Mechanisms of antimicrobial resistance in biofilms.

Most bacteria in nature exist in aggregated communities known as biofilms, and cells within a biofilm demonstrate major physiological changes compared to their planktonic counterparts. Biofilms are associated with many different types of infections which can have severe impacts on patients. Infections involving a biofilm component are often chronic and highly recalcitrant to antibiotic therapy as a result of intrinsic physical factors including extracellular matrix production, low growth rates, altered antibiotic target production and efficient exchange of resistance genes.

Modelling the influence of vitamin D and probiotic supplementation on the microbiome and immune response.

The intestinal microbiota play a critical role in human health and disease, maintaining metabolic and immune/inflammatory health, synthesizing essential vitamins and amino acids and maintaining intestinal barrier integrity. The aim of this paper is to develop a mathematical model to describe the complex interactions between the microbiota, vitamin D/vitamin D receptor (VDR) pathway, epithelial barrier and immune response in order to understand better the effects of supplementation with probiotics and vitamin D. This is motivated by emerging data indicating the beneficial effects of vitamin D and probiotics individually and when combined.

The impact of Cas9-mediated mutagenesis of genes encoding potato starch-branching enzymes on starch structural properties and in vitro digestibility.

The digestibility of starch is affected by amylose content, and increasing amylopectin chain length which can be manipulated by alterations to genes encoding starch-branching enzymes (SBEs). We investigated the impact of Cas9-mediated mutagenesis of SBEs in potato on starch structural properties and digestibility. Four potato starches with edited SBE genes were tested.

Investigation of the link between first-order kinetic models of the in vitro digestion of native starches and the accompanying changes in their crystallinity and structure.

Starch is the main source of dietary energy for humans. In order to understand the mechanisms governing native starch in vitro digestion, digestion data for six starches [wheat, maize, (waxy) maize, rice, potato and pea] of different botanical sources were fitted with the most common first-order kinetic models, i.e.

Menopause and Alzheimer's disease susceptibility: Exploring the potential mechanisms.

Alzheimer's Disease (AD), responsible for 62% of all dementia cases, is a progressive neurodegenerative condition that leads to cognitive dysfunction. The prevalence of AD is consistently higher in women suggesting they are disproportionately affected by this disease. Despite this, our understanding of this female AD vulnerability remains limited.

Assessing Functional Capacity in Myalgic Encephalopathy/Chronic Fatigue Syndrome: A Patient-Informed Questionnaire.

Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is an acquired disease with significant morbidity that affects both children and adults. Post-exertional malaise is a cardinal symptom of ME/CFS and impacts a patient's functional capacity (FC). The absence of effective tools to assess FC has significant consequences for timely diagnosis, clinical follow-up, assessments for patient disability benefits, and research studies.

FdeC expression regulates motility and adhesion of the avian pathogenic Escherichia coli strain IMT5155.

Adaptation of avian pathogenic E. coli (APEC) to changing host environments including virulence factors expression is vital for disease progression. FdeC is an autotransporter adhesin that plays a role in uropathogenic Escherichia coli (UPEC) adhesion to epithelial cells.

Cancer invasion and anaerobic bacteria: new insights into mechanisms.

There is growing evidence that altered microbiota abundance of a range of specific anaerobic bacteria are associated with cancer, including spp., spp., spp.

Characterization of clumpy adhesion of to human cells and associated factors influencing antibiotic sensitivity.

Unlabelled: intestinal infection pathotypes are characterized by distinct adhesion patterns, including the recently described clumpy adhesion phenotype. Here, we identify and characterize the genetic factors contributing to the clumpy adhesion of strain 4972. In this strain, the transcriptome and proteome of adhered bacteria were found to be distinct from planktonic bacteria in the supernatant.

imputomics: web server and R package for missing values imputation in metabolomics data.

Motivation: Missing values are commonly observed in metabolomics data from mass spectrometry. Imputing them is crucial because it assures data completeness, increases the statistical power of analyses, prevents inaccurate results, and improves the quality of exploratory analysis, statistical modeling, and machine learning. Numerous Missing Value Imputation Algorithms (MVIAs) employ heuristics or statistical models to replace missing information with estimates.

Collateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control .

The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen .

Bacteriophage Taxonomy: A Continually Evolving Discipline.

While taxonomy is an often underappreciated branch of science, it serves very important roles. Bacteriophage taxonomy has evolved from a discipline based mainly on morphology, characterized by the work of David Bradley and Hans-Wolfgang Ackermann, to the sequence-based approach that is taken today. The Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) takes a holistic approach to classifying prokaryote viruses by measuring overall DNA and protein similarity and phylogeny before making decisions about the taxonomic position of a new virus.

Profiling of the Helicobacter pylori redox switch HP1021 regulon using a multi-omics approach.

The gastric human pathogen Helicobacter pylori has developed mechanisms to combat stress factors, including reactive oxygen species (ROS). Here, we present a comprehensive study on the redox switch protein HP1021 regulon combining transcriptomic, proteomic and DNA-protein interactions analyses. Our results indicate that HP1021 modulates H.

Noninvasive Fecal Cytokine and Microbiota Profiles Predict Commencement of Necrotizing Enterocolitis in a Proof-of-Concept Study.

Background And Aims: Necrotizing enterocolitis (NEC) is a life-threatening disease and the most common gastrointestinal emergency in premature infants. Accurate early diagnosis is challenging. Modified Bell's staging is routinely used to guide diagnosis, but early diagnostic signs are nonspecific, potentially leading to unobserved disease progression, which is problematic given the often rapid deterioration observed.

Genomic characterization of enterohaemolysin-encoding haemolytic of animal and human origin.

Enterohaemolysin (Ehx) and alpha-haemolysin are virulence-associated factors (VAFs) causing the haemolytic phenotype in . It has been shown that chromosomally and plasmid-encoded alpha-haemolysin are characteristic of specific pathotypes, virulence-associated factors and hosts. However, the prevalence of alpha- and enterohaemolysin does not overlap in the majority of pathotypes.

Microbial metabolites as modulators of the infant gut microbiome and host-microbial interactions in early life.

The development of infant gut microbiome is a pivotal process affecting the ecology and function of the microbiome, as well as host health. While the establishment of the infant microbiome has been of interest for decades, the focus on gut microbial metabolism and the resulting small molecules (metabolites) has been rather limited. However, technological and computational advances are now enabling researchers to profile the plethora of metabolites in the infant gut, allowing for improved understanding of how gut microbial-derived metabolites drive microbiome community structuring and host-microbial interactions.

Faecal carriage of ESBL producing and colistin resistant in avian species over a 2-year period (2017-2019) in Zimbabwe.

Introduction: Extended spectrum beta-lactamase (ESBL) producing have become widespread among food producing animals. These strains serve as a reservoir of antibiotic resistance genes (ARGs) and act as a possible source of infection to humans as transmission can occur by direct or indirect contact.

Methods: This study investigated the faecal carriage of ESBL producing and colistin resistant in poultry over a 2-year period (2017-2019) from Zimbabwe.

Effects of Far-Infrared Radiation Drying on Starch Digestibility and the Content of Bioactive Compounds in Differently Pigmented Rice Varieties.

Far infrared radiation (FIR) was applied to six rice varieties with different coloring of the pericarp (purple, red or non-pigment). Changes were determined in amylose content, in gelatinization parameters, in the content of bioactive compounds, in antioxidant activity and in the in vitro digestibility of pigmented rice as affected by FIR. The highest contents of amylose, total phenolic (TPC), total flavonoid (TFC) and total anthocyanins (TAC) were found in the purple and red varieties.

Tumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients.

Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite its significance in the promotion of CRC, genomic studies of Fusobacterium is limited. We enrolled 43 Vietnamese CRC patients and 25 participants with non-cancerous colorectal polyps to study the colonic microbiomes and genomic diversity of Fusobacterium in this population, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome analysis.

Microbiome-based interventions to modulate gut ecology and the immune system.

The gut microbiome lies at the intersection between the environment and the host, with the ability to modify host responses to disease-relevant exposures and stimuli. This is evident in how enteric microbes interact with the immune system, e.g.

Benchmarks in antimicrobial peptide prediction are biased due to the selection of negative data.

Antimicrobial peptides (AMPs) are a heterogeneous group of short polypeptides that target not only microorganisms but also viruses and cancer cells. Due to their lower selection for resistance compared with traditional antibiotics, AMPs have been attracting the ever-growing attention from researchers, including bioinformaticians. Machine learning represents the most cost-effective method for novel AMP discovery and consequently many computational tools for AMP prediction have been recently developed.

Multilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level.

Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens could identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range, and risk to human health.

Microbiomes of Urine and the Prostate Are Linked to Human Prostate Cancer Risk Groups.

Background: Bacteria play a suspected role in the development of several cancer types, and associations between the presence of particular bacteria and prostate cancer have been reported.

Objective: To provide improved characterisation of the prostate and urine microbiome and to investigate the prognostic potential of the bacteria present.

Design, Setting, And Participants: Microbiome profiles were interrogated in sample collections of patient urine (sediment microscopy: n = 318, 16S ribosomal amplicon sequencing: n = 46; and extracellular vesicle RNA-seq: n = 40) and cancer tissue (n = 204).

Bifidobacterium castoris strains isolated from wild mice show evidence of frequent host switching and diverse carbohydrate metabolism potential.

Members of the gut microbiota genus Bifidobacterium are widely distributed human and animal symbionts believed to exert beneficial effects on their hosts. However, in-depth genomic analyses of animal-associated species and strains are somewhat lacking, particularly in wild animal populations. Here, to examine patterns of host specificity and carbohydrate metabolism capacity, we sequenced whole genomes of Bifidobacterium isolated from wild-caught small mammals from two European countries (UK and Lithuania).