Comparative nasal and anal microbiomes in sympatric ringed and harbour seals: insights into host adaptation and niche differentiation

Abstract Understanding the microbiomes of marine mammals is essential to explore their health, ecological roles and responses to environmental change. We investigated the nasal and anal microbiota of two sympatric subarctic seals, the harbour seal (Phoca vitulina) and the ringed seal (Pusa hispida), using 16S rRNA gene sequencing. We analysed 34 samples (17 nasal and 17 anal), identifying 741 bacterial amplicon sequence variants. Microbial composition varied by anatomical site and host species. Anal samples were dominated by Firmicutes, while nasal samples were primarily composed of Proteobacteria, especially in harbour seals. At the genus level, Fusobacterium was markedly more abundant in ringed seals, whereas Psychrobacter and Suttonella were more common in harbour seals. Ringed seals showed higher richness in both anal and nasal microbiota. Nasal microbial composition differed significantly between species (PERMANOVA, R² = 0.23, p = 0.001). These patterns suggest distinct microbiome assemblies linked to host physiology and ecology. Our results highlight the importance of anatomical site and species identity in shaping microbial communities and provide initial data for understanding host–microbiome interactions in subarctic marine ecosystems. This study contributes to ongoing efforts to characterize wildlife-associated microbiomes and supports future work exploring their potential associations with health and disease outcomes.