In their natural environment, plants are part of a rich ecosystem including numerous and
diverse microorganisms in the soil. It has been long recognized that some of these microbes …

The rumen is a complex ecosystem composed of anaerobic bacteria, protozoa, fungi,
methanogenic archaea and phages. These microbes interact closely to breakdown plant …

Genome-scale metabolic models are mathematically-structured knowledge bases that can
be used to predict metabolic pathway usage and growth phenotypes. Furthermore, they can …

Since the first two complete bacterial genome sequences were published in 1995, the
science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is …

Biological entities are involved in intricate and complex interactions, in which uncovering the
biological information from the network concepts are of great significance. Benefiting from …

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

The prediction of cellular function from a genotype is a fundamental goal in biology. For
metabolism, constraint-based modelling methods systematize biochemical, genetic and …

Precise control over microbial cell growth conditions could enable detection of minute
phenotypic changes, which would improve our understanding of how genotypes are shaped …

Background Several genome-scale metabolic reconstruction software platforms have been
developed and are being continuously updated. These tools have been widely applied to …

FBA has limitations, however. Because it does not use kinetic parameters, it cannot predict
metabolite concentrations. It is also only suitable for determining fluxes at steady state …