metagenomics

Integrating Microbial Ecology and Sustainability: Linking Agricultural Waste Gas Streams to Microbial Community Shifts in a Photobioreactor

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

Material context and TGF-β blockade timing determine retained matrix in patient-derived bioprinted keratoconus stroma

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.

A Minimal Synthetic Cleavage Module Enables Selective Degradation of Pathogenic r(CUG) Repeats in Cells

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

Application of metagenomic sequencing to improve sessile serrated lesion detection using the faecal immunochemical test

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.

Contrastive Learning Improves Generalization on M2OR Olfactory Binding Dataset

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

A new Serratia taxon found in a trombidiform mite shows genomic evidence of host adaptation but is phylogenetically distinct from Serratia symbiotica

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

Unprecedented urban freshwater microviral survey highlights shift from sewage to river water communities

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: A Framework and Suite of Fine-tuned Language Models for Genomic Sequences

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

Sourmash accurately profiles strains from long-read metagenomes preserving gene content

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

Effects of Reduced Watering Regimes on Hops Growth and Rhizospheric Microbial Communities

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.

Phylogeny-Guided Global-Local Shrinkage for Microbiome Feature Selection

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

Individual-specific recovery of the healthy human gut microbiota after antibiotics

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

Farm exposure is associated with human breast milk immune profile and microbiome

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.

Interpreting graph neural networks reveals microbial association patterns in inflammatory bowel diseases

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

Host specificity, seasonality, and urbanicity shape the gut microbiome of a synanthropic insect

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.

Differing patterns in community composition and diversity of biofilm-forming bacteria and fungi along a large salinity gradient

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.

Stream and lake network position structures freshwater microbial communities across multiple catchments

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

Temporal Dynamics Outweigh Fungicide Treatment in Shaping the Turfgrass Phyllosphere Resistome

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

ESX-5 Deletions in Mycobacterium tuberculosis Alter Macrophage Cytokine Signaling and Bacterial Heavy Metal Response

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.

Population-scale dietary signatures of the oral microbiome

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

AP2-L-Dependent Processes Promote PVM Maintenance and Plasmodium Liver-stage Development

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

Antimicrobial use contributes to resistance gene enrichment across cattle groups on commercial dairy farms

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.

Comparisons among Yanomami populations reveal transitional gut microbiome configurations under urban influence

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.

Perturbation-based propagation of bacterial composition uncertainty improves robustness and reproducibility of microbiome differential abundance analysis.

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

Early tuberculosis treatment remodels blood mRNA and small RNA, and a baseline host signature is associated with early culture conversion

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

CULTURE AND ISOLATION OF BACTERIA ASSOCIATED WITH MEDITERRANEAN CORALS

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.

Integrated microbiome and metabolomic profiling reveals alterations across the adenoma-colorectal cancer sequence

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

Understanding cognitive function in post-COVID-19 condition with fatigue: an interdisciplinary multimodal investigation

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

There are cores, indicators, and differences - a high-throughput and quantitative PCR study of the Ambrosia artemisiifolia L. leaf, root, and seed endophytic bacterial microbiomes within the European invasive range

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

Most metagenomic vanT calls are not vancomycin resistance genes

The paper shows that most metagenomic vanTG gene calls are misannotations of alanine racemases, not vancomycin resistance genes.