Abstract
Cats are essential companions to humans, offering emotional support while potentially harboring infectious agents. Understanding the gut microbiota of domestic cats (Felis catus) is critical for advancing feline health and examining environmental influences on microbial composition. This study utilized 16S and 18S rRNA sequencing to investigate bacterial and eukaryotic communities in the feces of 30 cats from two Colombian regions: urban Bogotá and rural Boyacá. Key bacterial taxa included Collinsella, Bifidobacterium, and Alloprevotella in Bogotá, while Romboutsia, Clostridium sensu stricto 1, and Turicibacter predominated in Boyacá. Similarly, fungal genera such as Candida and Malassezia were prevalent across all samples, with geographic variations observed for Blastocystis, which was more abundant in Bogotá, and Pseudomonocystis, which dominated Boyacá. Despite no significant clustering in alpha‑ and beta‑diversity analyses, subtle shifts in the relative abundance of specific taxa were observed and are hypothesized to be influenced by differences in lifestyle and diet, with urban cats tending to remain indoors and consume commercial feeds, while rural cats often scavenge or consume human food. This work also highlights the value of 18S rRNA analysis in characterizing microeukaryotic communities, providing foundational insights into the interactions between feline microbiota and their environments. This study delineates the gut microbiota composition of healthy cats, providing a valuable reference for future feline health research.