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Animal manure can be a source of antibiotic resistant genes (ARG) and pharmaceutical residues; however, few studies have evaluated the presence of ARG in pasture-raised animal production systems. The objective of this study was to examine changes in microbiome diversity and the presence of antibiotic residues (ABR) on three farms that contained a diverse range of animal species: pasture-raised poultry (broiler and layer), swine and beef cattle. Total bacterial communities were determined using 16S rRNA microbiome analysis, while specific ARG (sulfonamide [Sul; Sul1] and tetracycline [Tet; TetA]) were enumerated by qPCR. Results indicated that the ARG abundances (Sul1 [P &amp;lt; 0.05] and TetA [P &amp;lt; 0.001]) were higher in layer hen manures (16.5 x 10 -4 and 1.4 x 10 -4 µg kg -1, respectively) followed by broiler chickens (2.9 x 10 -4 and 1.7 x 10 -4 µg kg -1, respectively), swine (0.22 x 10 -4 and 0.20 x 10 -4 µg kg -1, respectively) and beef cattle (0.19 x 10 -4 and 0.02 x 10 -4 µg kg -1, respectively). Average fecal TetA ABR tended to be greater (P = 0.09) for broiler chickens (11.4 µg kg -1) than for other animal species (1.8-0.06 µg kg -1), while chlortetracycline, lincomycin, and oxytetracycline ABR were similar among animal species. Furthermore, fecal microbial richness and abundances differed significantly (P &amp;lt; 0.01) both among farms and specific species of animal. This study indicated that the microbial diversity, ABR, ARG concentrations, and types in feces varied from farm-to-farm and from animal species-to-animal species. Future studies are necessary to perform detailed investigations of the horizontal transfer mechanism of antibiotic resistant microorganisms (ARM) and ARG.

Antibiotic resistance, antimicrobial residues and bacterial community diversity in pasture-raised poultry, swine and beef cattle manures