A RBA model for the chemostat modeling

TL;DR

This paper introduces a constraint-based genome-scale bacterial model for chemostats, replacing traditional Monod models, significantly enhancing prediction accuracy of bacterial internal states and chemostat behavior under various limiting sources.

Contribution

It extends the RBA bacterial model from batch to chemostat conditions, improving predictive capabilities and including internal bacterial states as outputs.

Findings

Enhanced prediction of chemostat behavior

Accurate modeling of bacterial internal states

Effective predictions for various limiting sources

Abstract

The purpose of this paper is to show that it is possible to replace Monod's type model of a chemostat by a constraint based model of bacteria at the genome scale. This new model is an extension of the RBA model of bacteria developed in a batch mode to the chemostat. This new model, and the associated framework, leads to a dramatic improvement in the prediction capacities of the chemostat behaviour. Indeed, for example, the internal states of the bacteria are now part of the prediction outputs and the chemostat behaviour can now be predicted for any limiting source. Finally, the first interests of this new predictive method are illustrated on a set of classic situations where predictions are already close of the well-known biological observations about chemostat. This paper is an extended version of [8] that includes a discussion on the modeling assumptions.