metagenomics

Two decades of EU pesticide substitution have not reduced impacts on stream invertebrates

This study shows that two decades of EU pesticide substitution have not reduced environmental harm to stream invertebrates, as toxic pressure and impairment remained stable over time.

TestNet-PA: Sampling-Zero-Aware Inference of Microbial Presence-Absence Networks

TestNet-PA addresses sampling zeros in microbial presence-absence networks by modeling them as structural or sampling zeros, improving FDR control and sensitivity compared to Fisher's exact test.

Residual barcode-like sequences and barcode-associated artifacts after Dorado and Barbell preprocessing of metagenomic reads

The paper evaluates Dorado and Barbell preprocessing tools for metagenomic reads, finding Barbell reduces barcode-like sequences more effectively while retaining most reads.

Hybrid RY-mers increase aDNA alignment sensitivity

This paper introduces hybrid RY-mers to improve aDNA alignment sensitivity and efficiency, showing higher accuracy and reduced runtime compared to existing methods.

CauloBrowser 2.0: an AI powered update

CauloBrowser 2.0 updates the systems-biology database for Caulobacter crescentus with AI-powered tools for querying and visualizing experimental data.

Interspecific social contacts spread gut microbiota in wild rodent communities

This study shows that social interactions between different rodent species can spread gut microbiota, with stronger transmission from wood mice to yellow-necked mice.

Continental scale genetic diversity supports geo-clustered ecoregions connectivity

The paper examines genetic diversity and connectivity between ecoregions, finding a divide between eastern and western regions with restricted gene flow in the west.

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.

Sexing carnivores from faecal metagenomes: calibrating Rx for stone marten and red fox

The paper evaluates the use of the X-to-autosome ratio (Rx) for sexing carnivores from faecal metagenomes, finding it effective above a certain read depth.

Metatranscriptomic Profiling of Viral Diversity in Aquatic Environments with a Focus on Microalgal Viruses

The paper uses metatranscriptomics to analyze viral diversity in freshwater and marine environments, identifying new RNA viruses associated with microalgae and proposing a new genus within Marnaviridae.

RoDPAA: A Robust Dissimilarity-Based Principal Angle Analysis Framework for Multi-View Microbiome Data Integration

RoDPAA integrates multi-view microbiome data using dissimilarity-based principal angle analysis, recovering shared structure in IBD cohorts where log-ratio methods failed.

High reproducibility demonstrated in a direct-to-consumer microbiome testing workflow under real-world conditions using fecal reference material

This study demonstrates high reproducibility in a DTC microbiome testing workflow using NIST fecal reference material across multiple processing steps and real-world conditions.

NanoPAMDA enables rapid PAM characterization of metagenome-derived Cas9 effectors

The paper identifies novel Cas9 orthologs from metagenomic data and develops NanoPAMDA to rapidly characterize their PAM preferences.

Wild wood mouse gut microbiota are influenced by captivity and cross-fostering

This study examines how captivity and cross-fostering affect gut microbiota in wood mice, finding that microbial diversity and functional potential shift with host history and environment.

Long-read shotgun metagenomics identifies distinct urogenital microbial community states associated with functional potential and urinary tract infection during pregnancy

This study uses long-read shotgun metagenomics to identify distinct urogenital microbial community states in pregnant women, linking them to functional potential and UTI risk.

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.

COSMOS: integrated vector-pathogen metagenomics for mosquito-borne disease

COSMOS integrates vector-pathogen metagenomics to monitor mosquito-borne diseases, detecting pathogens and mosquito communities in field samples with high accuracy.

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.

SeCAT (Sequence Consensus Amplicon Trimming): a simulation-informed Nextflow pipeline for cross-study harmonisation of 16S rRNA metabarcoding datasets

SeCAT is a Nextflow pipeline that harmonizes 16S rRNA metabarcoding datasets by identifying a consensus sequence window and testing its impact on community structure before merging datasets.

Particle-Associated Prokaryotic Community Structures in the Bering and Chukchi Seas

The paper examines particle-associated prokaryotic communities in the Bering and Chukchi Seas, finding that lifestyle and water-mass origin, not depth, structure these communities.

PLATE: a global atlas of food metaplasmidomes

PLATE provides a global resource of food metaplasmidomes, offering curated catalogs and annotations for studying plasmid diversity and function in food ecosystems.

Model-Agnostic Decomposition of the Difference in Mean Response Between Two Groups via Game-Theoretic Attribution with Minimum-Switching-Distortion Coupling

This paper introduces a model-agnostic decomposition method to analyze differences in mean response between groups, using game-theoretic attribution and optimal transport coupling.

Joint effects of climate change and urbanization accelerate plant biodiversity loss across urban green spaces

This study shows that climate change and urbanization together reduce plant biodiversity in urban green spaces, with allotments and ruderal areas being most affected.

Virus coinfection in plants determined by ecological responses to environmental heterogeneity

This study investigates virus coinfection in plants by analyzing environmental and ecological factors across multiple host species and communities, finding that most coinfections are random interactions driven by environmental responses.

HiFiTaxa: a reproducible analysis pipeline for full length 16S rRNA gene and ITS amplicon sequencing from PacBio reads

HiFiTaxa is a Nextflow pipeline for analyzing PacBio HiFi reads of 16S rRNA and ITS amplicons, offering multiple classifiers and benchmarking their performance on mock communities and holdouts.

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.

The ecological niche and seasonality of Theileria equi in Portugal

This study identifies spatio-temporal dynamics and ecological niche factors influencing Theileria equi infection in Portugal using field-surveillance data and environmental variables.

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.

A baseline for aquatic parasite diversity in West African mangroves: host-parasite records, DNA barcodes, and an experimental design for future use

This study provides the first comprehensive survey of macroparasite communities in West African mangroves, identifies new species and host records, and establishes a baseline for future ecological monitoring.