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Although the pig has been introduced as an advanced animal model of genital tract infections in women, almost no knowledge exists on the porcine vaginal microbiota, especially in barrier-raised Göttingen Minipigs. In women, the vaginal microbiota plays a crucial role for a healthy vaginal environment and the fate of sexually transmitted infections such as  Chlamydia trachomatis  infections. Therefore, knowledge on the vaginal microbiota is urgently needed for the minipig model. The aim of this study was to characterize the microbiota of the anterior vagina by 16 s rRNA gene sequencing in prepubertal and sexually mature Göttingen Minipigs during an estrous cycle. The dominating phyla in the vaginal microbiota consisted of  Firmicutes, Proteobacteria ,  Actinobacteria ,  Bacteriodetes  and  Tenericutes . The most abundant bacterial families were  Enterobacteriaceae , unclassified families from  Gammaproteobacteria ,  Clostridiales  Family XI Incertae Sedis,  Paenibacillaceae ,  Lactobacillaceae ,  Ruminococcaceae  and  Syntrophaceae . We found a higher abundance of  Lactobacillaceae  in the prepubertal Göttingen Minipigs compared to sexually mature non-pregnant Göttingen Minipigs. However, correlation tests and diversity parameters revealed a very stable vaginal microbiota in the Göttingen Minipigs, both before and after sexual maturity and on different days throughout an estrous cycle. The vaginal microbiota in Göttingen Minipigs was not dominated by lactobacilli, as it is in women and according to our results the minipig vaginal microbiota is very stable, in opposite to women. These differences should be considered when using the minipig as a model of the genital tract in women.   Electronic supplementary material  The online version of this article (doi:10.1186/s13567-015-0274-0) contains supplementary material, which is available to authorized users.

The vaginal microbiome is stable in prepubertal and sexually mature Ellegaard Göttingen Minipigs throughout an estrous cycle