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United States Department of Agriculture

Agricultural Research Service

Research Project: ANIMAL INTESTINAL MICROBIOMES, FOODBORNE PATHOGENS, AND ANTIMICROBIALS Title: Gene expression changes in the swine microbiota with the in-feed antibiotic carbadox

Authors
item Looft, Torey
item Allen, Heather
item Severin, Andrew -
item Levine, Uri
item Bayles, Darrell
item Alt, David
item Stanton, Thaddeus

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: April 20, 2013
Publication Date: May 10, 2013
Citation: Looft, T.P., Allen, H.K., Severin, A., Levine, U.Y., Bayles, D.O., Alt, D.P., Stanton, T.B. 2013. Gene expression changes in the swine microbiota with the in-feed antibiotic carbadox. [abstract]. 113th General Meeting, American Society for Microbiology. p. 200.

Technical Abstract: Administering antibiotics to livestock and poultry can treat and prevent disease while improving feed efficiency. Carbadox is an in-feed antibiotic, commonly used in swine production to prevent swine dysentery and promote animal growth. Carbadox has been shown to induce bacteriophages in some cultivated intestinal bacteria although its mode of action isn’t well defined. The goal of this study was to monitor the gene-expression levels (metatranscriptomics) in swine intestinal microbiota to determine the effect of carbadox on microbial communities and on bacteriophage induction in vivo. Six pigs (four weeks old) received feed containing carbadox and six received unamended feed. Fecal samples were collected from control and treated animals before antibiotic treatment and after 1, 2, and 7 days of continuous carbadox treatment. RNA and DNA were simultaneously extracted from each sample (n=48) and mRNA sequenced using an Illumina HiSeq. Data analysis included: assembly of reads, alignment of reads back to assembly, differential expression analysis, and annotation with the MetaHIT human microbiome gene catalog. A total of 1.7 billion curated reads were assembled, with 1.1 billion (65%) of the reads contributing to the assembly. 1,183 genes were more highly expressed in samples from controls than in treated animals, which contrasts with only 92 genes with greater expression in the carbadox treated animals (p less than 0.05). Among the highly expressed genes in the medicated communities, several putative phage genes were identified on the same contig and may demonstrate increased phage production in the swine gut after exposure to carbadox. Ongoing analyses of these microbiomes will inform whether the effects of carbadox on the microbiota are due to shifts in bacterial diversity or are limited to differential gene expression. Analysis of the phage populations may highlight how phage diversity is impacted by carbadox use and if bacterial genes are being packaged into phage particles. These results suggest that microbial activity in animals fed carbadox was reduced while putative phage genes were increased. Understanding how the microbiota of agricultural animals responds to antibiotic use can help us predict the effects outside of growth promotion and disease prevention and aid the search for alternatives to antibiotic.

Last Modified: 10/25/2014
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