Cross-feeding interactions and nutrient provision revealed by metabolic modelling of a sponge microbiome

Marine sponges harbor diverse communities of microorganisms that are essential for the host survival and function. Omics analyses have in recent years described the functional diversity and potential of sponge symbionts, however it is unclear if and how they interacted with each other and the host to provide essential metabolites for growth. To address this knowledge gap, we generated and curated genome-scale metabolic model (GSMM) for 19 bacterial symbionts that account for 95 % of the community abundance in the sponge Phyllospongia foliascens. We next employed spatio-temporal resolved flux-balance analysis to the community of models using sponge-derived substrates identified by metabolomics as nutrient constraint. We identified nutrient conditions that resulted in stable community structures that reflected observed those seen in nature. Under those conditions, cross-feeding of multiple metabolites were found to be important for sustaining the community structure. The exchange of B-vitamins and amino acids also resulted in excess metabolite production potentially available for the sponge. Our analysis reveals the metabolic dependencies and interactions that are important for the symbiont community and how this can provide benefit to the host.