To Se or not to se: Secretor phenotype effects on milk-microbial interactions

Abstract

Bacteria in the infant gut ferment human milk oligosaccharides (HMOs), producing short-chain fatty acids (SCFA) and other metabolites, such as lactate. SCFA can be recovered as an energy source for the host. Maternal secretor status, controlled by the FUT2 (Se) gene, affects HMO production and recent data indicate maternal energetic status may also affect HMO production. Milk oligosaccharides in humans are unique in their structure and diversity. As HMOs are largely indigestible to the infant and lactation is a very costly aspect of reproduction, it is highly likely HMO production is maintained in the human lineage because of fitness benefits. While HMOs have frequently been investigated for their potential to protect infants against pathogens, their potential energetic effects via shaping the infant gut microbiome and SCFA production are largely unknown. Since FUT2 status and HMO profile vary globally, and HMO production can be influenced by maternal environment, we hypothesized milk profiles may shape the infant gut microbiome to affect infant energetic availability via metabolite production. Chapter 1 reviews what is previously known about the evolution and function of HMOs and SCFA production in humans and how they are influenced by secretor status and outlines the hypotheses this dissertation addresses. In Chapter 2, we attempted to create minimally invasive techniques for probiotic administration to mice, to inform future in vivo studies of the gut microbiome that require administration of dietary compounds. In Chapter 3, in vitro growth of six common infant gut microbes on secretor HMO was quantified and mock infant microbial communities formed from those strains were exposed to mock milk profiles representative of Malawian, Gambian, or Western United States women. Finally, in Chapter 4, mother-infant dyads were recruited from the Greater Boston area. Mother’s milk and infant fecal samples were used to assess in vitro effects on infant gut microbial communities exposed to their own mother’s milk, pooled milk from mothers of the same secretor status, and pooled milk from mothers of the opposite secretor status. Fecal samples were then pooled into secretor or non-secretor inocula based on maternal secretor status, gavaged into germ-free mice, and mice were given diets of standard infant formula or standard infant formula supplemented with a secretor HMO. Our findings repeatedly indicated that initial microbiome composition, and not HMO exposure, had the largest effect on metabolite production. However, we did find in vitro that infant microbiomes from non-secretor mothers produced the highest total SCFA when grown in their own mother’s milk, compared to pools of secretor or non-secretor milk. Infant microbiomes from secretors produced the highest SCFA when grown in pooled secretor milk, not their mother’s milk. We also found in vivo that infant microbiomes from non-secretor mothers produced increased butyrate and infant microbiomes from secretor mothers produced increased propionate and total SCFA. Additionally, we found differences in predicted functional pathway abundances for secretor and non-secretor inocula in vitro and in vivo. Together, the experiments presented in this dissertation represent the first test of a functional hypothesis that HMO variation in the human lineage based on secretor status affects infant energy acquisition via the gut microbiome. We provide plausible evidence that the FUT2 polymorphism may differentially shape the infant gut microbiome and microbial SCFA production for both energetic and immunological effects.