Glycoside hydrolase–mediated glucomannan catabolism in Segatella copri, a target of microbiota-directed foods for malnourished children

Evidence is emerging that perturbed postnatal gut microbiota development is causally related to childhood undernutrition. Clinical trials in undernourished Bangladeshi children found that a polysaccharide-rich, microbiota-directed complementary food (MDCF-2) designed to repair this perturbation produced superior ponderal and linear growth compared to a standard ready-to-use supplementary food. Subsequent analyses disclosed several candidate bioactive polysaccharides in the MDCF and their bacterial targets, notably strains of Segatella copri that possess carbohydrate-active enzymes (CAZymes) organized into polysaccharide utilization loci (PULs) targeting these glycans. A Bangladeshi S. copri isolate (BgF5_2) containing these PULs metabolized MDCF-2 glycans and promoted MDCF-dependent weight gain in a gnotobiotic mouse model emulating the clinical trials. Identifying prebiotic mixtures that mimic the effects of MDCF-2 would offer new options for treatment and prevention. Here, we describe a CAZyme-based approach to characterize the effects of glucomannan, a component of MDCF obtainable from sustainable sources, on growth and gene expression in S. copri BgF5_2 in vitro and in gnotobiotic mice. Biochemical characterization of purified CAZymes expressed by two of its MDCF-2 and glucomannan-targeted PULs disclosed a multifunctional GH26|GH5_4 CAZyme, inducible by glucomannan, that degrades several bioactive MDCF-2 glycans; glucomannan, arabinoxylan, xyloglucan, and mixed-linkage β-glucan. Our data suggest that this CAZyme functions as a multisubstrate “sentinel” that can produce diverse oligosaccharides from a variety of β-linked glycans, with each oligosaccharide able to induce corresponding PULs and non-PUL enzymes. This observation, plus the restricted distribution of the multifunctional CAZyme among S. copri strains, may partially explain strain responsiveness to MDCF-2.