Microscopic fungi occupy a vast number of habitats, are taxonomically diverse, degrade complex substrates, and have stood out for their capacity to biosynthesize a plethora of specialized metabolites. Such molecules are structurally diverse, and many have applications in fundamental and applied sciences, for example, in medicine, material sciences, food chemistry, textile and pharmaceutical industries, and agronomy, among other fields. However, despite the tremendous biotechnological value of fungi, these organisms are understudied, limiting the knowledge to their taxonomy, chemistry, and some putative applications. Notably, some specific habitats remain unexplored in terms of their mycobiota. Based on these considerations, this review describes the known fungal diversity associated with ants/nests, their metabolic potential, and the possible applications of their specialized metabolites in drug discovery programs focused on developing treatments for human diseases. According to this revision, fungal diversity has been studied by applying conventional methodologies such as isolation and morphological identification of soil fungi from mounds and nest chambers, and indirectly from ants’ cuticles and glands. The subfamilies, genera, taxonomical information, and geographical origin of ants from which filamentous fungi and yeast are commonly isolated are also described. Furthermore, some important information is presented concerning the difference between the ant-associated mycobiota and that in the surroundings, discarding the extrapolation of the chemical and biological information known for soil fungi. Altogether, this review evidenced the lack of information regarding the chemical composition of ant-associated fungi, encouraging research focused on exploring the chemistry biosynthesized from ants’ mycobiota, as well as the elucidation of their allelopathic potential inside the nests.
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