Novel Method for Collecting Skin Microbiome Samples From Free‐Ranging Bottlenose Dolphin

Abstract

Cetacean skin microbiome samples are traditionally collected by swabbing the skin of captured animals or using skin tissue from remote biopsies. The effects of different sampling methods are not well understood, and factors such as swab type and storage methods may affect the microbiome. The objective of this study was to determine if samples collected by swabbing biopsied skin from bottlenose dolphins yield sufficient microbial DNA for gene sequencing, while testing if commonly used sampling and storage methods affect the skin microbiome. Skin swab samples were collected during remote biopsy surveys with either a nylon flocked swab and flash frozen with liquid nitrogen or with a cotton swab and stored in RNAlater. Sequencing of the V3–V4 region of the 16S rRNA gene revealed swabs from dolphin skin biopsies yielded sufficient DNA to characterize the microbiome. We found no significant difference between the two sampling and storage methods tested, suggesting that studies using different techniques may be comparable. This work also demonstrates a novel technique to collect samples for interpretation of the skin microbiome of free‐ranging animals. Benefits of this method are that it can be done without capture and preserves valuable and typically scarce biopsy skin samples for other analyses.

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