A well-balanced human dietincludes a significantintake of non-starch polysaccharides, collectively termed ‘dietary fibre’, from the cell walls of diverse fruits and vegetables1. Owing to the paucity of alimentary enzymes encoded by the human genome2, our ability to derive energy from dietary fibre depends on the saccharification and fermentation of complex carbohydrates by themassivemicrobial community residing in our distal gut3,4. The xyloglucans (XyGs) are a ubiquitous family of highly branched plant cell wall polysaccharides5,6 whose mechanism(s) of degradation in the human gut and consequent importance in nutrition have been unclear1,7,8. Here we demonstrate that a single, complex gene locus in Bacteroides ovatus confers XyG catabolism in this common colonic symbiont. Through targeted gene disruption, biochemical analysis of all predicted glycoside hydrolases and carbohydrate-binding proteins, and three-dimensional structural determination of the vanguard endo-xyloglucanase, we reveal the molecular mechanisms through which XyGs are hydrolysed to componentmonosaccharides for furthermetabolism.We also observe that orthologous XyG utilization loci (XyGULs) serve as genetic markers of XyG catabolism in Bacteroidetes, that XyGULs are restricted to a limited number of phylogenetically diverse strains, and that XyGULs are ubiquitous in surveyed human metagenomes. Our findings reveal that the metabolism of even highly abundant components of dietary fibre may bemediated by niche species,which has immediate fundamental and practical implications for gut symbiont population ecology in the context of human diet, nutrition and health9–12.
Despite our omnivory, a census of the glycoside hydrolases (GHs) encoded by the human genome indicates that our inherent ability to digest carbohydrates is restricted to starch and simple saccharides such asmalto-oligosaccharides, sucrose and lactose2 .Consequently, the human gut microbiota and its cohort of predicted carbohydrate-active enzymes are implicated in the conversion of otherwise indigestible plant polysaccharides to short-chain fatty acids2,7,13, which provide up to 10% of daily caloric intake in humans14,15, and are central to colonic heath4,9,11,16. Despite an increasing body of (meta)genomic sequence data13,17–20, the enzymatic pathways by which the most common dietary polysaccharides are digested in the human gut have not been elucidated7,13.
XyGs are widespreadin the vegetables we consume: dicot primary cell walls,for example those of lettuce, onions and tomatoes,may contain up to 25% XyG on a dry-weight basis1,5,6. The primary walls of commelinoid monocots, including the cereals, contain much lower (1–5%)—but still non-zero—amounts of XyGs1,6. Seed XyGs are also widely used as food-thickening agents and have been used as drug delivery matrices in the intestine21. This family of polysaccharides is typified by a b(1R4)-glucan main chain that is heavily substituted with pendant a(1R6)-linked xylosyl units. Depending on the species and tissue of origin, these branches may be further extended by additional monosaccharides, including galactose, fucose and/or arabinose5,22 (Fig. 1). As such, complete saccharification in the gut necessarily requires a cadre of enzymes to address the monosaccharide and linkage diversity of these complex polysaccharides.
We recently identified a polysaccharide utilization locus (PUL) in the genome of a common human gut symbiont, B. ovatus—but not in the closely related model species B. thetaiotaomicron17—that was transcriptionally upregulated in response to growth on galactoxyloglucan7. By homology with the archetypal starch utilization system (Sus) of B. thetaiotaomicron, this PUL was predicted to encode an outer membrane sugar-binding protein (SusD-like), a TonB-dependent sugar receptor/ transporter (SusC-like), and an inner membrane hybrid two-component sensor. Further analysis revealed that this PUL was also predicted to encode eight GHs from six enzymefamilies (Fig. 2),which tantalizingly suggested a collective role in XyG utilization by B. ovatus. To establish a direct causal link for growth on XyG7,8 and outline a pathway for its degradation, we performed an in-depth molecular characterization of the PUL through reverse genetics, in vitro protein biochemistry and enzymology, and structural biology.
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