Fig. 1

Potential sources of non-resident fungi in the gut mycobiota associated with wild animals. a Intake of non-resident fungi into an animal’s gastrointestinal tract can occur via active consumption, for example of dietary fungi or lichens, or via passive ingestion, for example of plant symbionts/pathogens, fungal spores from the environment, and/or by incidental ingestion of soil particles. b While inclusion of incidental fungi will elevate measures of alpha diversity, c the effect of inclusion of non-resident fungal sequence variant (SV) groups in analyses of beta diversity is unclear. In this hypothetical beta diversity analysis (e.g. principle coordinates analysis, PCoA) each point represents a single sample. Samples are coloured according to the host species (e.g. ‘orange’ and ‘blue’). Sample clustering pattern in the gut mycobiota associated with ‘orange’ and ‘blue’ hosts can be driven by a combination of the amount of environmental material ingested by the host and/or by variation in environmental fungal communities. Differences in sample grouping between the two ordinations illustrate the potential difficulties associated with inferring the likely causes of variation in wildlife gut mycobiota without identifying and filtering non-resident gut fungi