Daniel R. Mende

This study shows how a single bacterial enzyme, D4BMY8, influences the composition and metabolism of an infant gut microbial community through its preference for the HMO lacto-N-tetraose.

The paper identifies two previously unknown oral bacteria in infants and shows they co-occur and exchange nutrients through metabolic interactions.

This study shows microbiota-derived indole metabolites inhibit rotavirus infection in human infants and animal models through the AhR pathway.

The paper quantifies discoverable bacterial and archaeal diversity in metagenomes, finding many novel phyla and genera hidden in current data.

The paper evaluates metagenomic software tools using realistic datasets, highlighting improvements in assembly and taxon profiling while identifying remaining challenges in virus/archaea detection and reproducibility.

This study benchmarks phylogenetic workflows using simulated bacterial evolution, finding k-mer alignment methods are accurate alternatives to reference mapping and de novo assembly impacts accuracy.

GUNC detects and quantifies chimerism in prokaryotic genomes by analyzing contig lineage homogeneity, improving genome quality.

The paper introduces mOTUs3, a tool for reference genome-independent taxonomic profiling of metagenomes, improving accuracy and coverage for underexplored microbiomes.

The paper analyzes pigment and metatranscriptomic data to show synchronized diel patterns of phytoplankton light response across domains in the open ocean.

The paper analyzes pan-genomes of 155 prokaryotic species to assess how environmental and phylogenetic factors influence strain diversity and pan-genome features.