Identifying Prevotella copri-mediated effects of dietary glycan supplementation on microbial community and host metabolism - ABSTRACT Globally, undernutrition remains the largest source of mortality for children under five years of age. Stunting (impaired linear growth) and wasting (low weight-for-height) respectively affect 148 and 45 million children; both are associated with permanent sequelae, including impairments in immunity and neurodevelopment and susceptibility to infection. While undernutrition is preventable, existing interventions fail to prevent these long-term complications, highlighting the continuing need for treatment options. Microbiota-directed complementary food (MDCF) formulations are novel therapeutic foods that were designed to treat undernutrition by repairing delayed microbiota development observed in these children. A clinical trial of Bangladeshi children with moderate acute malnutrition demonstrated that one formulation, MDCF-2, improved weight gain compared to a standard nutritional intervention. Gnotobiotic animal studies have implicated Prevotella copri, an organism which is prevalent in non-Western populations and encodes diverse carbohydrate utilization machinery, in mediating beneficial effects of MDCF-2. In mice fed MDCF-2, P. copri colonization promotes weight gain and degradation of arabinan, an abundant glycan in MDCF-2, and shifted microbial community metabolism towards utilization of arabinose and amino acid synthesis. However, it remains unknown whether P. copri mediates MDCF-2’s growth-promoting effects through direct products of carbohydrate catabolism or other metabolic activities, and to what extent these effects depend on interactions with other organisms. The central hypothesis of this proposal is that the growth- promoting effects of MDCF-2 are mediated in part by other organisms which utilize arabinose liberated by P. copri to synthesize tryptophan and indole derivatives. To test this hypothesis, the first aim of this proposal will identify contributions of individual arabinose-utilizing organisms to differences in amino acid and microbial metabolite levels that are observed with P. copri colonization. This will involve analysis of existing metagenomic (MGX), metatranscriptomic (MTX), and mass-spectrometric datasets from mice colonized with and without P. copri, as well as validation of cross-feeding by co-culturing of P. copri and arabinose-utilizing organisms in vitro. Due to limitations of existing methods, this aim will also require development of new statistical methods for differential expression analysis of paired MGX and MTX sequencing data. To test whether dietary arabinan supplementation is sufficient to recapitulate the beneficial effects of MDCF-2, the second aim will utilize gnotobiotic mouse models to assess the effects of arabinan on host weight gain, intestinal gene expression, and microbial community composition and metabolism. Together, these studies will reveal mechanisms by which active ingredients in MDCF-2 mediate its effects, informing future therapeutics for undernutrition. They will also evolve methodology for deconvoluting functional activities of individual microbes from complex community dynamics with numerous applications beyond childhood undernutrition.
