Impact of Organic and Conventional Husbandry Systems on the Gut Microbiome and Resistome in Pigs

The gut microbiome of pigs is important for energy supply and impacts the animals' health. Additionally, the microbiota can act as a reservoir for antimicrobial resistance genes (ARG). Different husbandry systems in pig farming can influence the microbiome and the overall composition of the resistome, i.e., the complete collection of ARG. In this study, pooled fecal samples were collected repeatedly in one pig farm over a period of two years. One group of animals was kept in organic husbandry conditions with access to an outdoor run, while the other group was kept according to conventional standards. Shotgun metagenomic sequencing was performed on the samples. Additionally, E. coli isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing. Significant differences were observed in alpha and beta diversity in the microbiome between the two husbandry systems. Families enriched in the organic group included Prevotellaceae, Lachnospiraceae, and Cellulosilyticaceae, while Methanobacteriaceae showed a higher abundance in the conventional group. In the resistome, the differences were smaller, and the dominant genes were the same in both groups. However, there was a significant difference in beta diversity. In addition, the overall frequency of ARG, normalized by 16S rRNA gene content, was on average higher in the organic group. Overall, the husbandry system shaped the microbiome and-albeit to a lesser extent-the resistome in pigs from the same farm.