Characterization of the Genital Microbiota in Portuguese Native Goats.

Evaluating the reproductive microbiome in small ruminant livestock, such as goats and sheep, is crucial for improving breeding performance, promoting animal health, and optimizing pregnancy outcomes. A healthy microbiome in the reproductive tract inhibits infections, regulates immune activity, and reduces the risk of microbial imbalances that negatively affect pregnancy. Understanding this microbiome also supports better disease control, informs advanced animal husbandry practices for goats and sheep, and contributes to global food security. This study aimed to characterize the genital microbiome of three local Portuguese goat breeds-Preta de Montesinho, Serrana, and Serpentina-using 16S rRNA metabarcoding. Samples were collected from 39 goats and, for comparison, seven sheep from a local breed-Serra da Estrela. Microbiome differences were obtained when integrating breed and sex factors in goats. The predominant genera in both vaginal and preputial samples included Fusobacterium, Aerococcus, Corynebacterium, Sediminibacterium, Campylobacter, and Ralstonia. Significant compositional differences were observed across breed, sex, and species as indicated by Bray-Curtis dissimilarity. By characterizing the caprine reproductive microbiota through metabarcoding, this study fills an important knowledge gap and establishes a baseline for future research on disease-associated changes in the male and female urogenital tract microbiota of small ruminants.