Investigating the microbiota in wildlife organisms has become increasingly important due to rising human interaction. The surge in anthropogenic activities emphasizes the need to comprehend the composition of eukaryotic microorganisms in these microbiomes, given their potential as pathogenic agents and their implications for human health. This study is specifically focused on characterizing eukaryotic microorganisms in capybaras (Hydrochoerus hydrochaeris) from Casanare, Colombia. We utilized 18 anal and 18 buccal swab samples from individuals in the municipalities of Trinidad and Paz de Ariporo. A fragment of the 18S-rRNA ribosomal gene, spanning from the hypervariable regions V4 to a portion of V7, was sequenced. Using the taxonomic assignment tool Kraken2, the presence of microorganisms such as Lomentospora prolificans, Trypanosoma cruzi, Coccidioides posadasii, Eimeria necatrix, Fonsecaea pedrosoi, Fusarium oxysporum, Neurospora crassa, Penicillium rubens, Phytophthora palmivora, Sarcocystis neurona, among others, was identified. A clear pattern of low species diversity with distinct dominance among them emerged from our analysis. The presence of these microorganisms in the examined samples is attributed to the capybara's interaction with external carrier agents and the environmental surroundings in which these animals inhabit. This taxonomic approach provides a deeper understanding of the eukaryotic microbial community associated with capybaras (H. hydrochaeris) in the region, highlighting organisms of high relevance to animal and human health. The findings confirm the role of these rodents as potential carriers of pathogenic organisms with zoonotic potential and contribute to the ecoepidemiology of wildlife organisms, especially capybaras (H. hydrochaeris).
