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Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and

Adriana Garzon1, Rafael Portillo-Gonzalez2, Gregory Habing2

  • 1Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA.

Microorganisms
|November 27, 2025
PubMed

Insights

Antimicrobial resistance (AMR) in dairy cows is complex. Hospital pens show higher AMR gene diversity, suggesting factors beyond farm antibiotic use shape the resistome.

Area of Science:

  • Veterinary Microbiology
  • Genomics
  • Public Health

Background:

  • Antimicrobial resistance (AMR) is a significant global health concern, impacting treatment efficacy.
  • Limited understanding exists regarding the dairy cattle resistome, especially in lactating cows.
  • Dairy farms are potential reservoirs for AMR genes.

Purpose of the Study:

  • To investigate the bacterial microbiome and resistome in fecal samples from lactating dairy cows across different pen types.
  • To assess the impact of antimicrobial stewardship training on AMR gene profiles.
  • To explore factors influencing AMR gene distribution in dairy cattle.

Main Methods:

  • Shotgun metagenomic sequencing of pooled fecal samples from 18 conventional dairy farms in California and Ohio.
  • Sampling across hospital, fresh, and mid-lactation pens at baseline and post-intervention.
  • Analysis of bacterial species and antimicrobial resistance (AMR) genes.

Main Results:

  • Identified 10,221 bacterial species and 345 AMR genes across 22 antimicrobial classes.
  • Hospital pens exhibited significantly higher AMR gene diversity compared to fresh and mid-lactation pens.
  • Distinct AMR gene correlation profiles were observed across pens, with fewer interactions in hospital pens.

Conclusions:

  • Farm-level antimicrobial drug use may not be the sole driver of the dairy cattle resistome.
  • Pen environment and management practices likely influence AMR gene composition.
  • Further research is needed to elucidate the complex dynamics of AMR in livestock systems.
Keywords:
antimicrobial resistancebovinemetagenomicsnext-generation sequencingresistome

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