on-flare to treat-to-target, with the ultimate goal of modifying disease course. Several studies have shown a reduction in the risk of surgery associated with the concomitant increase in anti-tumor necrosis factor α (TNFα) drug prescription, thus inferring a positive impact of anti-TNFα therapy on IBD natural history. However, establishing a causal relationship is complex, as multiple factors influence disease progression. Methods: To investigate this relationship, a narrative review applying the Bradford-Hill criteria to the existing literature has been conducted. Results: The potential causal link between the introduction and increased use of biologic drugs, particularly anti-TNFα agents, and the reduction in surgical risk in patients affected by IBD are critically reviewed. Conclusions: Establishing a direct causal link between increased anti-TNFα prescriptions and long-term outcomes remains a difficult issue. Multiple factors like greater awareness, early diagnosis, multidisciplinary approaches, introduction of guidelines, and ongoing education also contribute to improved prognosis.

Fermented Dairy Products as Precision Modulators of Gut Microbiota and Host Health: Mechanistic Insights, Clinical Evidence, and Future Directions

Dairy products-encompassing yogurt, kefir, cheese, and cultured milk beverages-are emerging as versatile, food-based modulators of gut microbiota and host physiology. This review synthesizes mechanistic insights demonstrating how live starter cultures and their fermentation-derived metabolites (short-chain fatty acids, bioactive peptides, and exopolysaccharides) act synergistically to enhance microbial diversity, reinforce epithelial barrier integrity via upregulation of tight-junction proteins, and modulate immune signaling. Clinical evidence supports significant improvements in metabolic parameters (fasting glucose, lipid profiles, blood pressure) and reductions in systemic inflammation across metabolic syndrome, hypertension, and IBS cohorts. We highlight critical modulatory factors-including strain specificity, host enterotypes and FUT2 genotype, fermentation parameters, and matrix composition-that govern probiotic engraftment, postbiotic yield, and therapeutic efficacy. Despite promising short-term outcomes, current studies are limited by heterogeneous designs and brief intervention periods, underscoring the need for long-term, adaptive trials and integrative multi-omics to establish durability and causality. Looking forward, precision nutrition frameworks that harness baseline microbiota profiling, host genetics, and data-driven fermentation design will enable bespoke fermented dairy formulations, transforming these traditional foods into next-generation functional matrices for targeted prevention and management of metabolic, inflammatory, and neuroimmune disorders.

Role and mechanism of gut microbiota-host interactions in the pathogenesis of Crohn's disease

BACKGROUND

Crohn's disease (CD) is a chronic, nonspecific inflammatory bowel disease with a poor prognosis. Despite its increasing incidence, curing CD remains challenging due to its complex etiology and unclear pathogenesis.

METHODS

A comprehensive PubMed and Web of Science search was conducted using the keywords Crohn's disease, gut microbiota, dysbiosis, pathogenesis and treatment, focusing on studies published between 2014 and 2024.

RESULTS

Recent studies have demonstrated a close relationship between gut microbiota dysbiosis and the development of CD. Although many dysbioses associated with CD have not yet been proven to be causal or consequential, it has been observed that the gut microbiota in CD patients exhibits reduced diversity, a decrease in beneficial bacteria, and an increase in pathogenic bacteria. These changes may lead to decreased intestinal barrier function, abnormal immune responses, and enhanced inflammatory reactions, which are related to the disease's activity, phenotype, drug treatment efficacy, and postoperative therapeutic outcomes. Therefore, further exploration of the microbiota-host interactions and the pathogenesis of CD, the identification of biomarkers, and the development of targeted strategies for modulating the gut microbiota could offer new avenues for the prevention and treatment of CD.

CONCLUSIONS

This review highlights the pivotal role of gut microbiota dysbiosis in driving CD pathogenesis and its progression, while underscoring its potential as a therapeutic target through dietary modulation, microbial interventions, and integrative strategies to improve clinical management and prognostic outcomes.

Time to classify: a narrative and scoping review of the old and the new classifications of perianal Crohn's disease

Perianal Crohn's disease (pCD) is a complex manifestation of Crohn's disease. Classifying this patient cohort for both clinical purposes and for inclusion into research trials is challenging but crucial in order to improve outcomes. This review provides an overview of historical classifications of both fistulising and non-fistulising pCD, including the Park's, Cardiff-Hughes and American Gastroenterological Association (AGA) classifications, as well as recent advances including the Treatment Optimisation and CLASSification of perianal Crohn's disease (TOpClass) classification of fistulising pCD. Secondly, this article provides a scoping review of recent trials in pCD and describes how the cohorts in these trials relate to the TOpClass classification. Of the 19 studies relating to pCD that were identified, four could be confidently classified as class 2a. Seven could be classified as class 2a or 2b, but it was not possible to subdivide further, and seven to class 2a, 2b or 2c, but it was not possible to subdivide further. One study population was classified as class 2a or 2c. In eight studies, it was not specified whether patients with a defunctioning stoma were included or excluded. This review demonstrates the heterogeneous nature of some patient cohorts in previous clinical trials, and how the TOpClass classification may be used to group patients more accurately for clinical use and inclusion in research trials.