Characterization of the Skin Microbiome of Free-Ranging Bottlenose Dolphins (Tursiops truncatus) in a Dynamic Environment Using a Novel Technique

Abstract

The objectives of this study are to determine if: 1) skin swabs from dolphin biopsy samples yield sufficient microbial DNA for 16S rRNA gene sequencing analyses, 2) the dolphin skin microbiome relates to the ambient water microbial community, 3) dolphin skin microbial community composition is affected by environmental attributes, and 4) sample handling affects DNA concentration or microbial community composition. These objectives will be answered by extracting, amplifying, sequencing, and analyzing skin swabs from biopsy samples collected from dolphins in Mobile Bay, Perdido Bay, and the Gulf of Mexico. It is hypothesized that: 1) dolphin skin biopsy swab samples will yield sufficient DNA to characterize the microbiome, differing from those in ambient water, 2) there will be variation in microbial community composition relative to environmental factors, 3) samples collected with cotton swabs and stored in RNAlater® will have different community compositions than samples that were collected with nylon flocked swabs and flash frozen in liquid nitrogen. This study tests a novel technique to analyze the skin microbiome of free-ranging animals without capture that will also preserve biopsy skin samples for additional studies. This information is important to assure the best methodology for future studies relating dolphin microbiome to ecology and health.