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

Citation

Holman, D.B., Gzyl, K.E., Kommadath, A. (2023). The gut microbiome and resistome of conventionally vs. pasture-raised pigs. Microbial genomics, [online] 9(7), http://dx.doi.org/10.1099/mgen.0.001061

Plain language summary

Antimicrobial use in swine production continues to be a serious concern due to its potential association with the development and persistence of antimicrobial resistance. Most commercial pigs in North America are raised indoors with high stocking densities whereas a smaller segment of the swine sector raises pigs entirely outdoors on pasture. However, very little is known about how these two management systems affect the pig gut microbial community and antimicrobial resistance. In this study we show that pigs raised outdoors on pasture have very different gut microbiomes compared to conventionally-raised pigs housed indoors and that swine management systems may have large impacts on the microbiome and antimicrobial resistance in the pig gut. Furthermore, even in the absence of direct antimicrobial exposure, the conventionally-raised pigs carried a greater abundance of antimicrobial resistance genes in their gut.

Abstract

Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. 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-l actams, macrolides-l incosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain- I evel 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.

Publication date

2023-07-01