Patient-Specific Regulatory Network Rewiring in Inflammatory Bowel Disease: How Genetic Polymorphisms Divert Incoming Signals and Contribute to Disease Pathogenesis.

Background: Intestinal cells receive incoming signals from neighboring cells and microbial communities. Upstream signaling pathways transduce these signals to reach transcription factors (TFs) that regulate gene expression. In inflammatory bowel disease (IBD), most single nucleotide polymorphisms (SNPs) are in non-coding genomic regions containing TF binding sites.

The landscape of microbial associations in human cancer.

Oncomicrobes are estimated to cause 15% of cancers worldwide. When cancer whole-genome sequencing (WGS) data are collected, the microbes present are also sequenced, allowing the investigation of potential etiological and clinical associations. Interrogating the microbial community for 8908 patients encompassing 22 cancer types from the Genomics England WGS dataset revealed that only colorectal tumors exhibited unmistakably distinct microbial communities that can reliably be used to distinguish anatomical site [positive predictive value (PPV) = 0.

Cell surface polysaccharides in the gut microbiota: occurrence, structure and role.

The gastrointestinal (GI) tract is colonized by trillions of microorganisms living in a symbiotic relationship with the host. Commensal bacteria in the gut engage in cross-talks with epithelial and immune cells through effector molecules secreted or attached to the cell surface. Although cell surface polysaccharides have mainly been studied in the context of pathogen-host interactions, these are increasingly being recognized as important factors of the symbiotic interaction between the gut microbiota and the host conferring biological activities and physiological functions.

ICTV Virus Taxonomy Profile: 2025.

The realm includes viruses of archaea, bacteria and eukaryotes, with linear dsDNA genomes. Duplodnavirians share a distinct morphogenetic module of four hallmark genes encoding the HK97-fold major capsid protein, a genome packaging ATPase-nuclease (large terminase subunit), a portal protein and a capsid maturation protease. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the realm , which is available at ictv.

Genomics uncover resistant and virulent Klebsiella on foods: a potential risk to human health.

Klebsiella pneumoniae is a bacterium of public health importance due to its association with antimicrobial resistance (AMR) and its role as a major cause of both hospital- and community-acquired infections. While Klebsiella species have been detected in foods, our understanding of their diversity and the potential risks they pose from food is limited. This study aims to comprehensively evaluate the Klebsiella species population and their contribution to the burden of AMR, virulence, and heavy metal tolerance from diverse food samples.

Upcycling of Waste Cherries Produces an Anthocyanin-Rich Powder That Protects Against Amyloid-β Toxicity in .

Agricultural waste poses significant environmental and economic challenges, with the UK generating 135,000 tonnes annually. Upcycling plant-derived waste offers a sustainable approach to enhancing agricultural productivity while producing innovative, health-promoting foods. Cherries, particularly rich in anthocyanins and quercetin, possess antioxidant and anti-inflammatory properties linked to numerous health benefits.

On-Cell Saturation Transfer Difference NMR Spectroscopy on Ion Channels: Characterizing Negative Allosteric Modulator Binding Interactions of P2X7.

P2X7 receptors are important drug targets involved in pathologies ranging from psychiatric disorders to cancer. Being membrane embedded receptors, they are more challenging for structural characterization, and at present, we only have a small number of X-ray and cryo-EM structures for P2X7 bound to antagonists. We demonstrate that saturation transfer difference (STD) NMR on live mammalian cells (on-cell STD NMR) overexpressing P2X7 receptors allows further structural insight on the complexes of P2X7 with two potent negative allosteric modulators, namely, AZ10606120 and JNJ-47965567, via the determination of the binding epitope mapping of the interactions, e.

PNGaseL from targets a diverse range of N-glycan structures.

Peptide:N-glycosidases (PNGases) are used by a wide range of organisms to remove N-glycan structures from proteins for use as either nutrients or in glycoprotein processing. PNGaseF is the most well-characterized enzyme of this family and is widely used in glycobiology to allow study of the N-glycome of a specific protein, cell and tissues, for instance. Despite this, PNGaseF has limitations in the types of N-glycan structures it can target.

Interlaboratory validation of an optimized protocol for measuring α-amylase activity by the INFOGEST international research network.

The activity of α-amylases is frequently determined using a single-point assay at 20 °C. Previous work within INFOGEST "Working Group 5 - Starch digestion and amylases" identified significant interlaboratory variation with this protocol. The current study aimed to evaluate the repeatability (intralaboratory precision) and reproducibility (interlaboratory precision), measured as coefficients of variation (CVs), of a newly optimized protocol version based on four time-point measurements at 37 °C.

Engineering biology and chemical approaches to the construction of vitamin B analogues and antivitamins B as probes and therapeutic agents.

Vitamins are indispensable cofactors that expand the chemical capabilities of enzymes beyond the inherent limitations of amino acid side chains. Among them, vitamin B₁₂ is particularly remarkable due to its exceptional structural complexity, the presence of a cobalt-centered corrin ring, and its exclusive biosynthetic origin in prokaryotes. This review explores the biosynthesis, transport, and biological significance of B₁₂, with an emphasis on the growing toolbox of synthetic analogues designed for research and therapeutic use.

Differential Cell-Specific, Regulatory Roles of FcγRIIB through IgG in IgA Nephropathy.

Background: IgA nephropathy is the most common form of glomerulonephritis and a leading cause of kidney failure. Ample evidence confirms the deposition of IgA and IgG, as well as the infiltration of mononuclear leukocytes in kidney biopsy specimens from IgA nephropathy patients. Previously, we established an experimental IgA nephropathy model in B cell-deficient mice, implicating interactions between Fcγ receptors (FcγRs) in the pathogenesis of IgA nephropathy.

Peptide abundance correlations in metaproteomics enhance taxonomic and functional analysis of the human gut microbiome.

Mass spectrometry (MS)-based proteomics is widely used for quantitative protein profiling and protein interaction studies. However, most current research focuses on single-species proteomics, while protein interactions within complex microbiomes, composed of hundreds of bacterial species, remain largely unexplored. In this study, we analyzed peptide abundance correlations within a metaproteomics dataset derived from in vitro cultured human gut microbiomes subjected to various drug treatments.

Impact of early life antibiotic and probiotic treatment on gut microbiome and resistome of very-low-birth-weight preterm infants.

Preterm infants (<37 weeks' gestation) are commonly given broad-spectrum antibiotics due to their risk of severe conditions like necrotising enterocolitis and sepsis. However, antibiotics can disrupt early-life gut microbiota development, potentially impairing gut immunity and colonisation resistance. Probiotics (e.

Genomic diversity of non-typhoidal found in patients suffering from gastroenteritis in Norfolk, UK.

is a significant public health pathogen responsible for a wide spectrum of diseases, ranging from gastroenteritis to invasive non-typhoidal salmonellosis and enteric fever. Although advancements in whole-genome sequencing have improved surveillance and outbreak investigations, traditional single-colony sequencing methods overlook within-host diversity, potentially underestimating the complexity of infections. This study explores the genome-wide diversity of strains recovered from stool samples of eight patients, with up to 20 isolates analysed per sample.

Draft genome sequence of a kombucha isolate of .

(syn. ) is a fermentative yeast of importance to both the food and biotechnology industries, as well as being of significant clinical concern. Here, we report the draft genome sequence of NCYC 4488, a kombucha-derived isolate.

An absent WD domain in the autophagy protein ATG16L1 leads to auditory and vestibular dysfunction and otoconial deficits in mice.

Objectives: To examine the inner ear functions of mice that lack the WD domain (δWD) of autophagy protein ATG16L1.

Design: Mice were assessed with vestibular evoked potentials (VsEPs), auditory brainstem responses (ABRs) and four δWD mice were observed with electron microscopy to assess otolith otoconia loss, and cochlear hair cell loss.

Study Sample: Seven δWD mice and four control mice.

Summary of taxonomy changes ratified by the International Committee on Taxonomy of Viruses (ICTV) from the Bacterial Viruses Subcommittee, 2025.

This article summarises the activities of the International Committee on Taxonomy of Viruses Bacterial Viruses Subcommittee, detailing developments in the classification of bacterial viruses. We provide here an overview of all new, abolished, moved and renamed taxa proposed in 2024, approved by the Executive Committee, and ratified by membership vote in 2025. Through the collective efforts of 74 international contributors of taxonomy proposals in this round, 43 ratified proposals have led to the creation of one new phylum, one class, four orders, 33 families, 14 subfamilies, 194 genera and 995 species.

Virus taxonomy proposal summaries: a searchable and citable resource to disseminate virus taxonomy advances.

Taxonomic classification of cellular organisms requires the publication of descriptions and proposed names of species and the deposition of specimens. Virus taxonomy is developed through a different system of annual submission of formal taxonomy proposals (TPs) that can be submitted by anyone but are typically prepared by a study group appointed by the International Committee on Taxonomy of Viruses (ICTV) and consisting of experts on a particular group of viruses. These are initially evaluated by an expert subcommittee and by the executive committee (EC) of the ICTV.

'What's in a name? Fit-for-purpose bacterial nomenclature': meeting report.

Rapid and economical DNA sequencing has resulted in a revolution in phylogenomics. The impact of changes in nomenclature can be perceived as an absolute necessity of scientific rigour, coupled with the slight inconvenience of needing to re-learn names. In relation to practical aspects of microbiology, for example, infectious disease diagnosis, there may, however, be potential dangers.

Experimental systems are essential for strengthening ecological modeling of microbiomes beyond observational data.

Disentangling the ecological mechanisms shaping the assembly of complex communities with thousands of interacting species remains a significant challenge. Ecological models derived from observational data are valuable tools for describing community states and generating hypotheses. Integrating these models with experimental approaches is crucial for addressing the challenges of uncovering the complex mechanisms and dynamics underlying microbiome assembly.

Association of antimicrobial resistant Vibrio and species pathogenic to humans with aquacultured seafood.

Vibrio is a genus of bacteria commonly found on seafood products and includes many important human pathogens. Most seafood is produced using aquaculture systems, which frequently use antimicrobial agents. Here we aimed to determine if method of seafood production was associated with Vibrio pathogenic to humans and/or antimicrobial resistant (AMR) Vibrio.

Deciphering the microbiome-metabolome landscape of an inflammatory bowel disease inception cohort.

The gut microbiota contribute to the etiopathogenesis of inflammatory bowel disease (IBD), but limitations of prior studies include the use of sequencing alone (restricting exploration of the contribution of microbiota functionality) and the recruitment of patients with well-established disease (introducing potential confounders, such as immunomodulatory medication). Here, we analyze a true IBD inception cohort and healthy controls (HCs) via stool 16S rRNA gene sequencing and multi-system metabolomic phenotyping (using nuclear magnetic spectroscopy and mass spectroscopy), with subsequent integrative network analysis employed to delineate novel microbiota-metabolome interactions in IBD. Marked differences in β diversity and taxonomic profiles were observed both between IBD and HCs, as well as between Crohn's disease (CD) and ulcerative colitis (UC) patients.

Genomic epidemiology of SARS-CoV-2 in Norfolk, UK, March 2020-December 2022.

In the UK, the COVID-19 Genomics UK Consortium (COG-UK) established a real-time national genomic surveillance system during the COVID-19 pandemic, producing centralized data for monitoring severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As a COG-UK partner, Quadram Institute Bioscience in Norfolk sequenced over 87,000 SARS-CoV-2 genomes as part of the national effort, contributing to the region becoming densely sequenced. Retrospective analysis of SARS-CoV-2 lineage dynamics in this region may contribute to preparedness for future pandemics.

Profiling of Permethylated Mucin O-glycans Using Matrix-assisted Laser Desorption/Ionization Time-of-flight Mass Spectrometry.

Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a powerful tool for the profiling of mucin glycans that offers high sensitivity and throughput. Here, we provide a detailed protocol for the analysis of O-linked glycans from mucins using MALDI-TOF MS, encompassing glycan release, desalting, permethylation, and data acquisition and analysis. This study shows that desalting based on ion exchange chromatography leads to improved recovery of larger glycans and better quality of the produced spectra compared to solid-phase extraction using porous graphitized carbon (PGC).