Quantifying cross-feeding interactions in the gut microbiome.
We introduce the Metabolite Exchange Score (MES) to quantify cross-feeding interactions among gut microorganisms and identify the interactions most affected in disease. Using constraint-based metabolic models from over 1600 individuals, MES identified and ranked metabolic interactions affected by lost cross-feeding partners in the majority of diseases analysed. Applying our analytical framework to a Crohn's disease study revealed a lack of hydrogen sulphide-consuming species as the key microbiome difference. We propose that targeting the restoration of cross-feeding interactions may be a promising strategy to restore a healthy gut ecosystem.