Capybaras (Hydrochoerus hydrochaeris), the world's largest rodent species native to South America, play a vital ecological role in preserving biodiversity and ecosystem health. Additionally, they hold cultural significance and serve as a food source in the Colombian plain's region. Despite their importance, little is known about the composition of their microbiota. This study aims to characterize the bacterial communities within Capybaras from the Department of Casanare. Molecular biology tools, including PCR and next-generation sequencing (NGS), were employed to explore bacterial diversity by deep sequencing the 16SrRNA gene in paired blood, hisopados bucales, and stool samples collected from two municipalities in Casanare, Colombia. Results reveal a diverse microbiota in Capybaras, with distinct genera dominating different samples. Notably, Lactobacillus prevails in hisopados bucales, Xanthomonadales in feces, and Bdellovibrionales in blood. Bacteroides, essential for digestion and immune system fortification, was consistently present across all sample types. However, the identification of potentially zoonotic pathogens—Bacillus, Clostridium, and Enterobacterales—in all samples from both municipalities raises concerns for public health. This study marks the first comprehensive analysis of Capybaras microbiota in Colombia, providing crucial insights into their health and implications for public health. The presence of potential pathogens underscores the importance of implementing preventive measures to mitigate infection risks, safeguarding both human populations and the Capybaras' well-being.
