Cetacean respiratory microbiome study using UAV sampling

This project investigates the respiratory microbiome of bottlenose dolphins (Tursiops truncatus) using a non-invasive sampling method based on Unmanned Aerial Vehicles (UAVs). Exhaled breath condensate (blow) samples were collected from dolphins kept under human care using different sampling tools, including sterile shields, FTA cards, sponges, and filters, to evaluate their efficiency in capturing microbial communities. Environmental control samples (air and water) were also collected to distinguish the true respiratory microbiome from background microbial signals. DNA was extracted and the bacterial 16S rRNA gene (V3-V4 region) was amplified and sequenced on an Illumina MiSeq platform. Sequence data were processed with quality control and denoising pipelines to obtain Amplicon Sequence Variants (ASVs), and community composition was compared across sampling tools and between blow and environmental controls. The generated dataset provides the first standardized and reproducible resource for characterizing cetacean respiratory microbiomes using UAV-based non-invasive sampling. This study contributes to advancing marine mammal health monitoring by enabling minimally invasive microbial surveys, and establishes a methodological framework that can be applied in both managed and free-ranging populations.