The In-Feed Antibiotic Carbadox Induces Phage Gene Transcription in the Swine Gut Microbiome

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2017-08-08
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Looft, Torey
Severin, Andrew
Bayles, Darrell
Wommack, K. Eric
Howe, Adina
Allen, Heather
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Howe, Adina
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Severin, Andrew
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Agricultural and Biosystems Engineering

Since 1905, the Department of Agricultural Engineering, now the Department of Agricultural and Biosystems Engineering (ABE), has been a leader in providing engineering solutions to agricultural problems in the United States and the world. The department’s original mission was to mechanize agriculture. That mission has evolved to encompass a global view of the entire food production system–the wise management of natural resources in the production, processing, storage, handling, and use of food fiber and other biological products.

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In 1905 Agricultural Engineering was recognized as a subdivision of the Department of Agronomy, and in 1907 it was recognized as a unique department. It was renamed the Department of Agricultural and Biosystems Engineering in 1990. The department merged with the Department of Industrial Education and Technology in 2004.

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1905–present

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  • Department of Agricultural Engineering (1907–1990)

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Genome Informatics Facility
The Genome Informatics Facility serves as a centralized resource of expertise on the application of emerging sequencing technologies and open source software as applied to biological systems. Its mission is to integrate this knowledge into pipelines that are easy to understand and use by faculty, staff and students to enable the transformation of ‘big data’ into data that dramatically accelerates our understanding of biology and evolutionary processes.
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Abstract

Carbadox is a quinoxaline-di-N-oxide antibiotic fed to over 40% of young pigs in the United States that has been shown to induce phage DNA transduction in vitro; however, the effects of carbadox on swine microbiome functions are poorly understood. We investigated the in vivo longitudinal effects of carbadox on swine gut microbial gene expression (fecal metatranscriptome) and phage population dynamics (fecal dsDNA viromes). Microbial metagenome, transcriptome, and virome sequences were annotated for taxonomic inference and gene function by using FIGfam (isofunctional homolog sequences) and SEED subsystems databases. When the beta diversities of microbial FIGfam annotations were compared, the control and carbadox communities were distinct 2 days after carbadox introduction. This effect was driven by carbadox-associated lower expression of FIGfams (n = 66) related to microbial respiration, carbohydrate utilization, and RNA metabolism (q < 0.1), suggesting bacteriostatic or bactericidal effects within certain populations. Interestingly, carbadox treatment caused greater expression of FIGfams related to all stages of the phage lytic cycle 2 days following the introduction of carbadox (q ≤0.07), suggesting the carbadox-mediated induction of prophages and phage DNA recombination. These effects were diminished by 7 days of continuous carbadox in the feed, suggesting an acute impact. Additionally, the viromes included a few genes that encoded resistance to tetracycline, aminoglycoside, and beta-lactam antibiotics but these did not change in frequency over time or with treatment. The results show decreased bacterial growth and metabolism, prophage induction, and potential transduction of bacterial fitness genes in swine gut bacterial communities as a result of carbadox administration.

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This article is from mBio vol. 8 no. 4 (8 August 2017) e00709-17, doi:10.1128/mBio.00709-17.

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