With flu surging again, Stephen Reicher and colleagues draw on the experience of covid-19 to argue that predictable winter pressures demand more than individual responsibility, they also require syste...

Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...

Unified strain taxonomies are needed for the epidemiological surveillance of bacterial pathogens and international communication in microbiological research. Core genome multilocus sequence typing (cg...

A man in his 50s, normally fit and well, had an ischaemic thalamic stroke confirmed on MRI, manifesting with left-sided weakness, numbness and ataxia. Admission BP was 254/150 mm Hg. All tests for sec...

Carbapenemase blaIMP genes between 1996-2023 were analysed across 4,556 genomes, revealing variant-specific epidemiologies and endemicities. Horizontal gene transfer enabled broad inter-species transm...

Nature Methods - Scikit-bio: a fundamental Python library for biological omic data analysis

An interface to compute pairwise ANI of NCBI genomes using the GTDB taxonomy.

Baked sediment, heat-shattered artefacts and introduced pyrite in a 400,000-year-old Palaeolithic occupation site in Suffolk, UK provide evidence of intentional fire-making, marking a pivotal moment i...

Abstract. The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database is a phylogenomic resource for orthology inference, evol

GigaTIME leverages multimodal AI to generate virtual multiplex immunofluorescence (mIF) profiles from standard H&E slides, enabling comprehensive tumor immune microenvironment modeling across a large ...

Real-time monitoring of metabolites in bacterial cultures is crucial for advancing our understanding of microbial physiology, metabolic fluxes, and dynamic responses to environmental changes. This capability enables researchers to capture transient metabolic states that are often missed in endpoint measurements. The use of engineered periplasmic binding proteins as biosensors for this real-time metabolite monitoring represents a groundbreaking approach. By leveraging the natural specificity and high affinity of PBPs for small molecules, these biosensors can be engineered to detect a wide range of metabolites with exceptional sensitivity and temporal resolution. The integration of PBP-based biosensors into microbial research not only enhances our ability to study real-time metabolism but also provides a versatile tool for optimizing industrial bioprocesses and exploring bacterial infections and complex microbial ecosystems

Stable carbon isotope analysis of mouse organs reveals no evidence for gut microbial essential amino acid provisioning after microbiome reconstitution as demonstrated by the nearly identical isotope p...

Here, via longitudinal metagenomic analysis of 676 fecal samples from 338 individuals in the Lifelines-DEEP study, the authors identify ongoing gene-sharing among human gut bacteria that supports comm...

Romeijn et al. reveal that horizontal transposon transfer is widespread in fungi, contributing up to 70% of transposon content in some taxa. The authors uncover thousands of events across diverse line...

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes - tseemann/abricate

Here, with metagenomic analyses on longitudinal samples collected from 195 mother-infant pairs, the authors show that the breast milk microbiome contributes to infant gut assembly through bacterial st...

PhD Project - The overlapping microbiome: ecology, function and resilience beyond species boundaries at University of Bath, listed on FindAPhD.com