Characterization of a Core Fungal Community and Captivity‐Induced Gut “Mycobiome” Change in Fowler's Toad ( Anaxyrus fowleri )

ABSTRACT Amphibious animals, such as frogs, are found at the intersection of aquatic and terrestrial ecosystems. They may serve as keystone and sentinel species and play key roles in nutrient cycling and food webs. In recent decades, amphibians have experienced drastic population declines due to habitat loss, climate change, and disease. These declines have prompted investments in ex situ conservation and captive breeding programs, which aim to reduce extinction risk by creating assurance colonies and reintroducing individuals once threats are mitigated. A critical component of these programs is proper husbandry, which ensures the health and longevity of captive populations and their ability to produce offspring that can be reintroduced into the wild. The artificial environment in captivity can profoundly impact animal behavior and health, particularly in relation to diet and nutrition. Diet not only provides nutrients and energy but also shapes the host's gut microbial community, which in turn impacts digestive health. Complex microbial communities, collectively known as the microbiome, are characterized by a high diversity of prokaryotes, microscopic fungi, and viruses. The diet‐associated microbiome is increasingly studied for its role in captive animal health and behavior, although research has focused more on bacteria than fungal communities, or the “mycobiome”. Here, we investigated the core mycobiome using metabarcoding of fungal communities in 15 wild‐caught Anaxyrus fowleri (Fowler's Toad), documenting shifts as toads transitioned from wild to captive settings. We identified a core set of fungal taxa and observed distinct changes in non‐core fungi associated with dietary differences associated with captivity. The non‐core mycobiome exhibited an ecological guild functional shift of the saprotrophic dominance relative to wild individuals, indicating large losses in both mycobiome diversity and functionality. These findings highlight the dynamic nature of the amphibian mycobiome and the dramatic impact captivity can have on microbial composition, providing a framework for understanding the role of the amphibian mycobiome in future conservation efforts.