Title: Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin
Author: Wei Zhou, Michelle Spoto, Rachel Hardy, Changhui Guan, Elizabeth Fleming, Peter J. Larson, Joseph S. Brown, Julia Oh
Issue&Volume: January 30, 2020
Abstract: Metagenomic inferences of bacterial strain diversity and infectious disease transmissionstudies largely assume a dominant, within-individual haplotype. We hypothesize thatwithin-individual bacterial population diversity is critical for homeostasis of ahealthy microbiome and infection risk. We characterized the evolutionary trajectoryand functional distribution of Staphylococcus epidermidis—a keystone skin microbe and opportunistic pathogen. Analyzing 1,482 S. epidermidis genomes from 5 healthy individuals, we found that skin S. epidermidis isolates coalesce into multiple founder lineages rather than a single colonizer.Transmission events, natural selection, and pervasive horizontal gene transfer resultin population admixture within skin sites and dissemination of antibiotic resistancegenes within-individual. We provide experimental evidence for how admixture can modulatevirulence and metabolism. Leveraging data on the contextual microbiome, we assesshow interspecies interactions can shape genetic diversity and mobile gene elements.Our study provides insights into how within-individual evolution of human skin microbesshapes their functional diversification.