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Microorganisms
Volume 13
Issue 11
10.3390/microorganisms13112641
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Article

Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms

by
Adriana Garzon
1,
Rafael Portillo-Gonzalez
2,
Gregory Habing
2,
Bart C. Weimer
1,3,*,
Cory Schlesener
1,3,
Noelia Silva-del-Rio
1,4,
Betsy M. Karle
5,
Craig Miramontes
1 and
Richard V. Pereira
1,*
1
Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
2
Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210, USA
3
100K Pathogen Genome Project, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
4
Veterinary Medicine Teaching and Research Center, School of Veterinary Medicine, University of California, Tulare, CA 93274, USA
5
Cooperative Extension, Division of Agriculture and Natural Resources, University of California, Orland, CA 95963, USA
*
Authors to whom correspondence should be addressed.
Microorganisms 2025, 13(11), 2641; https://doi.org/10.3390/microorganisms13112641 (registering DOI)
Submission received: 30 September 2025 / Revised: 18 November 2025 / Accepted: 18 November 2025 / Published: 20 November 2025
(This article belongs to the Section Microbiomes)
Versions Notes

Abstract

Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Pooled fecal pat samples were collected as part of a larger field study using a quasi-experimental design that assigned farms to the training intervention group (six per state) or the control group (three per state). For the training intervention group, farm worker(s), identified as having the task of diagnosing and treating adult cows on the farm, participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 months after the intervention was completed on each participating farm (n = 18). A total of 10,221 bacterial species and 345 AMR genes conferring resistance to 22 antimicrobial classes were identified. The hospital pen exhibited a higher AMR gene diversity compared to fresh and mid-lactation pens (p < 0.05). Several AMR genes showed bimodal distribution, suggesting complex transmission mechanisms. Network analysis revealed distinct gene correlation profiles across pens, with the hospital pen showing fewer gene interactions. Our findings suggest that farm-level antimicrobial drug use may not be the sole or primary driver of resistome composition in pooled fecal samples from dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems.
Keywords: antimicrobial resistance; bovine; resistome; next-generation sequencing; metagenomics antimicrobial resistance; bovine; resistome; next-generation sequencing; metagenomics

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MDPI and ACS Style

Garzon, A.; Portillo-Gonzalez, R.; Habing, G.; Weimer, B.C.; Schlesener, C.; Silva-del-Rio, N.; Karle, B.M.; Miramontes, C.; Pereira, R.V. Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms. Microorganisms 2025, 13, 2641. https://doi.org/10.3390/microorganisms13112641

AMA Style

Garzon A, Portillo-Gonzalez R, Habing G, Weimer BC, Schlesener C, Silva-del-Rio N, Karle BM, Miramontes C, Pereira RV. Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms. Microorganisms. 2025; 13(11):2641. https://doi.org/10.3390/microorganisms13112641

Chicago/Turabian Style

Garzon, Adriana, Rafael Portillo-Gonzalez, Gregory Habing, Bart C. Weimer, Cory Schlesener, Noelia Silva-del-Rio, Betsy M. Karle, Craig Miramontes, and Richard V. Pereira. 2025. "Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms" Microorganisms 13, no. 11: 2641. https://doi.org/10.3390/microorganisms13112641

APA Style

Garzon, A., Portillo-Gonzalez, R., Habing, G., Weimer, B. C., Schlesener, C., Silva-del-Rio, N., Karle, B. M., Miramontes, C., & Pereira, R. V. (2025). Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms. Microorganisms, 13(11), 2641. https://doi.org/10.3390/microorganisms13112641

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