Supplementary Material for: Catabolic network of the fermentative gut bacterium Phocaeicola vulgatus (phylum Bacteroidetes) from a physiologic-proteomic perspective

Phocaeicola vulgatus (formerly Bacteroides vulgatus) is a prevalent member of human and animal guts, where it influences by its dietary fiber-fueled, fermentative metabolism the microbial community as well as the host health. To refine the current understanding of the P. vulgatus physiology, 14 different growth-supporting carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars, were selected for two major lines of investigation, which were based on substrate-adapted cells. Firstly, the range of growth performance was quantitatively assessed, revealing, e.g., doubling times [h] from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields [gCDW/mmolS] from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields [mMATP/mMC] from 0.21 (rhamnose) to 0.60 (glucuronate/xylan). Furthermore, fermentation product spectra were determined, ranging from broad and balanced (with xylan: acetate, succinate, formate, and propanoate) to rather one-sided (with rhamnose or fucose: mainly propane-1,2-diol). Secondly, based on proteogenomic analyses a fermentation network serving all tested compounds was reconstructed. This network is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate-specificity (e.g., conversion of arabinose to D-xylulose-3-phosphate) implicating a fine-tuned regulation. By contrast, central modules (e.g., glycolysis or the reaction sequence from PEP to succinate) were constitutively formed. Extensive formation of propane-1,2-diol from rhamnose and fucose involves rhamnulokinase (RhaB), rhamnulose-1-phosphate kinase (RhaD), and lactaldehyde reductase (FucO). Furthermore, sus-like systems are apparently the most relevant uptake systems and a complex array of transmembrane electron-transfer systems (e.g., Na+-pumping Rnf and Nqr complexes, fumarate reductase) as well as F- and V-type ATP-synthases were detected. Taken together, insights into the potential contribution of P. vulgatus to the gut metabolome and into the strain's biotechnological potential for sustainable production of short-chain fatty acids and alcohols are provided.