A glimpse into the first-ever sequenced gut microbiome of a South American wild canid : bacterial composition and antibiotic resistance genes

Abstract

The Pampa biome, located in the southern cone of South America, has been undergoing major changes due to the expansion of agriculture in the region. The Pampas fox (Lycalopex gymnocercus), a generalist-omnivorous canid, is one of the mammals that inhabits the Pampa biome. Generalist animals are generally more resistant to environmental changes and can serve as reservoirs of pathogens and vectors of zoonotic diseases. Although the species L. gymnocercus has been classified as Least Concern (LC) by the IUCN, modifications in the Pampa biome may alter its behavior, such as foraging habits, thus influencing the diet of the Pampas fox. Because they are more flexible concerning diet, they may exhibit alterations in gut bacterial diversity. In this study, we used high-throughput sequencing of 16S rRNA to characterize the bacterial composition of four pampas foxes and analyzed the presence of six antibiotic resistance genes (ARGs), aiming to give a first look into the Pampas foxes’ gut microbiome and analyze the level of anthropogenic contact. Regarding the bacterial composition, the dominant phylum observed was Proteobacteria. All samples were negative for the presence of the ARGs msr(C), blaCTX-M, and bla-TEM. Four samples presented the gene tet(M). The high abundance of Proteobacteria and the presence of tet(M) could be related to anthropic actions. Our study reinforces the importance of conducting research related to the impact of human activities on the Brazilian Pampa biome.