The taxonomic composition of the microbial community varied across tissue type and diet (Figure 2, Figure 3 and Figure S1). Figure 3 provides visualisation of fungal OTUs unique to each fish GI tract region and those that were shared between two or more regions. Different OTUs were detected within each region of each fish, but the core microbiome of the fish is dominated by sequences with high similarity to Sordariomycetes and Dothideomycetes in all regions with the former more prevalent in the midgut and hindgut of the mixed-diet fed fish and the latter dominated in the midgut and hindgut of the wood-diet fed fish (Figure 3). Sequences with high sequence similarity to Fusarium oxysporum were the major OTUs detected in all tissue regions, except the wood-fed hindgut, which was dominated by sequences similar to Cirrenalia macrocephala. Other sequences present throughout the GI tracts of both dietary regimens included Aureobasidium pullulans and Debaryomyces prosopidis (both more abundant in wood-fed fish), and Malassezia restricta.