R. A. Daly

Mapping the soil microbiome functions shaping wetland methane emissions

The paper maps soil microbiome functions in wetlands to understand methane emissions by analyzing microbial communities and gene expression across spatial and temporal gradients.

Time resolved multi-omics reveals diverse metabolic strategies of Salmonella during diet-induced inflammation

This study uses multi-omics to analyze Salmonella's metabolic strategies in mice on different diets over time, identifying phase-specific gene expression linked to infection stages and therapeutic targets.

Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics

This study uses genome resolved metatranscriptomics to reveal dominant nitrogen metabolisms in a warm, seasonally anoxic tropical lake, identifying key microbial taxa and functional pathways involved in nitrogen cycling.

A functional microbiome catalog crowdsourced from North American rivers

The paper creates GROWdb, a microbiome database from North American rivers, revealing microbial community structures and functional traits across watersheds.

Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream

The paper analyzes spatial and temporal metagenomic data from a wastewater-impacted river to reveal viral and microbial community dynamics and their potential roles in biogeochemical cycles.

Human-gut phages harbor sporulation genes

The paper identifies sporulation genes in human gut phages that may influence bacterial spore formation and host microbiome health.

Exposing New Taxonomic Variation with Inflammation-A Murine Model-Specific Genome Database for Gut Microbiome Researchers

The paper presents a genomic catalog of the CBA/J murine gut microbiome, revealing taxonomic and functional changes during Salmonella-induced inflammation.

Genome-resolved metaproteomics decodes the microbial and viral contributions to coupled carbon and nitrogen cycling in river sediments

The paper integrates metagenomic, metaproteomic, and metabolomic data from river sediments to uncover microbial and viral roles in carbon and nitrogen cycling, creating a genomic resource called HUM-V.

Variation in root exudate composition influences soil microbiome membership and function

This study shows that different root exudate compositions from sorghum genotypes alter soil microbial community structure and function, with implications for crop production.

Playing with FiRE: A genome resolved view of the soil microbiome responses to high severity forest wildfire

The paper analyzes soil microbiome responses to high severity wildfires using genome-resolved data, finding Actinobacteria dominance and microbial traits enhancing post-fire survival.

DRAM for distilling microbial metabolism to automate the curation of microbiome function

DRAM automates microbiome function curation by translating genomic data into microbial traits, accurately assigning metabolic roles in soil and gut communities.

Cryptic inoviruses are pervasive in bacteria and archaea across Earth's biomes

The paper identifies 10,295 inovirus-like genomes across diverse ecosystems, revealing their widespread presence and complex interactions with bacterial and archaeal hosts.