Tissue-specific and sex-dependent microbiome structure in East African cattle ticks (Amblyomma gemma and Rhipicephalus pulchellus) and their bovine hosts.

Ticks and their vertebrate hosts share intimate ecological interactions that shape microbial community composition, with implications for tick fitness and pathogen transmission. However, the extent and specificity of tick-host microbial interactions remain poorly understood, particularly in East African tick species. Here, we characterised microbial communities across multiple tissue types from two economically important tick species (Amblyomma gemma and Rhipicephalus pulchellus) and their shared bovine host using 16S rRNA V1-V2 gene sequencing. We profiled haemolymph, midgut, salivary glands, and gonads from individual ticks (25 Am. gemma and 8 Rh. pulchellus), alongside 12 bovine blood samples. Microbiota were dominated by Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota, with Coxiella, Rickettsia, and Acinetobacter as the most abundant genera. Despite substantial taxonomic overlap, Am. gemma harboured more unique bacterial genera than Rh. pulchellus, suggesting species-specific microbial associations. Alpha and beta diversity analyses indicated distinct community structures between tick species and host blood. Tissue-level analyses revealed striking sexual dimorphism in both species: males exhibited stable microbial communities across tissues, whereas females showed strong tissue-dependent variation in richness, diversity, and composition. Co-occurrence network analyses, restricted to Am. gemma due to limited Rh. pulchellus sample size, identified sex- and tissue-specific putative keystone taxa, including Georgenia in male midguts, Serratia in female salivary glands, Enhydrobacter in ovaries, and Gemmatimonas in testes, suggesting roles in community stability. These findings highlight tissue-specific and sex-dependent factors as key determinants of tick microbial community composition, with implications for pathogen maintenance and transmission in East African livestock systems.