Metabarcoding analysis of three small ruminant flocks naturally infected by Coxiella burnetii and comparation to serological and q-PCR results.
Background: This study investigates Q fever in sheep and goats, key reservoirs for human infection, by analyzing microbiota through metabarcoding and comparing it with q-PCR and serology. Samples were collected from 26 goats and sheep (aborted and normal-delivery) and six males across three herds affected by Q fever.  Results: One sheep herd (10% abortion rate) showed 50% seropositivity but no C. burnetii detection, while the second ovine herd (40% abortion rate) showed 80% seropositivity with C. burnetii detected in three vaginal samples. In the goat herd (70% abortion), 100% of the animals were seropositive and C. burnetii was detected in 90% of the animals, where nasal and vaginal samples showed the highest frequency of detection. Metabarcoding results showed significant differences in alpha diversity with a higher richness in blood and evenness in milk from normal-delivery sheep and, higher evenness in faeces from aborted sheep. Beta diversity analyses revealed a greater richness and distinct vaginal microbiota of normal-delivery females compared to aborted. The most abundant phylum observed was Firmicutes (34.07%). The genera with the highest relative abundance were Moraxella, Mannheimia and Lactobacillus (nasal); Mycoplasma, Staphylococcus and Anaplasma (blood); Streptococcus, Pseudomonas and Staphylococcus (milk); Ureaplasma, Escherichia-Shigella, and Histophilus (vaginal); Ureaplasma, Streptobacillus, and Porphyromonas (preputial); Rikenellaceae RC9 gut group, Bacteroides and UCG-005 (faeces). Significant differences in bacterial genera and species, including increased vaginal pathogens linked to infertility, were found between females' groups, alongside the discovery of new bacterial species and tropisms. Taxonomic analysis identified the genus and the C. burnetii specie in vaginal, milk and environmental samples. Conclusion: This first report of C. burnetii in the caprine nasal cavity suggests a possible underestimated tropism and could enhance the diagnosis of Q fever. Moreover, control measures against Q fever should be implemented in the entire herd, including males and non-aborted females. Our findings contribute to understanding the negative impact of this pathogen on the microbiota of goats and sheep, which had not been previously reported, and represent a novel approach to studying infectious diseases in this sector through microbiota analysis in small ruminants and their environment.