Fungal sequences corresponding to the ITS1 and ITS2 regions were PCR amplified from all GI tract regions of both diets. A total of 256,280 sequences, clustering into 207 OTUs, were obtained from the ITS2 amplification and analysed using USEARCH. The ITS1 sequence analysis was found to be considerably less sensitive and useful for this study and the results for this region are included in supplementary information (Table S1). For the ITS2 analysis, OTUs were binned into taxonomic groupings allowing comparison of fungal community alpha diversities across tissues and diet.