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Subclinical doses of antimicrobials are commonly used in the swine industry to control infectious diseases and growth performance. Accumulating evidence suggests that swine administered with antibiotics are susceptible to disease development due to disruption of the beneficial gut microbial community, which is associated with host immune regulation, nutrient digestion, and colonization resistance against pathogens. In this study, we found that finishing swine administered with lincomycin showed gut dysbiosis and increased diarrhea incidence compared with control swine. 16S rRNA amplicon sequencing was used to analyze the gut microbiota in finishing swine administered with lincomycin. The relative abundance of detrimental microbes, such as species of  Clostridium ,  Aerococcus ,  Escherichia-Shigella , and  Corynebacterium  was increased in the feces of lincomycin-administered finishing swine, but that of bacteria associated with fiber degradation, such as species of  Treponema ,  Succinivibrio, Fibrobacter , and  Cellulosilyticum  was decreased. Moreover, administration of lincomycin significantly increased the enrichment of metabolic pathways related to pathogenicity and deficiency of polysaccharide degradation. These results suggest that lincomycin treatment could cause severe disruption of the commensal microbiota in finishing swine.

Alteration of Gut Microbiota After Antibiotic Exposure in Finishing Swine