metagenomics

The paper characterizes the RNA virome of oysters from five continents, identifying many previously unknown viruses, including those potentially infecting vertebrates.

This study examines Arcellinida diversity across Bulgaria's ecosystems, finding that stable humidity and intermediate soil carbon stocks enhance richness, while acidic peatlands host unique taxa.

The paper examines root-associated fungal communities of white spruce trees across Alaskan treelines, finding that site and soil pH strongly influence fungal composition, while treeline effects are context-dependent and not linked to tree growth.

The paper examines microbiome instability in red flour beetles, showing ecological drift driven by environmental factors and its impact on host fitness benefits.

The paper evaluates clustering methods for multivariate longitudinal data using a real-world eCDF-Copula resampling framework to address missing data and improve benchmarking.

The paper introduces MGM2, a multimodal foundation model for microbial communities that predicts responses to interventions and interprets community changes using shared representations of molecular identity and context.

This study combines metagenome-assembled genomes and clinical genomes to reveal Acinetobacter diversity and transmission between public transport and clinical settings, identifying antibiotic resistance genes across multiple species.

This study shows the ketogenic diet does not reduce seizures or neuroinflammation in a virus-induced epilepsy mouse model, despite altering gut microbiota.

The paper uses longitudinal metagenomics to show rapid, convergent evolution in honey bee worker microbiomes despite ecological stability.

The paper introduces a latent variable mediation framework to analyze the gut microbiome's indirect effects on clinical outcomes through compositional data structures.

The paper develops classifiers to detect modified 16S rRNA sequences that pass SILVA database quality controls by using conserved motifs and achieves over 90% sensitivity and specificity.

The paper investigates how viral anti-defense systems vary with genomic traits, host immunity, and environmental stress across microbial ecosystems.

This study evaluates how different extraction methods and sequencing protocols affect nematode biodiversity metrics in soil samples.

This study shows that Schistosoma mansoni infection increases insertion sequence activity in the gut microbiome of mice, suggesting enhanced microbial genome plasticity.

This study evaluates the reliability of using wing biopsies to detect blood-borne pathogens in bats, finding lower detection rates compared to blood but still viable for initial pathogen discovery.

This study examines how soil viral communities respond to drought and recovery in an artificial rainforest, finding they are more influenced by soil heterogeneity than moisture changes.

This study investigates the gut microbiota of black soldier fly larvae, revealing a plastic midgut microbiota and a stable hindgut microbiota, with implications for their polyphagous behavior.

This study examines factors influencing gut microbiome composition and its response to a dietary intervention in a multi-ethnic cohort living in a shared environment.

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

The paper quantitatively analyzes lipid-protein interactions, showing how membrane curvature and composition influence protein association and function, and highlights new tools for studying these relationships.

The paper introduces the Ocean Microbiomics Database (OMDB) to analyze microbial thermal niches and predict their response to ocean warming, showing richness declines faster than abundance.

This paper presents a coupled strategy for enzyme discovery, evolution, and yeast chassis adaptation to improve microbial biopolymer valorisation, demonstrating it with laccases for lignin depolymerisation.

This study compares microfluidic droplet technology (MDT) with conventional plate methods (CPM) for isolating Arctic soil microbes, finding MDT significantly improves recovery rates, taxonomic richness, and evenness.

This study identifies a bacterial protease that influences phage susceptibility and links it to host epithelial responses in ulcerative colitis.

The paper quantifies chemical fluxes between gut microbiota and host by identifying measurable host parameters that influence flux magnitudes.

This study uses iNaturalist and herbarium data to show urban areas in the tropics have longer plant reproductive durations and weaker seasonality compared to rural areas.

The paper integrates holo-omic data from porcine hosts and gut microbiomes to predict host-microbiome interactions, identifying both known and novel relationships.

The paper identifies an IFN-induced PD-L1 splice variant, PD-L1Δ3, which is retained intracellularly and fails to suppress T cell activation, altering β cell immune communication in type 1 diabetes.

The paper investigates how zooplankton diversity and composition affect host-associated and environmental microbiomes, finding contrasting effects on microbiome diversity depending on host species.