Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome


Lee, C., Zaheer, R., Munns, K., Holman, D.B., Van Domselaar, G., Zovoilis, A., McAllister, T.A. (2023). Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome. Microorganisms, [online] 11(12), http://dx.doi.org/10.3390/microorganisms11122982

Plain language summary

In this study, researchers investigated the impact of using antibiotics in the livestock industry, specifically in beef cattle feedlots. They focused on comparing cattle raised conventionally with antibiotics and those raised naturally without antibiotics. The study used a method called shotgun metagenomics to analyze the microbiome (microorganisms in the gut), resistome (collection of antibiotic-resistant genes), and mobilome (genetic elements that can move between organisms).

The results showed that in naturally raised cattle, there was a significant decrease in certain microbial genera in the gut compared to conventionally raised cattle. However, this difference was not observed in environmental samples from catch basins. The resistome at the class level (types of antibiotic resistance) did not show significant differences between the two feedlot practices. In fecal samples, the study found a decrease in reads for specific antibiotic-resistant genes in naturally raised cattle.

Interestingly, antibiotic-resistant genes associated with plasmids (genetic structures that can transfer between bacteria) were more common in feces from conventionally raised cattle. The study also noted that macrolide resistance genes were more stably conserved in both natural and conventional feedlots, whether associated with chromosomes or plasmids.

In conclusion, the research suggests that the impact of antibiotic use in the past persists in the resistomes of cattle even after ceasing antibiotic use in natural production systems. This highlights the long-lasting effects of generational selection of antibiotic resistance genes in livestock.


Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of “natural” feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.