Respiratory microbiota as a health biomarker in blue, fin and humpback whales: Pilot study in the Gulf of St-Lawrence (Québec, Canada)

1. Summary Amplicon-based profiling of airway microbiota is increasingly used to assess respiratory health in mammals, yet baseline data for free-ranging baleen whales remain scarce. We characterised the exhaled-breath (“blow”) microbiota of rorqual whales in the Gulf of St. Lawrence (Canada) and examined associations with individual health indicators. Blow samples were collected opportunistically from six whales (two blue, two fin and two humpback), with seawater and air controls. The V4 region of the 16S rRNA gene was sequenced on an Illumina MiSeq platform and processed in R (v4.5) using the DADA2 pipeline for quality filtering, denoising and amplicon sequence variant (ASV) inference. Alpha diversity varied among individuals (Shannon = 2.72 – 4.33) and beta-diversity analyses revealed a significant effect of environment (whale blow vs. seawater) on community composition (PERMANOVA: R 2 = 0.140, F = 1.31, p = 0.030). The relative abundance of pathobionts (22.8–48.8%) was negatively correlated with alpha diversity (Spearman ρ = −0.88 to −0.94, p < 0.05), while higher diversity correlated positively with good skin condition (ρ = 0.84, p = 0.03). These findings provide the first baseline description of rorqual respiratory microbiota in the Gulf of St. Lawrence and support blow microbiome metrics as non-invasive health biomarkers.