Fecal Microbiome Changes Following Coccidia Infection in Black Footed Ferrets

The black-footed ferret (Mustela nigripes) is a native North American ferret species that has been endangered since 1967. Among the threats faced by M. nigripes is the eukaryotic parasite, Coccidia, which causes gastrointestinal diseases and contributes to substantial population loss. In this study, metagenomic sequencing was used to characterize the fecal microbiomes of two black-footed ferrets as the Coccidia infection progressed. The detected Coccidia species belong to the genus Cystoisospora. Although no significant changes in alpha and beta diversity were observed between the Coccidia-negative and Coccidia-positive fecal samples, distinct compositional shifts were evident. Specifically, the relative abundance of Bacteroides, Enterococcus, Fusobacterium, and Peptostreptococcus increased in the presence of Coccidia. Peptostreptococcus russellii was significantly enriched in Coccidia-positive samples, whereas several commensal and potentially beneficial bacteria were significantly depleted as the infection progressed, suggesting a shift toward gut dysbiosis and increased susceptibility to secondary bacterial infections.