Interspecies malate-pyruvate shuttle drives amino acid exchange in organohalide-respiring microbial communities

Most microorganisms in the biosphere live in communities and develop coordinated metabolisms via trading metabolites. In this study, we sought to deconstruct the metabolic interdependency in the organohalide-respiring microbial communities enriched with Dehalobacter restrictus (Dhb), using a complementary approach of computational metabolic modeling and experimental validation. Dhb possesses a complete set of genes for amino acid biosynthesis yet requires amino acid supplementation. We reconciled this discrepancy using Flux Balance Analysis with consideration of cofactor availability, enzyme promiscuity, and shared protein expression patterns of several Dhb strains. Experimentally, 13C incorporation assays, growth assays, and metabolite analysis of strain PER-K23 cultures were performed to validate the model predictions. The model resolved that Dhb amino acid dependency results from restricted NADPH regeneration and diagnosed that malate supplementation can replenish intracellular NADPH using malic enzyme. Interestingly, we observed unexpected export of glutamate and pyruvate in parallel to malate consumption in the strain PER-K23 cultures. Further experiments on Dhb-enriched consortium ACT-3 suggested an interspecies malate-pyruvate shuttle between Dhb and a glutamate-auxotrophic Bacteroides sp., reminiscent of mitochondrial malate shunt pathway in eukaryotic cells. Altogether, this study reveals that redox constraints and metabolic complementarity are important driving forces for amino acid exchange in anaerobic microbial communities.