Association with a sea anemone alters the skin microbiome of clownfish

Host-associated microbes play important roles in animal health. Clownfish and anemones form a mutualistic relationship where external surfaces are in constant contact with one another. The effects of this mutualism on the skin mucosal microbiome of clownfish are unknown. We monitored the mucosal microbiome of the clownfish Amphiprion clarkii before, during and after association (hosting) with the anemone Entacmaea quadricolor. Microbiome composition differed significantly between hosting and non-hosting clownfish. Upon separation of clownfish from anemones, the microbiome of post-hosting fish converged to resemble that of non-hosting fish. Bacterial sequence variants that significantly distinguished hosting from non-hosting clownfish were more abundant in the anemone microbiome and that of hosting fish, compared to non-hosting fish, suggesting transfer from or enrichment by the anemone. These results show that direct contact mutualism results in significant but reversible microbiome shifts, raising questions about a potential microbial role in mediating the fish-anemone interaction.