Humans

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new …

Proteobacteria explain significant functional variability in the human gut microbiome

BACKGROUND: While human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that …

Automated and accurate estimation of gene family abundance from shotgun metagenomes

Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw …