My Digital Gut: a tool set for microbiome-mediated precision nutrition - Pacific event

Methods that rely on flux balance analysis require a detailed knowledge of metabolism. Over the last century, extensive knowledge of central metabolism in various organisms has been accumulated. Flux balance analysis involves encoding a biochemical network into a system of equations using matrices and vectors. The stoichiometric matrix S and flux vector V are key components in this formalism. The steady state assumption is that S times V equals zero, ensuring a balance between material influx and outflux.

Constraints on fluxes can be imposed based on thermodynamics or metabolite availability, leading to constraint-based analysis or modeling. The S matrix represents a simple biochemical reaction network, with reactions metabolizing different compounds. The goal of flux balance analysis is to estimate the flux vector V, indicating the amount of mass flowing through each reaction.

Solving these high-dimensional systems to find unique solutions can be challenging. By maximizing or minimizing certain fluxes, unique solutions can be identified within the allowable space defined by the steady state assumption. In the case of biomass production maximization, the assumption is that organisms aim to grow as much as possible within given constraints.

Originally developed for a single organism, flux balance analysis has been traditionally applied in this context.