A snapshot of the microbiome of blood and ticks of captive cheetahs (Acinonyx jubatus) from selected conservation facilities in South Africa.

Cheetahs (Acinonyx jubatus) are listed as vulnerable on the IUCN Red List, with populations declining across their native range due to anthropogenic pressures. To support conservation, breeding programs have been established in South Africa and globally. However, captivity introduces new ecological challenges, including increased exposure to ticks and tick-borne pathogens (TBPs). Translocation of cheetahs may further facilitate the spread of pathogens, potentially affecting animal health and introducing infections into new environments. Despite these risks, little is known about the blood and tick microbial communities of captive and free-ranging cheetahs in South Africa. This study investigated the composition, abundance, taxonomic classification, of bacteria detected in captive cheetahs and associated ticks in South Africa. Full-length 16S rRNA gene sequencing was performed on samples originating from 10 adult cheetahs and 20 tick specimens representing 8 tick species from the genera Amblyomma, Haemaphysalis, Hyalomma, and Rhipicephalus across five provinces of South Africa. Sequencing was conducted using the PacBio platform, and reads were classified to genus level using the SILVA microbial database at a 99% confidence threshold. Amplicon Sequence Variant (ASV) analysis identified both known and unknown bacterial taxa, including genera harboring potential zoonotic pathogens. Proteobacteria was the dominating bacterial phylum in both the host and tick microbiota, however ticks had a larger proportion of Proteobacteria than hosts. At the genus level, the tick bacterial microbiomes were dominated by the genus Coxiella, while host microbiomes were dominated by Bacillus and Stenotrophomonas. The compositions of dominant genera in female ticks constituted a higher abundance of Coxiella and Methylobacterium-Methylorubrum compared to males. Accounting for the low-biomass nature and contamination risks of blood, resulted in the Shannon and Simpson diversity indices being significantly higher for host samples, while ticks maintained significantly higher observed ASV richness. Beta-diversity analysis further revealed significant differences in microbial community structure between hosts and ticks (p < 0.05), making sample type to be the primary factor shaping bacterial composition. In contrast, sex, province, and tick species did not significantly influence Beta-diversity. Overall, these findings highlight distinct bacterial community patterns between hosts and ticks and emphasize the importance of sample type in structuring tick-associated microbiomes and the importance of continuous surveillance and monitoring of TBPs during wildlife translocation to reduce risks to wildlife, livestock, and human health.