metagenomics

The paper investigates how freshwater microbial communities influence viral inactivation, finding that specific bacterial taxa, rather than community diversity, drive differences in virus removal rates.

The paper analyzes gut microbiome metadata from the NCBI SRA to assess its structure, completeness, and reusability for large-scale studies and AI model development.

This study shows that elevated temperatures reshape phenotypic selection on plant traits and their plasticity, with effects depending on biotic interactions.

The paper investigates bacterial communities in Ae. aegypti breeding habitats and their role in oviposition behavior during arboviral outbreaks in Pune, India.

This paper designs a synthetic gene circuit that improves salt tolerance in Arabidopsis and rice by mimicking natural endodermal barriers and adding modules to mitigate adverse effects and osmotic stress.

The paper shows that voluntary exercise improves glucose tolerance in some BXD mouse strains on a high-fat diet, independent of caloric intake, and suggests gut microbiota may mediate this effect.

LOAM is a family of genomic language models trained on long-read soil metagenomes, showing competitive performance despite a small training corpus and highlighting the importance of model scale and training data composition.

The paper investigates redox distribution of Asgard archaea and co-occurring taxa in microbial mats from an early Proterozoic ecosystem analog, revealing their ecological niches and potential roles in early eukaryogenesis.

The paper identifies microbiome resilience to climate stress using network analysis of amplicon sequencing data, showing that keystone microbes and baseline network properties predict community stability.

This study tracks rhizosphere microbiome assembly in tomato plants during early development, showing inoculum-constrained succession with increased phylogenetic clustering and diversity.

The paper identifies a novel virus lineage, IME1, found in Dehalococcoides-containing cultures, characterized by features similar to filamentous bacterial viruses.

The paper analyzes human ascites fluid to identify immune dysregulation features associated with poor outcomes in cirrhosis, finding that B cell dysfunction, not microbial translocation, defines high-risk cases.

This study examines how Phytophthora cinnamomi affects avocado rhizosphere fungal communities, finding shifts in composition and potential antagonists.

MetaUmbra infers genome-level presence from metaproteomic peptides using statistical methods, accurately recovering expected genomes in benchmark tests.

This study uses eDNA metabarcoding to reconstruct trophic webs in an Arctic fjord, revealing differences between coastal and offshore domains and demonstrating the method's utility for ecosystem monitoring.

The paper identifies a molecular signature of age-related decline in vervet monkey skeletal muscle through multi-omics analysis, highlighting miRNA and epigenetic changes associated with sarcopenia.

LOL identifies phenotype-associated patterns and detects confounding factors in GEO transcriptomics data through leakage-safe preprocessing and diagnostic checks.

The paper examines Arcellinida diversity in the Peruvian Andes, finding lower abundance and diversity compared to extratropical biomes, with unique taxonomic composition shaped by elevation and canopy cover.

FAMUS improves protein annotation by using contrastive learning to compare query sequences against multiple profiles, outperforming existing tools in KEGG and PANTHER annotations.

The paper examines how dissolved organic matter (DOM) responds to temperature changes in the ocean and predicts increased diversity of thermal responses at deeper depths, potentially enhancing the deep-ocean carbon sink.

This paper presents an optimized DNA extraction protocol for adhesive samplers to enable culture-independent ITS2-based metabarcoding of fungal bioaerosols, revealing site-specific and seasonal fungal community dynamics.

The paper introduces a latent Gaussian dynamic graphical model for longitudinal non-Gaussian data, showing it can recover both contemporaneous and lag-one temporal dependence structures in microbiome data.

This paper evolves microbial strains to efficiently produce D-allulose from D-glucose, achieving a 15% yield at 30°C using engineered enzymes and a chassis strain.

The paper investigates how season and fertilization affect soil microbiome dynamics and interactions with Bdellovibrio-and-Like Organisms (BALOs) in agricultural fields.

The paper analyzes how viral infections affect microbial transcript profiles across insect species using meta-transcriptomic data, revealing host-specific and conserved patterns of virus-microbiome interactions.

This study uses lipid hydrogen stable isotope probing to estimate archaeal generation times in hot spring sediments, finding decadal-scale rates in Yellowstone and slower rates in El Tatio.

The paper develops and validates a quantitative PCR assay for detecting dugong eDNA, showing reliable performance across different environments and populations.

The paper shows that redox oscillation frequency increases antibiotic resistance gene expression in a freshwater microbial community through metabolic and ecological selection, without altering resistance gene sequences.

This paper shows that horizontally acquired mgtC genes can have different physiological roles depending on genomic and biochemical contexts in Salmonella enterica and other bacteria.

EsViritu is a viral pathogen profiler that accurately detects and reconstructs virus genomes from metagenomes with high sensitivity and specificity.