Annex Publishers | www.annexpublishers.com Volume 5 | Issue 3 Gut Microbiomes of Pigs Grown in Organic and Conventional Dietary Regimens DebRoy C *1 , Hegde NV 1 , Schilling M 2 , Kapur V 2 and Katani R 2 1 E. coli Reference Center, Department of Veterinary and Biomedical Sciences, Te Pennsylvania State University, University Park, PA, USA 2 Department of Animal Science, Te Pennsylvania State University, University Park, PA, USA * Corresponding author: DebRoy C, E. coli Reference Center, Department of Veterinary and Biomedical Sciences, Te Pennsylvania State University, University Park, PA 16803, USA, E-mail: rcd3@psu.edu Citation: DebRoy C, Hegde NV, Schilling M, Kapur V, Katani R (2017) Gut Microbiomes of Pigs Grown in Organic and Conventional Dietary Regimens. J Vet Sci Ani Husb 5(3): 301 Research Article Open Access Volume 5 | Issue 3 Journal of Veterinary Science & Animal Husbandry ISSN: 2348-9790 Introduction 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. Te microbiomes of gut in swine grown under these two dietary regimens exhibited little diference 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. Tis 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. Keywords: Swine Ricrobiome; Antibiotic Resistance Genes; Phylotypes; Metagenomic Library Antibiotics have been administered at sub-therapeutic and therapeutic levels for animal production for many years in the United States for disease prevention and growth promotion. It has been demonstrated that antimicrobial resistance in foodborne pathogens may arise due to use of antimicrobials in agriculture that may spread to humans through contaminated food [1-4]. To address the concern, United States Department of Agriculture (USDA) established the National Organic Program in 1990 that has grown by almost 20% annually. Organic production focuses on animal health, good environmental practices, production quality and do not use antibiotics, hormones or animal byproducts in feed as mandated by USDA. (http://www.usda.gov/wps/portal/ usda/usdahome?navid=organic-agriculture). Conventional farming practices generally focus on reducing costs and maximizing production by feeding antimicrobials and dietary supplements to animals. Antibiotics in the diet plays a major role in modulating gut microfora by providing selective pressure on microbial community leading to the emergence of drug resistant bacteria. Te selection pressure may also facilitate persistence and the transfer of resistance determinants between bacterial species [5,6]. It is now known that non-pathogenic commensal microorganisms may develop antibiotic resistance and also transmit the resistance determinants to other microbes [7,8]. Te emergence and dissemination of antibiotic resistance in bacterial pathogens is a serious emerging problem worldwide [7,9]. In swine production, association between antimicrobial use and antimicrobial resistance is well documented [10-14]. Antimicrobial resistant bacteria are consumed by humans through contaminated food, or can be acquired by direct contact with animals, or from the environment due to release of contaminated animal waste [15]. To prove that antimicrobial usage in swine production may be directly correlated with antimicrobial-resistant infections in the human population has been challenging. However, diseases in humans, caused by multidrug-resistant Salmonella enterica serotype Typhimurium DT104 in Denmark [16], S. enterica serotype Typhimurium DT104 in England [17], and Enterococcus faecium in China [18] were found to have originated from swine herds. Received Date: May 22, 2017 Accepted Date: October 23, 2017 Published Date: October 25, 2017