Highly-resolved within-species dynamics in the human facial skin microbiome

Abstract

AbstractHuman facial skin microbiomes (FSMs) on adults are dominated by just two bacterial species,Cutibacterium acnesandStaphylococcus epidermidis.Underlying this apparent simplicity, each FSM harbors multiple strains of both species whose assembly dynamics on individuals are unknown. Here, we use 4,055 isolate genomes and 360 metagenomes to trace the dynamics of strains on individuals and their transmission. Strains are shared amongst family members of all ages, but each individual harbors unique strain consortia. Strain stability changes upon formation of the adult-type FSM:S. epidermidislineage turnover slows, and the rate ofC. acnescolonization increases before stabilizing, suggesting this transitional window could facilitate engraftment of therapeutic strains. Our work reveals previously undetectable community dynamics and informs the design of therapeutic interventions.One-Sentence SummaryPreviously undetectable gain and loss of individual strains underlies the species stability of important microbiome bacteria.