Investigating the mechanism of dietary fibre breakdown by the human and animal gut microbiota

Abstract

The intestinal tracts of mammalian species are inhabited by a complex community of microbes, known collectively as the gut microbiota. Many bacterial members of the gut microbiota play an important role in the degradation of complex dietary carbohydrates. Hemicelluloses are plant polysaccharides, often degraded by the gut microbiota; however these are generally tightly associated with cellulose, which is more recalcitrant to breakdown. Xylans are amongst the most abundant hemicelluloses within the human and animal diet. Here, we initially investigated the xylan-degrading capabilities of members of the Bacteroidota phylum and show that ability to utilise different types of xylan is widespread but not ubiquitous. Furthermore, we demonstrate the ability to bioinformatically predict xylan utilisation capabilities for gut Bacteroidota. Highly decorated xylans, such as those from cereal brans, are generally recalcitrant to breakdown by endoxylanases but have previously been shown to be cleaved by a GH98 enzyme from the human gut symbiont Bacteroides ovatus. GH98 enzymes have also been shown to be β1,4-galactosidases targeting blood group sugars. Here we present structural and functional studies into Bo98 endoxylanase to investigate the mechanism of complex cereal xylan targeting by this enzyme and reveal how the same family can possess specificity for both xylans and blood group sugars. We also show that that other gut and non-gut derived GH98 enzymes display the same specificity as Bo98. Furthermore, these GH98 endoxylanases possess a conserved CBM35 domain, which we show is a functional carbohydrate binding protein, recognising a range of arabinose-containing hemicelluloses at a novel binding site for the family. Finally, we show that human gut Bacillota Ruminococcus champanellensis is capable of growth on cellulose and a whole corn cell wall substrate. We present plans for future experiments examining gene upregulation during growth on these substrates. These data will provide insights into the plant cell wall degrading strategy of this keystone Bacillota from the human gut. This investigation demonstrates that members of the gut microbiota have developed diverse glycan utilising strategies and preferences, allowing survival of individual species in a highly populated ecological niche