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Volume 9, Issue 7

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

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 , and were relatively more abundant in the gut microbiomes of pasture-raised pigs and and 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 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-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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): antimicrobial resistance , metagenomics , pasture-raised and pigs
Funding
This study was supported by the:
  • Agriculture and Agri-Food Canada
    • Principle Award Recipient: DevinB Holman
© 2023 Crown Copyright
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2023-07-13
2024-12-02
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The gut microbiome and resistome of conventionally vs. pasture-raised pigs
M Gen 9, 001061 (2023); https://doi.org/10.1099/mgen.0.001061
/content/journal/mgen/10.1099/mgen.0.001061
/content/journal/mgen/10.1099/mgen.0.001061
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