Models

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 …

Yeast cells can access distinct quiescent states

We conducted a phenotypic, transcriptional, metabolic, and genetic analysis of quiescence in yeast induced by starvation of prototrophic cells for one of three essential nutrients (glucose, nitrogen, or phosphate) and compared those results with …

Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations

Microbes tailor their growth rate to nutrient availability. Here, we measured, using liquid chromatography-mass spectrometry, textgreater100 intracellular metabolites in steady-state cultures of Saccharomyces cerevisiae growing at five different …