Temporal Dynamics of the Vaginal Microbiome in Sows (Sus scrofa domesticus) Across Late Gestation, Farrowing, and Post-Farrowing

This project utilizes 16S rRNA gene amplicon sequencing to characterize the composition and temporal dynamics of the vaginal microbiota in healthy pregnant sows. The primary objective was to establish a baseline of microbial communities during key reproductive stages and to identify specific shifts associated with gestational age, farrowing, and the post-partum period. Vaginal swab samples were collected from a cohort of 108 Landrace x Yorkshire sows housed at the University of Guelph's Arkell Swine Research Facility. Sampling was conducted at three critical timepoints: in the final weeks of gestation (week 13), during the week of farrowing (week 16), and two weeks post-farrowing (week 18). Environmental controls, including swabs from farrowing crate walls and sterile saline, were also collected and sequenced to account for potential background contamination. The V4 hypervariable region of the 16S rRNA gene was amplified and sequenced on an Illumina MiSeq platform, generating paired-end 300bp reads. Raw sequencing data was processed using the QIIME 2 (version 2023.8) pipeline. Sequences were quality-filtered, denoised, merged, and chimera-checked using DADA2 to generate a high-resolution table of amplicon sequence variants (ASVs). Taxonomy was assigned against the SILVA 138 reference database. This dataset provides a comprehensive resource for researchers in swine reproduction, microbial ecology, and animal health. It serves as a foundational reference for future studies investigating the link between the vaginal microbiome and critical reproductive outcomes, such as offspring health and sow productivity.