Gut Microbiomes of Pigs Grown in Organic and Conventional Dietary Regimens

Abstract

In animal production, antibiotics are used at sub-therapeutic and therapeutic levels for growth promotion and disease prevention. Using antibiotics can result in selecting for drug resistant microorganisms that may spread to humans through consumption of contaminated food. Lately, an increased interest in organic farming, where animals are grown without antibiotics, has been popular amongst the consumers. It is believed that organic farming will reduce antimicrobial resistance in microorganisms. However, the animals grown organically may be prone to diseases, and other microorganisms may thrive in the gut, that may be potentially harmful to humans. We analyzed the DNA of fecal samples of pigs grown under conventional and organic dietary regimens and detected the presence of genes that causes antibiotic resistance. The microbiomes of gut in swine grown under these two dietary regimens exhibited little difference in composition and exhibited the presence of Bacteriodetes, Firmicutes and Proteobacteria at the phyla level and Prevotella, Lactobacillus, Barnesiella, Proteus, Fecalibacteria, Escherichia coli and Shigella at the genus level. Presence of eighty seven antibiotic resistance genes, tested by real-time PCR, exhibited the presence of more antibiotic resistance genes in guts of swine grown in conventional diet than under organic conditions. This pilot study may lead to comprehensive research on the composition of microbiomes in pigs in large production environment allowing formulation of strategies that may eventually reduce prevalence and dissemination of antibiotic resistance genes in the guts of animals