Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

Milton Thomas,Joy Scaria,Sudeep Ghimire,Jane Christopher-Hennings,Derek Brake,Megan Webb,Alex Thomas Fonder,Kenneth Olson,Gavin John Fenske,Amanda Blair

doi:10.1038/s41598-017-12481-6

Milton Thomas, Joy Scaria + Show 8 more

Open Access

https://doi.org/10.1038/s41598-017-12481-6

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Journal: Scientific Reports	Publication Date: Sep 25, 2017
Citations: 107	License type: open-access

Affiliation: South Dakota State University

Abstract

In North America, antibiotic feed additives such as monensin and tylosin are added to the finishing diets of feedlot cattle to counter the ill-effects of feeding diets with rapidly digestible carbohydrates. While these feed additives have been proven to improve feed efficiency and reduce liver abscess incidence, how these products impact the gastrointestinal microbiota is not completely understood. In this study, we analyzed the impact of providing antibiotic feed additives to feedlot cattle using metagenome sequencing of treated and control animals. Our results indicate that use of antibiotic feed additives does not produce discernable changes at the phylum level. However, treated cattle had reduced abundance of gram-positive bacteria at the genus level. The abundance of Ruminococcus, Erysipelotrichaceae and Lachnospiraceae in the gut of treated steers was reduced. Functional analysis of the data indicates that there was only minimal impact due to the treatment in the rumen. Genes involved in detoxification were significantly increased in the rumen of AB steers. But the relative abundance of these genes was < 0.3%. However, our results did not show any correlation between the presence of antimicrobial resistance genes in the gut microbiota and the administration of antibiotic feed additives.

Highlights

Commensal microbes inhabiting the mammalian gut are associated with immune development[1], nutrient supply[2], prevention of pathogenic diseases[3], and overall health of the host
The methodologies used in these studies were anaerobic culture, terminal restriction fragment length polymorphism (TRFLP), and 16S rRNA-based polymerase chain reaction (PCR)
Shotgun metagenomics sequencing of the gastrointestinal tract (GIT) microbiome of antibiotic feed additive treated and control feedlot cattle was utilized to determine the influence of these feed technologies on the microbiome and antibiotic resistome

Summary

Introduction

Commensal microbes inhabiting the mammalian gut are associated with immune development[1], nutrient supply[2], prevention of pathogenic diseases[3], and overall health of the host. Cattle in feedlots are generally fed a finishing ration that contains up to 90% rapidly digestible carbohydrates This elevates incidences of acidosis[6] and liver abscesses[7], which have a detrimental effect on animal health and beef production. This study provides a snapshot of the structure and functional characteristics of the GIT microbiome and resistome of steers that are adapted to a rapidly fermentable carbohydrate-rich diet and were finished with or without antibiotic feed additives. To our knowledge, this is the first report that uses shotgun metagenomic sequencing for studying the microbiome and resistome alterations in the GIT of steers.

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Results

Conclusion