Temporal dynamics of SARS-CoV-2 shedding in feces and saliva: a longitudinal study in Norfolk, United Kingdom during the 2021-2022 COVID-19 waves.

Unlabelled: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was originally described as a respiratory illness; however, it is now known that the infection can spread to the gastrointestinal tract, leading to shedding in feces potentially being a source of infection through wastewater. We aimed to assess the prevalence and persistence of SARS-CoV-2 in fecal and saliva samples for up to 7 weeks post-detection in a cohort of 98 participants from Norfolk, United Kingdom using RT-qPCR. Secondary goals included sequencing the viral isolates present in fecal samples and comparing the genetic sequence with isolates in the saliva of the same participant.

Genome sequence of AM6, isolated from a Parkinson's disease patient.

Here, we report the genome sequence of AM6, isolated from a fecal sample obtained from a Parkinson's disease patient. The bacterial genome was sequenced using Illumina technology on a NextSeq 500 platform. The assembled genome of comprises 4,318,463 base pairs with a G + C content of 47.

Cognitive Dysfunction in Myalgic Encephalomyelitis/Chronic Fatigue Syndrome-Aetiology and Potential Treatments.

Systemic infection and inflammation impair mental function through a combination of altered attention and cognition. Here, we comprehensively review the relevant literature and report personal clinical observations to discuss the relationship between infection, peripheral inflammation, and cerebral and cognitive dysfunction in patients with myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS). Cognitive dysfunction in ME/CFS could result from low-grade persistent inflammation associated with raised pro-inflammatory cytokines.

S-Methyl Methanethiosulfonate, the Main Human Metabolite of S-Methyl-L-Cysteine Sulfoxide, Alters Energy Metabolism in Prostate Cancer Cells.

Cruciferous and allium vegetables contain the sulfur compound S-methyl-L-cysteine-sulfoxide (SMCSO). Considering SMCSO is found at a higher abundance compared to the glucosinolates, there are limited reports on its effect on health, with the majority of the evidence on the beneficial effects on glucose metabolism in rodent models. In the current study, we investigated the metabolic effects of SMCSO and its metabolite, S-methyl methanethiosulfonate (MMTSO), on prostate cancer metabolism.

IL-17RA signaling provides dual tumor-suppressor function during late-stage colorectal carcinogenesis.

Expression of interleukin (IL)-17 family cytokines is associated with tumor-promoting inflammation. We found that low expression of IL17RA associated with worse prognosis in late-stage colorectal cancer (CRC) patients. Deletion of Il17ra in intestinal epithelial cells (IECs) in a murine model of CRC enhanced epithelial-to-mesenchymal transition (EMT) via increased expression of the epidermal growth factor receptor and subsequent activation of the kinase Src.

Gut in Tube─Continuous Measurement of Metabolic Crosstalk between Cell Populations in Heterogeneous Samples by NMR Imaging.

In complex living systems, such as the human gut, the interplay between the multiple cell types present is governed by the exchange of small molecule metabolites. However, at present, we lack techniques capable of monitoring this crosstalk in real time and with spatial resolution. Here, we present a model of the human gut in a 5 mm NMR tube that accounts for the intraluminal, mucosal, and colonocyte spaces.

Assessing Bias and Reproducibility of Viral Metagenomics Methods for the Combined Detection of Faecal RNA and DNA Viruses.

Whole transcriptome amplification (WTA2) and sequence-independent single primer amplification (SISPA) are two widely used methods for combined metagenomic sequencing of RNA and DNA viruses. However, information on the reproducibility and bias of these methods on diverse viruses in faecal samples is currently lacking. A mock community (MC) of diverse viruses was developed and used to spike faecal samples at different concentrations.

Genomic insights into the beneficial potential of and strains isolated from Cameroonian infants.

A healthy early-life gut microbiota plays an important role in maintaining immediate and long-term health. Perturbations, particularly in low- to middle-income communities, are associated with increased infection risk. Thus, a promising avenue for restoring a healthy infant microbiota is to select key beneficial bacterial candidates from underexplored microbiomes for developing new probiotic-based therapies.

Metagenomic analyses of gut microbiome composition and function with age in a wild bird; little change, except increased transposase gene abundance.

Studies on wild animals, mostly undertaken using 16S metabarcoding, have yielded ambiguous evidence regarding changes in the gut microbiome (GM) with age and senescence. Furthermore, variation in GM function has rarely been studied in such wild populations, despite GM metabolic characteristics potentially being associated with host senescent declines. Here, we used 7 years of repeated sampling of individuals and shotgun metagenomic sequencing to investigate taxonomic and functional changes in the GM of Seychelles warblers () with age.

Microvascular endothelial cells display organ-specific responses to extracellular matrix stiffness.

The extracellular matrix was originally thought of as simply a cellular scaffold but is now considered a key regulator of cell function and phenotype from which cells can derive biochemical and mechanical stimuli. Age-associated changes in matrix composition drive increases in matrix stiffness. Enhanced matrix stiffness promotes the progression of numerous diseases including cardiovascular disease, musculoskeletal disease, fibrosis, and cancer.

A pragmatic pipeline for drug resistance and lineage identification in Mycobacterium tuberculosis using whole genome sequencing.

Delays in accurate diagnosis of drug resistant tuberculosis (DR-TB) can hinder treatment. Whole genome sequencing (WGS) provides more information than standard molecular and phenotypic testing, but commonly used platforms are expensive to implement, and data interpretation requires significant expertise. We aimed to optimise a TB WGS diagnostic pipeline balancing user-friendliness, cost-effectiveness and time to results, whilst ensuring accuracy.

The nisin O cluster: species dissemination, candidate leader peptide proteases and the role of regulatory systems.

Nisin O is an antimicrobial peptide encoded by the human gut bacterium A2-162 which has antimicrobial activity against clinically relevant organisms. The nisin O biosynthetic gene cluster (BGC) varies from other nisin BGCs as it lacks a leader-peptide cleaving protease and contains two bacterial two-component response regulator-histidine kinase (RK) systems. The dissemination of the nisin O cluster, the final proteolytic biosynthesis step and the regulation of nisin O are currently unknown and are the foci of this study.

Vitamin B12 Levels Association with Functional and Structural Biomarkers of Central Nervous System Injury in Older Adults.

Objective: Vitamin B12 (B12) plays a critical role in fatty- and amino-acid metabolism and nucleotide synthesis. While the association between B12 deficiency and neurological dysfunction is well-known, the exact threshold for adequacy remains undefined in terms of functional impairment and evidence of injury. The objective was to assess whether B12 levels within the current normal range in a cohort of healthy older adults may be associated with measurable evidence of neurological injury or dysfunction.

Expansion and Assessment of a Web-Based 24-Hour Dietary Recall Tool, Foodbook24, for Use Among Diverse Populations Living in Ireland: Comparative Analysis.

Background: Currently, the methods used to collect dietary intake data in Ireland are inflexible to the needs of certain populations, who are poorly represented in nutrition and health data as a result. As the Irish population is becoming increasingly diverse, there is an urgent need to understand the habitual food intake and diet quality of multiple population subgroups, including different nationalities and ethnic minorities, in Ireland. Foodbook24 is an existing web-based 24-hour dietary recall tool, which has previously been validated for use within the general Irish adult population.

Exploration of the genetic landscape of bacterial dsDNA viruses reveals an ANI gap amid extensive mosaicism.

Average nucleotide identity (ANI) is a widely used metric to estimate genetic relatedness, especially in microbial species delineation. While ANI calculation has been well optimized for bacteria and closely related viral genomes, accurate estimation of ANI below 80%, particularly in large reference data sets, has been challenging due to a lack of accurate and scalable methods. To bridge this gap, we introduce MANIAC, an efficient computational pipeline optimized for estimating ANI and alignment fraction (AF) in viral genomes with divergence around ANI of 70%.

Antimicrobial peptide glatiramer acetate targets Pseudomonas aeruginosa lipopolysaccharides to breach membranes without altering lipopolysaccharide modification.

Antimicrobial peptides (AMPs) are key components of innate immunity across all domains of life. Natural and synthetic AMPs are receiving renewed attention in efforts to combat the antimicrobial resistance (AMR) crisis and the loss of antibiotic efficacy. The gram-negative pathogen Pseudomonas aeruginosa is one of the most concerning infecting bacteria in AMR, particularly in people with cystic fibrosis (CF) where respiratory infections are difficult to eradicate and associated with increased morbidity and mortality.

Protocol for predicting host-microbe interactions and their downstream effect on host cells using MicrobioLink.

Analyzing host-microbe interactions is essential for understanding how microbiota changes disrupt host homeostasis. Here, we present a protocol for predicting host-microbe protein-protein interactions and their downstream effects using MicrobioLink. We describe steps for setting up the environment, installing software, and preparing human transcriptomic and bacterial proteomic data.

Clinical Microbiome Analysis by Mass Spectrometry-Based Metaproteomics.

Mass spectrometry-based proteomics and metaproteomics have long been used in the study of human microbiomes, with the potential of metaproteomics only recently being fully harnessed. This progress is due to the advancements of high-performance mass spectrometers, innovative proteomics strategies, and the development of dedicated bioinformatics tools. In this review, we critically examine the recent technological developments that enhance the application of metaproteomics in clinical microbiome analysis.

Avian pathogenic Escherichia coli-targeting phages for biofilm biocontrol in the poultry industry.

Avian pathogenic Escherichia coli (APEC) is a principal etiologic agent of avian colibacillosis, responsible for significant economic losses in the poultry industry due to high mortality and disease treatment with antibiotics. APEC and its ability to form biofilms on food and processing surfaces contributes to its persistence within farms. Bacteriophages are promising antibacterial agents for combating APEC.

Acute Myeloid Leukaemia and Acute Lymphoblastic Leukaemia Classification and Metabolic Characteristics for Informing and Advancing Treatment.

Acute myeloid leukaemia (AML) and acute lymphoblastic leukaemia (ALL) remain significant challenges in haematological oncology. This review examines the pathophysiology, classification, and risk stratification of these aggressive malignancies, emphasising their impact on treatment strategies and prognosis. We discuss current standard-of-care treatments, including chemotherapy regimens and targeted therapies, while addressing the associated adverse effects and hypersensitivity reactions.

FAecal micRobiota transplantation in primary sclerosinG chOlangitis (FARGO): study protocol for a randomised, multicentre, phase IIa, placebo-controlled trial.

Introduction: Primary sclerosing cholangitis (PSC) is the classical hepatobiliary manifestation of inflammatory bowel disease (IBD). The strong association between gut and liver inflammation has driven several pathogenic hypotheses to which the intestinal microbiome is proposed to contribute. Pilot studies of faecal microbiota transplantation (FMT) in PSC and IBD are demonstrated to be safe and associated with increased gut bacterial diversity.

Association of gut microbiota and gut metabolites and adverse outcomes in biliary atresia: A longitudinal prospective study.

Background: The Kasai portoenterostomy (KPE) aims to re-establish bile flow in biliary atresia (BA); however, BA remains the commonest indication for liver transplantation in pediatrics. Gut microbiota-host interplay is increasingly associated with outcomes in chronic liver disease. This study characterized fecal microbiota and fatty acid metabolites in BA.

Ecological insights into the microbiology of food using metagenomics and its potential surveillance applications.

A diverse array of micro-organisms can be found on food, including those that are pathogenic or resistant to antimicrobial drugs. Metagenomics involves extracting and sequencing the DNA of all micro-organisms on a sample, and here, we used a combination of culture and culture-independent approaches to investigate the microbial ecology of food to assess the potential application of metagenomics for the microbial surveillance of food. We cultured common foodborne pathogens and other organisms including , spp.