Abstract
This study investigates Q fever in sheep and goats, key reservoirs for human infection, by metabarcoding and comparing it with q-PCR and serology. Samples from 26 small ruminants (aborted and normal-delivery) and six males across three Q fever-affected herds were analyzed. In sheep herds, seropositivity was 50 and 80 % respectively, with Coxiella (C.) burnetii shedding detected vaginally in the second herd. In goats, 100 % seropositivity and 90 % C. burnetii detection were observed, with nasal and vaginal samples showing the highest detection rates. Metabarcoding revealed significant differences in alpha diversity, with greater richness in blood and evenness in milk from normal-delivery sheep and higher evenness in faeces from aborted sheep. Beta diversity showed distinct vaginal microbiota in normal-delivery females compared to aborted ones. Firmicutes was the most abundant phylum observed. Dominant genera included: Moraxella (nasal), Mycoplasma (blood), Streptococcus (milk), Ureaplasma (vaginal and preputial), Rikenellaceae RC9 gut group (faeces). Significant differences in bacterial composition, including infertility-linked vaginal pathogens, were found across female groups in all herds in the anatomical locations studied, revealing new species and tropisms. Moreover, taxonomic analysis identified C. burnetii in vaginal, milk and environmental samples. This first report of C. burnetii in the caprine nasal cavity suggests an underestimated tropism that may improve Q fever diagnosis. These findings underscore the need for herd-wide Q fever control measures, including males and normal-delivery females. Our findings contribute to new insights into the pathogen's impact on small ruminant microbiota and a novel approach to studying infectious diseases in this sector.