metagenomics

This study examines microbial community dynamics in a photobioreactor using agricultural waste gas streams, showing spatially structured communities and partial nitrogen recovery.

This study shows that timing of TGF-β blockade and material context affect matrix retention in bioprinted keratoconus stroma, with optimal regimens improving collagen retention and reducing contractile gene expression.

This study develops a synthetic cleavage module that selectively degrades pathogenic r(CUG) repeats in cells, reducing DM1-associated pathology without DNA damage.

This study investigates whether FIT samples can reveal a microbial signature of sessile serrated lesions, finding no significant differences in community structure but suggesting potential functional differences.

The paper evaluates contrastive learning on VOC-OR binding datasets, showing improved generalization and reduced performance inflation from identity leakage.

The paper identifies a new Serratia taxon in mites with genomic signs of host adaptation but phylogenetically distinct from S. symbiotica.

The paper surveys microviruses in urban freshwater environments, finding shifts in community composition from sewage to river water, with wastewater treatment plants acting as filters.

MicrobeRT is a framework of fine-tuned language models for metagenomic analysis, achieving strong performance in taxonomic classification, antibiotic resistance detection, and pathogenicity assessment.

This study evaluates Sourmash's ability to profile microbial strains from long-read metagenomes, showing accurate gene content recovery and abundance estimation.

This study examines how reduced watering affects hops growth and rhizospheric microbial communities across five cultivars, finding differential plant responses and consistent microbial associations with cultivar type.

This paper introduces PGL, a Bayesian regression method for microbiome feature selection that uses phylogenetic trees to improve detection of exposure-associated ASVs.

The paper shows that the human gut microbiota recovers to an individual-specific state after antibiotics, not to a generic healthy state.

The paper compares immune profiles and microbiomes of breast milk from mothers with different farm exposures to identify associations with immune development and atopic disease.

The paper uses graph neural networks to interpret microbial association patterns in IBD, showing that coordinated associations, not just abundance shifts, are predictive.

This study examines how host plant, season, and urbanization affect the gut microbiome of soapberry bugs, finding that host plant is the primary driver of microbial community structure.

The paper examines how bacterial and fungal biofilm communities respond to salinity gradients, finding distinct patterns in diversity and environmental drivers between the two groups.

The paper shows bacterial community composition changes consistently across hydrological network positions in freshwater systems.

This study shows that temporal changes in the phyllosphere microbiome have a greater impact on antibiotic resistance gene abundance than fungicide treatment.

This study shows that ESX-5 deletions in Mtb reduce cytokine secretion in macrophages via a post-transcriptional mechanism and alter heavy metal response genes.

The paper examines diet-oral microbiome associations using metagenomic data from 5,824 participants, finding shared microbial signatures across dietary patterns.

This study shows AP2-L is essential for Plasmodium liver-stage development by regulating PVM formation and host-cell interactions.

The paper links antimicrobial use (AMU) on dairy farms to variations in resistance gene profiles across cattle groups, showing that higher AMU correlates with increased resistance to certain drug classes.

The paper compares gut microbiomes of Yanomami populations with varying urban influence and a Belgian urban cohort, finding urban-associated features and shifts in microbial composition and function.

PARALLAX improves microbiome differential abundance analysis by addressing compositional data, uncertainty, and experimental design through a unified framework with stability-based metrics.

This study identifies blood-based biomarkers that predict early tuberculosis culture conversion by analyzing mRNA and small RNA changes during treatment.

The paper isolates and cultures bacteria from four Mediterranean corals, identifying 84 pure isolates, including novel species, to better understand their roles in the coral holobiont.

This study identifies microbial and metabolic changes across the adenoma-carcinoma sequence in colorectal cancer using 16S rRNA sequencing and metabolomic profiling.

This study investigates cognitive symptoms in post-COVID-19 condition with fatigue, finding subtle neurobiological changes not captured by standard assessments.

The paper profiles endophytic bacterial microbiomes in Ambrosia artemisiifolia L. tissues across Europe, finding tissue type shapes community structure more than region or habitat.