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Background Bats are important long-distance dispersers of many tropical plants, yet, by consuming fruits, they may disperse not only the plant’s seeds, but also the mycobiota within those fruits. We characterized the culture-dependent and independent fungal communities in fruits of  Ficus colubrinae  and feces of  Ectophylla alba  to determine if passage through the digestive tract of bats affected the total mycobiota. Results Using presence/absence and normalized abundance data from fruits and feces, we demonstrate that the fungal communities were significantly different, even though there was an overlap of ca. 38% of Amplicon Sequence Variants (ASVs). We show that some of the fungi from fruits were also present and grew from fecal samples. Fecal fungal communities were dominated by  Agaricomycetes , followed by  Dothideomycetes ,  Sordariomycetes, Eurotiomycetes , and  Malasseziomycetes , while fruit samples were dominated by  Dothideomycetes , followed by  Sordariomycetes ,  Agaricomycetes, Eurotiomycetes , and  Laboulbeniomycetes . Linear discriminant analyses (LDA) show that, for bat feces, the indicator taxa include  Basidiomycota  (i.e.,  Agaricomycetes: Polyporales  and  Agaricales ), and the ascomycetous class  Eurotiomycetes  (i.e.,  Eurotiales ,  Aspergillaceae ). For fruits, indicator taxa are in the  Ascomycota  (i.e.,  Dothideomycetes :  Botryosphaeriales ;  Laboulbeniomycetes :  Pyxidiophorales ; and  Sordariomycetes :  Glomerellales ). In our study, the differences in fungal species composition between the two communities (fruits vs. feces) reflected on the changes in the functional diversity. For example, the core community in bat feces is constituted by saprobes and animal commensals, while that of fruits is composed mostly of phytopathogens and arthropod-associated fungi. Conclusions Our study provides the groundwork to continue disentangling the direct and indirect symbiotic relationships in an ecological network that has not received enough attention: fungi-plants-bats. Findings also suggest that the role of frugivores in plant-animal mutualistic networks may extend beyond seed dispersal: they may also promote the dispersal of potentially beneficial microbial symbionts while, for example, hindering those that can cause plant disease.

Fungal communities in feces of the frugivorous bat Ectophylla alba and its highly specialized Ficus colubrinae diet