Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …

Genome-scale metabolic models (GEMs) computationally describe gene-protein-reaction
associations for entire metabolic genes in an organism, and can be simulated to predict …

Genome-scale stoichiometric modeling of metabolism has become a standard systems
biology tool for modeling cellular physiology and growth. Extensions of this approach are …

Plant-associated endophytes define an important symbiotic association in nature and are
established bio-reservoirs of plant-derived natural products. Endophytes colonize the …

The importance of microbial communities (MCs) cannot be overstated. MCs underpin the
biogeochemical cycles of the earth's soil, oceans and the atmosphere, and perform …

Constraint-based reconstruction and analysis (COBRA) methods at the genome scale have
been under development since the first whole-genome sequences appeared in the mid …

High-throughput DNA sequencing has proven invaluable for investigating diverse
environmental and host-associated microbial communities. In this Review, we discuss …

Microbial communities populate most environments on earth and play a critical role in
ecology and human health. Their composition is thought to be largely shaped by …

Metabolic exchange mediates interactions among microbes, helping explain diversity in
microbial communities. As these interactions often involve a fitness cost, it is unclear how …

Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic
methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the …