Alterations in the gut microbiome, including diet-driven changes, are linked to the rising prevalence of food allergy. However, little is known about how specific gut bacteria trigger the breakdown of oral tolerance. Here we show that depriving specific-pathogen-free mice of dietary fibre leads to a gut microbiota signature with increases in the mucin-degrading bacterium Akkermansia muciniphila. This signature is associated with intestinal barrier dysfunction, increased expression of type 1 and 2 cytokines and IgE-coated commensals in the colon, which result in an exacerbated allergic reaction to food allergens, ovalbumin and peanut. To demonstrate the causal role of A. muciniphila, we employed a tractable synthetic human gut microbiota in gnotobiotic mice. The presence of A. muciniphila within the microbiota, combined with fibre deprivation, resulted in stronger anti-commensal IgE coating and innate type-2 immune responses, which worsened symptoms of food allergy. Our study provides important insights into how gut microbes can regulate immune pathways of food allergy in a diet-dependent manner.

Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets of genetic changes that confer to the virus higher transmissibility and ability to evade existing immunity. The continuous evolution of SARS-CoV-2 may pose challenges for current treatment options and diagnostic tools. In this study, we have first evaluated the performance of the 14 WHO-recommended real-time reverse transcription (RT)-PCR assays currently in use for the detection of SARS-CoV-2 and found that only one assay has reduced performance against Omicron. We then developed a new duplex real-time RT-PCR assay based on the amplification of two ultra-conserved elements present within the SARS-CoV-2 genome. The new duplex assay successfully detects all of the tested SARS-CoV-2 variants of concern (including Omicron sub-lineages BA.4 and BA.5) from both clinical and wastewater samples with high sensitivity and specificity. The assay also functions as a one-step droplet digital RT-PCR assay. This new assay, in addition to clinical testing, could be adopted in surveillance programs for the routine monitoring of SARS-CoV-2’s presence in a population in wastewater samples. Positive results with our assay in conjunction with negative results from an Omicron-specific assay may provide timely indication of the emergence of a novel SARS-CoV-2 variant in a certain community and thereby aid public health interventions.

Alterations in the gut microbiome, including diet-driven changes, are linked to the rising prevalence of food allergy, yet little is known about how specific gut bacteria incite breakdown of oral tolerance. Here, we show that depriving specific-pathogen-free mice of dietary fiber leads to an increase of the mucolytic bacterium Akkermansia muciniphila, which is associated with a surge in the colonic type 2 immune cells and IgE-coated commensals, and microbiota-mediated gut mucosal barrier dysfunction. These changes manifest into exacerbated sensitization to food allergens, ovalbumin and peanut. To demonstrate the causal role of A. muciniphila, we employed a tractable synthetic human gut microbiota in gnotobiotic mice. The presence of A. muciniphila within the microbiota, combined with fiber deprivation, resulted in stronger anti-commensal IgE coating and type 2 immune responses, which worsened symptoms of food allergy. Our study supports a mechanistic link between diet and a mucolytic gut microbe in regulating food allergy.

Dietary fibers can alter microbial metabolic output in support of healthy immune function, however, the impact of distinct fiber sources and immunomodulatory effects beyond short-chain fatty acid production are underexplored. In an effort to discern the effects of diverse fibers on host immunity, we employed five distinct rodent diets with varying fiber content and source in specific-pathogen-free, gnotobiotic (containing a 14-member synthetic human gut microbiota), and germ-free mice. Broad-scale metabolomic analysis of cecal contents showed a reduction in microbiota-produced B vitamins during fiber deprivation. Fiber deprivation shifted the ratio of transcripts corresponding to bacterial enzymes involved in B vitamin synthesis versus downstream utilization, resulting in a net reduction of host-available B vitamins. Broad immunophenotyping identified that the local gut effector immune populations and activated T cells accumulate in a microbiota-dependent manner. Supplementation with the prebiotic inulin recovered the availability of microbial-produced B vitamin and restored immune homeostasis. Our findings highlight the biotechnological potential of defined fiber polysaccharides to boost microbiota-derived B vitamin availability to the host and regulate local innate and adaptive immune populations, which may have critical implications for immune homeostasis in a variety of diseases.

Background: Antimicrobial resistance (AMR) is an increasing global threat. Effective surveillance is central for a successful public health response. Policy initiatives have called for a coordinated, data-driven response, yet a systematic method to track and contextualise progress in AMR surveillance is lacking. We aimed to establish a standardised, comparative framework designed to: demonstrate ongoing AMR surveillance, identify surveillance gaps, and monitor progress towards policy commitments across Europe.Methods: We developed a structured questionnaire and performed a cross-sectional inventory of national AMR surveillance systems for human health in spring 2025. The collected data was integrated into a dashboard called JAMREYE. We analysed the data to identify surveillance gaps and country progress towards meeting selected policy recommendations from the 2023 EU Council Recommendation on AMR. Findings: Our framework allowed us to map the national AMR surveillance landscape for the human sector across 30 European countries. Robust surveillance was generally seen for invasive infections and carbapenem-resistant pathogen, but critical gaps were identified for additional culture materials and AMR priority pathogens. For example, surveillance of carbapenem-resistant E. coli from blood was mandatory in 73% of countries compared to 53% for urine. Through a progress analysis, we established a European baseline for policy commitments, enabling the identification of additional actions to support their implementation.Interpretation: To meet surveillance policy commitments by 2030, European countries must advance on several recommendations. We suggest focusing on closing surveillance gaps for both invasive and non-invasive infections and optimising the use of surveillance data to enhance patient outcomes.