metagenomics

The paper establishes a fecal microbiota biobank in southern Brazil and evaluates metagenomic sequencing for donor safety assessment, identifying antibiotic resistance genes in selected donors.

The paper identifies pks12 as an in vivo essential gene in Mtb by combining genomic, metabolomic, and phenotypic analyses, revealing its role in mycolyl lipid synthesis and host-pathogen interface structure.

The paper evaluates learned fungal ITS embeddings against correctly configured alignment and finds alignment performs better in open-world settings due to evaluation choices.

This paper identifies a new microalga, Desmodesmus ecotolerans, that shows superior growth and bioelectrochemical performance under low-light and variable temperature conditions for biophotovoltaic applications.

This study uses environmental predictors to predict antibiotic resistance gene occurrence in urban wastewater, achieving 78% of the predictive performance of metagenomic sequencing.

A back-splicing circRNA reporter yields linear trans-spliced artifacts; in orthogonal assays three reported cellular IRESes are inactive, and Iso-Seq 5' ends agree with nAnT-iCAGE start sites.

The paper investigates microbial community response to aeration and its cessation in a eutrophic estuary, showing shifts in community structure and dominance of algae during aeration shutdown.

This study benchmarks 16S rRNA gene analysis pipelines in high-diversity datasets, revealing trade-offs between clustering accuracy, species recovery, and abundance reconstruction.

The paper identifies global hotspots of plankton-based ecosystem services by integrating satellite data with metagenomic functions and machine learning.

This paper presents a semi-automated workflow using sequence clustering and varVAMP to design broad-range RT-qPCR primers for diverse viruses, improving representation and reducing redundancy.

The paper identifies genetic traits of low-light adapted Prochlorococcus in the Equatorial Pacific, showing loss of nitrite assimilation and use of an iron-independent HemG isoform.

The paper examines how energy quantity and quality influence biodiversity in coastal oceans, finding that high-quality energy sources support greater species richness and planktonic diversity.

This study detects and characterizes coronaviruses in rodents and bats from four European countries, identifying new viral lineages and highlighting potential zoonotic risks.

This study updates the understanding of form I-related RuBisCOs by analyzing their phylogenetic relationships and identifying a form I RuBisCO gene in an archaeal MAG, highlighting uncertainties in their evolutionary history.

The paper detects putative Cyclospora cayetanensis in wastewater metagenomic data using 31-mers, finding 3.5% of runs positive and seasonal patterns matching cyclosporiasis.

Minerva extracts RNA base-pairing, protein-contact and repeat maps from a genome language model without alignments, flagging unannotated structured loci and a phage ncRNA array reverse-transcribed into short cDNAs.

The paper examines gut microbiome changes in chronic systolic heart failure patients, linking microbiome alterations to disease severity and clinical improvement.

The paper investigates the inactivation kinetics and mechanisms of three enteric viruses in lakewater, showing differences in their decay rates and the role of microbial proteases and capsid integrity.

The paper investigates phytoplankton and giant virus dynamics during HAB events in a eutrophic mariculture area, revealing associations between phytoplankton and giant viruses and seasonal influences on their community structure.

This study analyzes microbial community changes in traditional Swiss cheese over 142 years, showing shifts linked to production practices and antibiotic use.

This study links gut microbiome features to brain development in infants using multimodal neuroimaging and metagenomics.

The paper investigates CO and H2 as energy sources for microbes in the Mariana Trench, finding higher H2 oxidation rates at depth compared to CO.

DeepCDS improves coding sequence prediction in short prokaryotic sequences using deep learning and protein language model embeddings, outperforming existing methods across various sequence lengths and error profiles.

The paper presents two LC-MS workflows using MazF endoribonuclease to characterise mRNA sequence identity, 5' capping efficiency, and poly(A) tail length and heterogeneity.

This study examines the short-term effects of BDD electrochemical treatment on wastewater effluent, showing changes in dissolved oxygen and microbial community structure without major physicochemical shifts.

The paper introduces a lossless compression algorithm for protein databases, improving memory efficiency and classification accuracy in Centrifuger for metagenomic analysis.

The paper identifies two new bat coronavirus subgenera and potential species from Neotropical bats using metatranscriptomic sequencing and phylogenetic analysis.

The paper examines how microbial community characteristics predict soil respiration across a forest-to-marsh gradient, finding that the fungal:bacterial biomass ratio is more effective than taxonomic or functional gene indicators.

π-MNovo improves de novo peptide sequencing for metaproteomics by adapting to microbial spectra and selecting candidates based on evidence, achieving higher recall than existing models.

Long-read 16S-ITS-23S tracking in 17 sow-piglet families shows maternal putative-strain sharing peaks in late lactation, which supplies most maternally derived strains persisting post-weaning.