A Study of the Community Relationships Between Methanotrophs and Their Satellites Using Constraint-Based Modeling Approach

Biotechnology continues to drive innovation in the production of pharmaceuticals, biofuels, and other valuable compounds, leveraging the power of microbial systems for enhanced yield and sustainability. Genome-scale metabolic (GSM) modeling has become an essential approach in this field, which enables a guide for targeting genetic modifications and the optimization of metabolic pathways for various industrial applications. While single-species GSM models have traditionally been employed to optimize strains like <i>Escherichia coli</i> and <i>Lactococcus lactis</i>, the integration of these models into community-based approaches is gaining momentum. Herein, we present a pipeline for community metabolic modeling with a user-friendly GUI, applying it to analyze interactions between <i>Methylococcus capsulatus</i>, a biotechnologically important methanotroph, and <i>Escherichia coli</i> W3110 under oxygen- and nitrogen-limited conditions. We constructed models with unmodified and homoserine-producing <i>E. coli</i> strains using the pipeline implemented in the original BioUML platform. The <i>E. coli</i> strain primarily utilized acetate from <i>M. capsulatus</i> under oxygen limitation. However, homoserine produced by <i>E. coli</i> significantly reduced acetate secretion and the community growth rate. This homoserine was taken up by <i>M. capsulatus</i>, converted to threonine, and further exchanged as amino acids. In nitrogen-limited modeling conditions, nitrate and ammonium exchanges supported the nitrogen needs, while carbon metabolism shifted to fumarate and malate, enhancing <i>E. coli</i> TCA cycle activity in both cases, with and without modifications. The presence of homoserine altered cross-feeding dynamics, boosting amino acid exchanges and increasing pyruvate availability for <i>M. capsulatus</i>. These findings suggest that homoserine production by <i>E. coli</i> optimizes resource use and has potential for enhancing microbial consortia productivity.