Bioactive glycans in a microbiome-directed food for malnourished children
Authors: Hibberd Matthew C. , Webber Daniel M. , Rodionov Dmitry A. , Henrissat Suzanne , Chen Robert Y. , Zhou Cyrus , Lynn Hannah M. , Wang Yi , Chang Hao-Wei , Lee Evan M. , Lelwala-Guruge Janaki , Kazanov Marat D. , Arzamasov Aleksandr A. , Leyn Semen A. , Lombard Vincent , Terrapon Nicolas , Henrissat Bernard , Castillo Juan J. , Couture Garret , Bacalzo Nikita P. , Chen Ye , Lebrilla Carlito B. , Mostafa Ishita , Das Subhasish , Mahfuz Mustafa , Barratt Michael J. , Osterman Andrei L. , Ahmed Tahmeed , Gordon Jeffrey I. 
Published: August 2023

Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition1–4. Designing effective microbiome-directed therapeutic foods to repair these perturbations requires knowledge about how food components interact with the microbiome to alter its expressed functions. Here we use biospecimens from a randomized, controlled trial of a microbiome-directed complementary food prototype (MDCF-2) that produced superior rates of weight gain compared to a conventional ready-to-use supplementary food (RUSF) in 12-18-month-old Bangladeshi children with moderate acute malnutrition (MAM)4. We reconstructed 1000 bacterial genomes (metagenome-assembled genomes, MAGs) present in their fecal microbiomes, identified 75 whose abundances were positively associated with weight gain (change in weight-for-length Z score, WLZ), characterized gene expression changes in these MAGs as a function of treatment type and WLZ response, and used mass spectrometry to quantify carbohydrate structures in MDCF-2 and feces. The results reveal treatment-induced changes in expression of carbohydrate metabolic pathways in WLZ-associated MAGs. Comparing participants consuming MDCF-2 versus RUSF, and MDCF-2-treated children in the upper versus lower quartiles of WLZ responses revealed that twoPrevotella copriMAGs positively associated with WLZ were principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilization of its component glycans. Moreover, the predicted specificities of carbohydrate active enzymes expressed by polysaccharide utilization loci (PULs) in these two MAGs correlate with the (i)in vitrogrowth of BangladeshiP. copristrains, possessing differing degrees of PUL and overall genomic content similarity to these MAGs, cultured in defined medium containing different purified glycans representative of those in MDCF-2, and (ii) levels of carbohydrate structures identified in feces from clinical trial participants. In the accompanying paper5, we use a gnotobiotic mouse model colonized with age- and WLZ-associated bacterial taxa cultured from this study population, and fed diets resembling those consumed by study participants, to directly test the relationship betweenP. copri, MDCF-2 glycan metabolism, host ponderal growth responses, and intestinal gene expression and metabolism. The ability to identify bioactive glycan structures in MDCFs that are metabolized by growth-associated bacterial taxa will help guide recommendations about use of this MDCF for children with acute malnutrition representing different geographic locales and ages, as well as enable development of bioequivalent, or more efficacious, formulations composed of culturally acceptable and affordable ingredients.