metagenomics

This study shows milk urea increases during lactation, is conserved across mammals, and supports infant gut microbiome establishment through urea-metabolizing bacteria.

This study uses multi-omics data to show that Candidatus Accumulibacter buffers transcriptional dynamics at the protein level, maintaining stable proteomes during cyclic EBPR operations.

The paper uses multi-marker DNA metabarcoding to assess parasitism rates and identify parasitoids of cabbage stem flea beetle larvae across England, revealing regional differences and novel interactions.

The paper shows cavefish have evolved unique host-microbiota interactions that support growth in nutrient-scarce environments through specific microbial metabolites.

The paper shows bacterial invasion and neutrophil immunosuppression drive adenoma progression in a porcine FAP model using single-cell RNA sequencing and spatial transcriptomics.

This study characterizes a native Heterorhabditis indica-Photorhabdus akhurstii complex and identifies virulence factors contributing to its insecticidal activity against Spodoptera species.

The paper uses large language models to discover a novel family of reverse transcriptases with tandem repeat arrays from metagenomic data.

FastaLake constructs compact metaproteomic databases from sequence resources to improve peptide identification without requiring matched metagenomic sequencing.

This study uses eDNA metabarcoding to show that bottom trawling affects prokaryotic and Animalia benthic communities, with long-term impacts on Animalia diversity and unexpected effects on community structure.

This study shows that removing rRNAs and tobamoviruses from wastewater metatranscriptomes improves detection of low-abundance viruses and pathogens.

This study uses RNA HTS to analyze the virome of Caliothrips phaseoli, identifying 18 novel viruses across multiple families.

The paper investigates the genomic diversity and metabolic traits of Fructilactobacillus isolates from honeypot ant crop microbiomes and identifies factors contributing to their dominance.

This study shows that soil-based eDNA metabarcoding can detect rare plant species and track community composition changes in grasslands, but filtering choices affect its accuracy.

Winnow-tax improves taxonomic profiling of low-coverage shotgun metagenomes by combining sensitive read-level classification with genome-level confirmation, achieving better precision-sensitivity balance than existing methods.

The paper analyzes a dairy starter microbiome with low species richness using genomic and metagenomic data to reveal hidden population complexity and phage resilience.

This study uses multi-species qPCR to identify human and animal fecal sources in Mobile Bay, finding human waste as a major contributor.

This study identifies aromatic hydrocarbon catabolic machinery in gut commensals using murine models, metaproteomics, and chemoproteomics, revealing functional differences between intestinal compartments.

The paper analyzes gut microbiome data from Vietnamese adults to show two enterotypes reflecting industrialization stages, similar to global patterns.

This study evaluates the effectiveness of nitrifying supplements containing Nitrospira and ammonia-oxidizing archaea in freshwater aquaria, showing they reduce ammonia and nitrite more effectively than conventional supplements.

This study examines how varying concentrations of PQQ affect the tobacco rhizosphere microbiome using metagenomic sequencing, revealing non-monotonic changes in taxonomic and functional profiles.

This study shows marine bacteria are attracted to fucoidan at high concentrations, suggesting it guides them to macroalgal surfaces, influencing carbon cycling.

The paper identifies two TBDTs in Marinobacter nauticus that mediate Fe-petrobactin uptake, showing distinct regulatory mechanisms and evolutionary trajectories, and demonstrates Fe-petrobactin's role in stimulating prokaryotic growth in Southern Ocean communities.

This study investigates water kefir grains as a model for microbial multicellularity, revealing an emergent growth function in multispecies biofilms.

The paper compares two viral sequencing pipelines from wastewater influent and solids, finding that solids capture more DNA viruses while influent captures more RNA viruses, with probe-capture enrichment providing comparable results across fractions.

This study evaluates phenotypic diversity in Argentine maize landraces, finding substantial variation and associations between traits and altitude.

This study examines microbiome strain sharing among zoo-housed great apes, finding that phylogenetic structure persists despite shared environments and that spore-forming bacteria may drive cross-exhibit transmission.

The paper examines Symbiodiniaceae diversity in Acropora corals on Kiritimati atoll seven years post-2015-2016 heatwave, finding low symbiont diversity and dominance by a single lineage.

The paper introduces fastEmu, a scalable method for estimating differential abundance in microbial metagenomics data, achieving faster runtime with minimal impact on error rates.

The paper compares viromes of two galaxiid fish with different life-history strategies, finding that the river-resident species has higher viral diversity than the migratory species.

This study examines how leaf damage from disease or environmental stress alters the microbiome composition and abundance in the phyllosphere of Spartina alterniflora, showing increased microbial abundance and diversity in damaged leaves.