Distinct Gut and Skin Microbiomes of a Carnivorous Caecilian Larva (Ichthyophis bannanicus) Show Ecological and Phylogenetic Divergence from Anuran Tadpoles

The amphibian microbiome plays a vital role in host health, yet the bacterial communities of caecilians (Order: Gymnophiona) remain largely uncharacterised. We investigated this by providing the first characterisation of the gut and skin microbiome of larval <i>Ichthyophis bannanicus</i>, a carnivorous caecilian, using 16S rRNA gene metabarcoding. Our analyses show distinct communities between the faecal samples and skin, with significant enrichment of <i>Laribacter</i> in faeces and <i>Flavobacterium</i> on skin. Despite significant variation in their community structures, the core genera <i>Escherichia-Shigella</i> were shared between both regions, suggesting similar microbial exchange in the aquatic environments. Skin bacterial diversity exhibited relatively higher richness, but lower evenness than that of faeces. Further, the skin bacterial community exhibited more complex interactions, suggesting stronger resilience to changes. The relationships and interactions of skin and faecal bacterial communities suggest their interactive effects on the host's overall health. Compared with anuran tadpoles, the <i>I. bannanicus</i> larval microbiome showed taxonomic overlap, but possessed certain unique core bacteria. This work on an understudied amphibian lineage is foundational, highlighting how diet, phylogeny, and aquatic environment shape microbial communities and informing future research into amphibian health and disease.