The Social Microbiome. An Exploration of Bacteria in Vertical and Horizontal Systems in Humans and Baboons

Abstract

The collection of bacteria, fungi and viruses that comprise the microbiome can have large effects on the host over the course of its lifetime. Changes in microbiome composition are associated with various human diseases, including diabetes, colorectal cancer, and inflammatory bowel disease. Many factors can influence the composition of the gut microbiome, including diet, host genetics, host social interactions, and even the maternal microbiome. Here, I focus on two factors that have been shown to influence microbiome composition: maternal transmission via breast milk, and horizontal transmission via host social interactions. Although the maternal microbial contribution to the infant’s initial gut microbiome assembly has been studied extensively, with emphasis on the role of the mother’s oral, intestinal and vaginal microbiomes, the human breast milk microbiome remains largely understudied. To investigate the maternal milk microbiome taxonomic composition and functional potential in relation to the infant gut microbiome, we collected metagenomic shotgun samples from breast milk and infant stools postpartum, as part of the Mother and Infants LinKed for health (MILK) cohort. A total of 507 samples were collected from 195 healthy and gestational diabetes mother-infant pairs. Mothers with gestational diabetes and their infants did not significantly differ in terms of species composition and functional potential from healthy mother-infant pairs. Overall, the infant gut microbiome was dominated by the presence of Bifidobacteria (mostly B. longum, B. breve and B. bifidum), a pattern which is also reflected in the paired maternal milk samples. We identified both commensal and pathogenic bacterial strains that are shared between the maternal milk and the infant’s gut. Finally, we wanted to better understand the underlying dynamics of social transmission of gut microbiota. Since long-term microbiome transmission studies are impractical in humans, we turned to a longitudinal study on wild populations of baboons from Amboseli National Park, Kenya. We analyzed metagenomic shotgun sequencing samples from two baboon social groups, Mica and Viola. Preliminary results indicate that there are differences in the microbial species composition between the two social groups. With these two projects, we are able to start to disentangle the complex relationship of social connections and environmental influences on gut microbiota.