metagenomics

TACTIC: hybrid denoising and clustering for robust 16S amplicon diversity estimates

The paper introduces TACTIC, a tool that combines denoising and clustering to improve 16S rRNA diversity estimates by reducing inflation caused by within-species sequence variation.

Detection of merbecoviruses in Danish bats using a novel broad-range RT-qPCR assay

The paper develops a broad-range RT-qPCR assay to detect merbecoviruses in Danish bats and identifies two new infections, including a novel lineage in Nathusius' pipistrelle.

Global distribution and host specificity of plastid-bearing microeukaryotes across coral holobionts

The paper analyzes 16S rRNA gene datasets to study the diversity and distribution of plastid-bearing microeukaryotes in corals, finding widespread symbionts and host-specific patterns.

Biogeographical context mediates land-use impacts on tropical soil multitrophic diversity

The paper examines how biogeographic context influences land-use impacts on soil multitrophic diversity in tropical dry forests, finding region-specific responses to forest-to-pasture conversion.

Differential sensitivity of k-mer based identification tools using closely related database sequences affects relative abundance estimation

This study evaluates how k-mer based tools affect abundance estimation in metagenomic data with closely related references, showing differential performance based on sample-reference distance and reference similarity.

Biome-specific genome catalogues reveal functional potential of shallow sequencing

The paper introduces BioSIFTR, a tool that uses shallow shotgun sequencing and biome-specific databases to generate accurate taxonomic and functional profiles, validated against deep sequencing data.

Fecal virome addition promotes biofilm biomass and produces distinct bacterial responses in biofilm and planktonic communities in an in vitro colon model

This study shows that adding fecal virome to an in vitro colon model increases biofilm biomass and alters bacterial community composition differently in biofilm and planktonic communities.

Single-Amplicon Sequencing of Coding-Complete Enteroviruses and Rhinoviruses Genomes from Clinical Specimens

The paper develops a single-amplicon sequencing method to recover coding-complete genomes of enteroviruses and rhinoviruses from clinical specimens, showing higher fidelity and lower cost than hybridization capture.

CPMsi: a data-driven Computational Pipeline for fast, large-scale Mass Spectrometry Imaging analysis

CPMsi is a computational pipeline that efficiently processes and integrates large-scale MSI data, enabling faster analysis and discovery of molecular patterns across tissue sections.

Gain and loss of gut symbionts during stingless bee diversification is linked to host group size

The paper investigates how group size in stingless bees influences the presence of gut symbionts, finding that larger colonies are more likely to harbor specific bacteria.

Plant microbiomes have a greater effect than plant size on flowering and growth in Asclepias syriaca

This study shows that microbiomes, not plant size, more strongly influence flowering and growth in milkweed, with leaf microbiomes predicting growth and soil microbiomes predicting flowering.

Environmental drivers of soil virus diversity across UK habitats

This study identifies soil pH and habitat type as key drivers of viral diversity and community structure in UK soils, showing strong coupling with bacterial communities.

The impact of strain heterogeneity on genomic profiling accuracy in mixed-strain Escherichia coli metagenomes

The paper evaluates how strain heterogeneity affects the accuracy of genomic profiling in mixed-strain Escherichia coli metagenomes using simulated data and various bioinformatic tools.

Molecular evidence of the eukaryotic parasites Perkinsea and Stylocephalidae in lizard muscle tissue

The paper identifies novel Alveolate parasites in lizard tissues using 18S rRNA metabarcoding and phylogenetic analysis, revealing sequences related to Stylocephalidae and Perkinsea not previously found in reptiles.

GlyEnzEA: reaction-informed enrichment of enzyme-centered glycan sets from glycomics data

GlyEnzEA constructs enzyme-specific glycan sets from glycomics data and identifies significant changes in specific enzyme groups.

Genome-resolved metagenomics reveals seasonally defined life strategies in hypersaline sediments

This study uses genome-resolved metagenomics to show that hypersaline sediments use different osmoadaptation strategies seasonally, with biosurfactant production occurring at the cell envelope rather than being secreted.

A Cis-Element in magu-2 Mediates Apical mRNA Localization via Active Transport in C. elegans

A trans-splicing model for poly(A)-tail addition during VSG mRNA maturation in Trypanosoma brucei

The paper identifies a splicing enhancer sequence that recruits factors for VSG mRNA maturation and proposes a model where polyadenylated SL RNA precursors are substrates for trans-splicing.

The microbiota of a wild butterfly species over three decades of climate change

The paper examines how climate change affects the microbiota of Glanville fritillary butterflies over 28 years, finding gradual shifts and recovery after a drought event.

An update on the mosquito fauna of Aguascalientes, Mexico: morphological and molecular identifications, host-feeding patterns, and the removal of Aedes idahoensis (Theobald) from Mexico

The paper updates the mosquito fauna of Aguascalientes, Mexico, through morphological and molecular analysis, revealing new species records and host-feeding patterns.

Benchmarking and integration of viral prediction tools to uncover viral dark matter across divergent low abundance metagenomes

The paper benchmarks viral prediction tools in low-abundance metagenomes and finds that combining tools improves viral detection while reducing false positives.

Benchmarking Microbiome Methods for Improved Metagenomic Sequencing of Lower Respiratory Tract Samples

The paper benchmarks microbiome methods to improve metagenomic sequencing of lower respiratory tract samples by optimizing DNA purification strategies.

Enhancement of gut-microbiome-based classification of prodromal Parkinson's Disease cases by hyperparameter tuning, integration of multimodal data, and meta-analysis.

This study improves classification of prodromal Parkinson's Disease using gut microbiota data and clinical features, achieving an AUC of 0.917 with integrated multimodal data.

Sex specificity of root exudates and their effects on rhizosphere microorganisms in a rare and endangered plants, Taxus cuspidata

This study compares root exudates and rhizosphere microbial communities between male and female Taxus cuspidata plants across developmental stages, revealing sex-specific differences in chemical composition and microbial diversity.

Advances in 16S Taxonomic Classification: Impacts on Species-Level Resolution of Female Bladder Microbiota

The paper evaluates updated 16S rRNA sequencing methods and databases for improved species-level classification of the urinary microbiome.

Bee phylosymbiosis: the relative importance of host phylogeny, behavioral traits, and environment

This study examines phylosymbiosis in bees, finding moderate patterns with lineage-specific microbial communities and weak ecological trait effects on microbiomes.

Innate Immune Dysregulation Precedes Clinical Onset in Neuromyelitis Optica

The paper identifies innate immune activation and CMV-specific antibody reactivity as early markers of preclinical NMOSD, preceding clinical onset by over 12 years.

Epiphytic cryptogam communities differ little despite strong variation in coastal fog exposure

The paper examines how coastal fog exposure affects epiphytic cryptogam communities and finds little variation in abundance, reproduction, and community composition despite strong microclimate differences.

A synthetic MALDI-TOF MS atlas for microbial classification across hospitals

The paper creates a synthetic MALDI-TOF MS atlas to improve microbial classification across hospitals by addressing dataset fragmentation and variability.

An optimized flow cytometry sorting-sequencing workflow reduces storage, sorting and extraction bias in sorted microbial communities

The paper optimizes a flow cytometry sorting-sequencing workflow to reduce contamination and bias in microbial community analysis.