Gill-associated microbiome as indicators of population stress and condition in Eastern Baltic Cod

The skin microbiome contributes to host health by facilitating pathogen exclusion, priming the immune system modulation and maintaining skin homeostasis. We examined how the composition of the skin microbiota is associated with body size and condition in two populations of eastern Baltic cod (Gadus morhua callarias), at Bornholm basin (ICES subdivision 25) and in the [A]land Sea (subdivision 29). These locations are characterized by differences in body size and experience distinct hydrographic conditions, including salinity, oxygen and temperature. We used 16s rRNA gene metabarcoding to compare skin microbiota diversity and composition in these populations. We found significant differences between the populations in both alpha and beta diversity, with higher microbial diversity observed in the [A]land cod characterized by larger body size. Moreover, we identified a greater number of significantly enriched Gene Ontology (GO) metabolic pathways in [A]land cod as compared to those from the Bornholm Basin, with many pathways absent in Bornholm. However, other GOs, such as those associated with the nervous system, were uniquely detected in the Bornholm cod. Differences in microbial communities can be influenced by external environmental factors, determined by the habitats where individual cod reside. These results indicate a potential relationship between the skin microbiome and host health; however, direct evidence for a causal impact remains limited, highlighting the importance of incorporating host skin microbiota interactions in studies of aquatic populations.