metagenomics

This study investigates host-microbiota interactions during bovine respiratory disease, finding that antimicrobial treatment has a greater impact on microbial communities and metabolic functions than infection alone.

The study examines URT microbiome features linked to S. pneumoniae colonisation in older children in The Gambia, identifying microbial associations and environmental factors influencing colonisation.

The paper uses shotgun metagenomic sequencing to compare bacterial communities in plaque, saliva, and tumor samples from OSCC patients and healthy controls, identifying distinct microbial profiles.

The paper compares insect biodiversity captured from different environmental substrates and finds they represent complementary aspects of biodiversity rather than equivalent ones.

This study shows compost application changes soil and rhizosphere microbial communities but does not affect plant resistance to aphids, highlighting the disconnect between community structure and functional outcomes.

LGTM couples a neural topic model with additive basis-function Gaussian processes, learning microbial co-abundance topics and how covariates relate to their trajectories in longitudinal gut microbiome data.

SCiMS predicts host chromosomal sex from metagenomic data, outperforming existing tools at low host coverage and across species.

This study tracks SARSr-CoV evolution in Rhinolophus bats over 10 years, revealing host factors driving viral diversification and adaptation.

This study shows that targeting catecholate siderophore systems reduces AIEC colonization in colitis by immunization, preserving gut microbiome composition.

The paper characterizes viral communities in urban waterfowl across New Zealand, finding widespread viral diversity and connectivity despite geographic distance.

The paper analyzes microbial community structure and phosphorus deficiency in a sediment core from Poza Roja 2, revealing compositional zones and extreme nutrient ratios.

This study compares oral and gut microbiomes in HIV patients and finds oral bacteria like Veillonella parvula contribute to systemic inflammation through epithelial barrier disruption and monocyte activation.

This paper identifies VCB1, a novel ACLY inhibitor, which overcomes TKI resistance in lymphoma by disrupting lipid and nucleotide metabolism, ISR, and redox homeostasis.

This study shows that floral visitation patterns do not fully reflect resource allocation to offspring in bees, revealing hidden resource-specific foraging strategies.

CHAIR provides an antigen-resolved immune resource for healthy adult aging by integrating PhIP-seq, clinical data, and immune phenotyping across multiple age groups.

The paper introduces π-MSNet, a large-scale proteomics dataset for AI training and benchmarking, showing performance improvements when models are retrained on it.

The paper investigates phage activity during vegetable fermentation and shows phages influence bacterial succession without disrupting fermentation stability.

StrainSpy fits zero-inflated beta mixed models to containment ANI, reaching >98% simulated sensitivity versus ~79% for logistic regression and detecting colorectal-cancer E. coli strain shifts.

This study shows mitochondrial dysfunction accelerates aging by disrupting gut microbiota structure and inducing immune dysregulation and inflammation through metabolic reprogramming.

The paper examines microbial community variability in Singapore Strait waters, showing that particle association and monsoon seasons shape bacterioplankton composition across different size fractions.

This paper shows that combining oral and gut microbiome data reveals complementary age-related signatures, detected through SHAP-based site attribution, despite no overall accuracy improvement.

The paper identifies rare Bacillus cereus group species in unassembled metagenomic samples, revealing their potential geographic distribution and genomic diversity.

This study evaluates how respiratory tract sampling methods affect inferred microbiome structure and identifies bronchial brushing as yielding a distinct but low-biomass microbial signal.

This study identifies bacterial NDH-1 as a target of metformin, showing it inhibits bacterial growth and carbohydrate fermentation, with implications for metformin's antidiabetic effects.

This study uses untargeted sequencing to analyze population genetics and pathogen surveillance in timber rattlesnakes, finding genetic distinctness and a color variation locus linked to ALDH4A1.

The paper shows that codon usage bias in metabolism-related genes reflects microbial adaptation to temperature and nutrient regimes in ocean communities.

The paper tests synthetic microbial communities on radish seeds to protect against a fungal pathogen, finding that multi-kingdom communities provide the best protection.

The paper tracks gene flow in the gut microbiome, showing diet and community ecology influence phage activation and horizontal gene transfer.