The gut microbiome and resistome of conventionally- vs. pasture-raised pigs

Abstract

Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors in lower stocking densities. Pigs in both production systems are usually fed a grain-based diet but pasture-raised pigs may also consume plants and soil. Antimicrobial use also differs with conventionally-raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai, and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally-raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally-raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their CAZyme profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1,043 dereplicated strain-level metagenome-assembled genomes ([≥] 90% completeness and <5% contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.