G C A T T A C G G C A T genes Article A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity Tim McCubbin 1, R. Axayacatl Gonzalez-Garcia 1, Robin W. Palfreyman 1 , Chris Stowers 2, Lars K. Nielsen 1 and Esteban Marcellin 1,* 1 Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia;
[email protected] (T.M.);
[email protected] (R.A.G.-G.);
[email protected] (R.W.P.);
[email protected] (L.K.N.) 2 Corteva Agriscience, Indianapolis, IN 46268, USA;
[email protected] * Correspondence:
[email protected] Received: 31 July 2020; Accepted: 10 September 2020; Published: 23 September 2020 Abstract: Propionibacteria have been studied extensively since the early 1930s 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 previously hampered the acquisition of quality sequence data, the accurate annotation of the available genomes, and the functional characterization of genes. The recent completion of the genome sequences for several species has led researchers to reassess the taxonomical classification of the genus Propionibacterium, which has been divided into several new genres. Such data also enable a comparative genomic approach to annotation and provide a new opportunity to revisit our understanding of their metabolism. Using pan-genome analysis combined with the reconstruction of the first high-quality Propionibacterium genome-scale metabolic model and a pan-metabolic model of current and former members of the genus Propionibacterium, we demonstrate that despite sharing unique metabolic traits, these organisms have an unexpected diversity in central carbon metabolism and a hidden layer of metabolic complexity.