M. Mehrshad

This study uses phylogenomic analysis of metagenome-assembled genomes to show that bacterial species rarely exist in multiple biomes and that cross-biome transitions involve proteome reorganization and gene content changes.

The paper analyzes antibiotic resistance genes in Caspian Sea metagenomes using HMM, homology alignment, and deep learning to classify ARGs by resistance category and link them to ecological strategies.

The paper investigates how dissolved organic matter (DOM) chemodiversity sustains taxonomic and functional diversity of aquatic heterotrophs across different model communities.

The paper analyzes microbial communities in the Persian Gulf along a pollution continuum, showing chronic oil exposure shifts microbial profiles and promotes oil-degrading microbes.

The paper analyzes genome size distribution across Earth's microbiomes and finds that environmental microorganisms have smaller genomes than lab-cultivated ones, with ecological and phylogenetic factors influencing genome size.

The paper analyzes the Black Sea's microbiome using genome-centric metagenomics, revealing distinct microbial communities across different water layers and their metabolic capabilities.

The paper analyzes global metagenomes to study metabolic specialization of freshwater Chlorobia, revealing widespread distribution and niche-specific adaptations.

The paper identifies a core microbiome in deep oligotrophic groundwater, showing cooperative microbial communities adapted to low-energy environments through ecological traits and partnerships.

This study uses ultra-deep metagenomics to reveal phage-centric ecological interactions in freshwater ecosystems, identifying phage genes that enhance microbial survival against grazing and showing spatiotemporal dynamics of phage and host abundances.

The paper uses phylogenetic analyses and metabolic reconstructions to infer the lifestyle and metabolic environment of the closest archaeal relatives of eukaryotes, revealing microoxic lifestyles and novel metabolic pathways.

This study uses ecogenomics to explore the evolutionary history and genome architecture of freshwater Planctomycetes, revealing niche-driven genome reduction and specialized lifestyles.

The paper examines the diversity and distribution of freshwater Chloroflexi in various pelagic habitats, revealing their genomic diversity and ecological roles.