Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.

Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured.

Microbial Interactions as Drivers of a Nitrification Process in a Chemostat.

This article deals with the inclusion of microbial ecology measurements such as abundances of operational taxonomic units in bioprocess modelling. The first part presents the mathematical analysis of a model that may be framed within the class of Lotka-Volterra models fitted to experimental data in a chemostat setting where a nitrification process was operated for over 500 days. The limitations and the insights of such an approach are discussed.

Insights from Microbial Transition State Theory on Monod's Affinity Constant.

Microbial transition state theory (MTS) offers a theoretically explicit mathematical model for substrate limited microbial growth. By considering a first order approximation of the MTS equation one recovers the well-known Monod's expression for growth, which was regarded as a purely empirical function. The harvest volume of a cell as defined in MTS theory can then be related to the affinity concept, giving a new physical interpretation to it, and a new way to determine its value.