Natural recolonization of the amphibian skin bacterial community following disruption by antibiotics

Despite the ubiquity of microbial communities, we lack a thorough understanding of how host-associated communities respond to disturbances. We explored the response of the skin bacterial communities of Notophthalmus viridescens (eastern, red-spotted newts) to disturbance by exposing newts to antibiotics, returning them to pond enclosures and assessing bacterial community composition through periodic skin swabs over 28 days. Through 16S rRNA gene amplicon sequencing and qPCR, we observed immediate shifts in bacterial abundance and community composition following antibiotic exposure. Bacterial communities recovered compositionally by the experiment’s conclusion; however, bacterial abundance did not recover to pre-exposure levels. Additionally, community composition on all newts shifted over the course of the experiment. Our results provide evidence for lasting consequences of disturbance on bacterial communities, highlight the potential disconnect between recovery in terms of community structure and bacterial abundance and emphasize the importance of incorporating natural community shifts into evaluations of community recovery.