ARS | Publication request: Metagenomic and 16S rRNA Analyses of Fecal Bacteria of Swine Given Diets Containing Antibiotics

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: May 2, 2010
Publication Date: N/A

Technical Abstract: Antibiotics are commonly given to livestock to treat disease and promote growth. For the most part, effects of these dietary additives on intestinal microbes and their ecology are unknown. The goal of this study was to evaluate how antibiotics influence the intestinal microbial communities in swine. ASP250 (chlortetracycline, sulfamethazine, and penicillin) is added to swine diets for both therapeutic and performance enhancing applications. Three pigs received ASP250 feed and three received feed without antibiotics. Feces were collected from the animals before treatment (zero time) and after 14 days of continuous treatment. Metagenomic and 16S rRNA gene (V3 region) sequence analysis was used to characterize the microbial communities from each timepoint and treatment. According to the V3 analysis, the majority of the reads grouped with the Bacteroidetes (53%) and Firmicutes (30%) phyla. After 14 days, the group given antibiotics showed a two-fold increase in Proteobacteria (9% to 18%) compared to the community of the same pigs at zero time. The largest shift within Proteobacteria was with Escherichia, which increased from 1% to 11% with antibiotic treatment. Comparisons between the antibiotic fed and control groups at 14 days reflected the same shift with the use of antibiotics. Metagenomic sequence analyses of the pooled DNA from each timepoint and treatment confirmed the 16S results. To assess the antibiotic resistance potential of the treated and untreated metagenomes, the antibiotic resistance gene database was used to identify resistance genes in the four metagenomes. At a cutoff of 35% amino acid identity, 190 antibiotic resistance genes were identified across all metagenomes, most of which were present regardless of antibiotic treatment. These results indicate swine can be a reservoir for resistance genes even in the absence of antibiotic use. The increase in Escherichia levels, with use of antibiotics suggests implications for food safety and animal disease.