SRA

This project collected 16S and shotgun metagenomic data from the swine food chain as part of the Circles project. The main objective was to optimize microbiome structure and circulation to improve productivity and quality in the swine food chain. The first step involved identifying the microbiota of high-performing farms. During the observational phase, 96 pigs were followed from birth until slaughter (9 months). From Site 1 (S1, farrowing unit – piglets from birth to 24±2 days of age), 4 pigs (2 males and 2 females) from 24 litters were selected. Piglets from S1 were equally allocated to two Sites 2 (S2, weaning units) and subsequently to two Sites 3 (S3, growing-finishing units). S2 and S3 were selected for their historical productivity, with good (H group) or poor (L group) scores. Fecal and environmental samples (i.e. environmental swabs, air, drinking water, soil and wastewater) were collected from pigs at six stages: 17 days (T1), 38-40 days (T2), 74-80 days (T3), 90-101 days (T4), and 272-279 days (T5), 291-298 days of life (T6, slaughterhouse). After identifying bacterial taxa associated with the H groups, two intervention trials were conducted to increase their presence. In the first intervention, the same experimental and sampling scheme was followed, with 150 pigs followed from birth to slaughter, divided into high sanitary (H) and low sanitary (L) groups, then further divided into Control (CO) and Treated (TRT) groups, with the latter receiving a diet supplemented with E. faecium, benzoic acid, and muramidase in the weaning phase and only benzoic acid during the growing-finishing period. In the second intervention, 160 piglets allocated to high sanitary (H) and low sanitary (L) weaning units were followed until the end of the weaning phase, here the control group received a standard diet, while the Treated group received a diet supplemented with chestnut extracts.