Experimental design

Five cynomolgus macaques were included in this study to characterize their vaginal and rectal microbiota. Blood, rectal, and vaginal swabs were sampled weekly during a period of 15 weeks. Four animals were housed in the same room and one animal in another. Room controls (air swab) were performed each week to check for possible contamination or other technical biases. After DNA extraction from the swab material, the bacterial 16S rRNA gene was sequenced using primers targeting the V3 and V4 regions. Sequenced reads were preprocessed and analyzed with QIIME for OTU detection and taxonomic assignment. Statistical analyses were then performed to identify relevant taxonomies.