Catabolic Network of the Fermentative Gut Bacterium <i>Phocaeicola vulgatus</i> (Phylum Bacteroidota) from a Physiologic-Proteomic Perspective

Abstract

<b><i>Introduction:</i></b> <i>Phocaeicola vulgatus</i> (formerly <i>Bacteroides vulgatus</i>) 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. Moreover, the fermentative metabolism of <i>P. vulgatus</i> bears potential for a sustainable production of bulk chemicals. The aim of the present study was to refine the current understanding of the <i>P. vulgatus</i> physiology. <b><i>Methods:</i></b> <i>P. vulgatus</i> was adapted to anaerobic growth with 14 different carbohydrates, ranging from hexoses, pentoses, hemicellulose, via an uronic acid to deoxy sugars. These substrate-adapted cells formed the basis to define the growth stoichiometries by quantifying growth/fermentation parameters and to reconstruct the catabolic network by applying differential proteomics. <b><i>Results:</i></b> The determination of growth performance revealed, e.g., doubling times (h) from 1.39 (arabinose) to 14.26 (glucuronate), biomass yields (g_CDW/mmol_S) from 0.01 (fucose) to 0.27 (α-cyclodextrin), and ATP yields (m<sc>M</sc>_ATP/m<sc>M</sc>_C) 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). The fermentation network serving all tested compounds is composed of 56 proteins (all identified), with several peripheral reaction sequences formed with high substrate specificity (e.g., conversion of arabinose to <sc>d</sc>-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. <b><i>Conclusions:</i></b> The present study provides insights into the potential contribution of <i>P. vulgatus</i> to the gut metabolome and into the strain’s biotechnological potential for sustainable production of short-chain fatty acids and alcohols.