A network-based analysis of bacterial growth on substrate mixtures uncovers glucose inhibition in Phaeobacter inhibens

Many bacteria exhibit the remarkable ability to thrive on a diverse range of nutritional substrates. This allows them to survive in environments with a complex composition of resources, even if their total availability is low. The optimal regulation of resource usage is crucial for the ecological success in such environments. Thus, understanding its regulatory facilities can help to understand the ecological function of a microbial species. However, in a complex regulatory context, changing substrate preferences can be challenging to detect from limited experimental data without a systematic analysis. In this work, our primary objective is to introduce a method to infer potential substrate interaction networks in single-species heterotrophic bacterial cultures growing on mixed substrates. Our approach compares substrate depletion curves and can reveal the most important pairwise interdependencies between uptake and presence of substrates. We applied our method to previously published batch culture experiments with the marine bacterium Phaeobacter inhibens, where a mixture of sugars and amino acids served as the exclusive carbon source. This analysis revealed a coexistence of diauxie and co-utilization of substrates illustrating complex regulatory strategies in this bacterium. Notably, we found an inhibition of glucose uptake by the availability of other sugars, i.e., mannitol and/or N-acetylglucosamine. This contrasts the well-documented prioritization of glucose in many other bacteria.