A pan-genome guided metabolic network reconstruction of five Propionibacterium species reveals extensive metabolic diversity

Abstract Background: Propionibacteria have been studied extensively since the early 1930’s due to their relevance to industry and importance as human pathogens. Still, their unique metabolism is far from fully understood. This is partly due to their signature high GC content which has hampered the acquisition of quality sequence data, the accurate annotation of the few available genomes and the functional characterization of genes. The recent completion of the genome sequences for several species enable a comparative genomic approach to annotation and provides a new opportunity to revisit our understanding of their metabolism. Results: Using pan-genome analysis combined with the reconstruction of the first high-quality Propionibacterium genome-scale metabolic model and a pan-Propionibacterium metabolic model we demonstrate that Propionibacterium have an unexpected diversity in central carbon metabolism and a hidden layer of metabolic complexity. This combined approach gave us new insights into the evolution of Propionibacterium metabolism and led us to propose a novel, putative ferredoxin-linked energy conservation strategy. The pan-genomic approach highlighted key differences in Propionibacterium metabolism that reflect adaptation to their environment. Results were mathematically captured in genome-scale metabolic reconstructions which can be used to further explore metabolism using metabolic modelling techniques. Conclusions: Overall, the data provides a platform to explore Propionibacterium metabolism and provides a tool for the rational design of strains.