Eukaryotic microbes that reside in the mammalian gut have an important role in maintaining metabolism, digesting nutrients, and regulating the immune system. Therefore, changes in the microbial composition of the gut may generate adverse impacts on animal health. Using high-throughput sequencing, the present study examined the fecal eukaryotic community of wild young South American (Arctocephalus australis) (n = 2) and Subantarctic fur seals (Arctocephalus tropicalis) (n = 3). The results indicated there was a distinct and diverse eukaryotic community in the fecal samples of young wild fur seals. Perhaps based on the migratory habits of certain species and the difficulty in obtaining samples, the microbiota of wild animals is poorly understood. This work reports a number of phyla and classes of microorganisms never noticed in the fecal samples of wild fur seals before and provide insight into the fecal eukaryotic community of wild young South American and Subantarctic fur seals
