Little is known about the development of the tonsillar microbiota and the factors determining the establishment and proliferation of disease-associated bacteria. In this study we sampled the tonsillar microbiota of 63 piglets from 21 different litters after birth and at week 1, 3, and 5 of life. The piglets were free from disease and antimicrobial treatment throughout the study period. 16S rRNA gene V3-V4 region Illumina NovaSeq sequencing produced a minimum of 42537 reads per sample after processing with DADA2. The dataset includes 252 piglet microbiota samples and 12 samples collected from unrelated sows at the same farm. Analysis revealed that a diverse tonsillar microbiota is established shortly after birth, and that gradual change takes place during the first 5 weeks of life without weaning having a large impact. We found a strong litter effect, with siblings sharing a more similar microbiota compared to non-sibling piglets. Co-housing in rooms, within which litters were housed in separate pens, also had a large impact on microbiota composition. Sow parity and pre-partum Streptococcus suis bacterin vaccination had weaker but significant associations with microbiota composition, with piglets of vaccinated sows having a lower S. suis abundance 1 week after birth.This dataset consists of 16S rRNA gene V3-V4 amplicon sequencing of tonsillar swabs of piglets. The piglets were sampled shortly after birth, at week 1, week 3, and (after being weaned at week 4), week 5. No antimicrobial treatment was applied, and all piglets were healthy; piglets that died during the experiment were not included for sequencing.

Date Submitted: 2021-11-04