Impact of parenteral antimicrobial administration on the structure and diversity of porcine fecal microbiota

Antibiotics administration in swine husbandry systems has been used for prevention and treatment of several forms of infections as well as a growth promoter, but concerns regarding the emergence of antibiotic-resistant and adverse effect on the microbial colonization have led to novel approaches in development of alternative strategies. Therefore, the purpose of this study was to characterize the impact of antibiotics administration on the composition and diversity of the resident fecal microbiotas in pigs. Five antimicrobial treatment groups each consisting of 4, 8 week old piglets were treated with one of the antimicrobials (Tulathromycin, Ceftiofur Crystalline free acid, Ceftiofur hydrochloride, Oxytetracycline, and Procaine Penicillin G) at label dose and route. Individual fecal swab was collected before antibiotics administration (d 0) and again on d 1, 3, 7, and 14. Genomic DNA was extracted, and the V1V3 region of 16S rRNA gene was amplified and sequenced using Illumina- based sequencing. Our result demonstrated that the core fecal microbiome was dominated by Firmcuties and Bacteroidetes. Discriminant analysis showed pronounced microbial shift in the fecal microbiota after different antibiotics administration. Prevotella, Ruminococcaceae, Streptococcus, Christensenellaceae, Clostridium, Lachnospiraceae and Oscillospira were the main bacterial taxa associated with the microbial shift after Tulathromycin, Ceftiofur Crystalline and Ceftiofur hydrochloride administration. Only minor alterations were noted after the administration of Oxytetracycline and Procaine Penicillin G. Based on our results, exposure to various antibiotics administration has distinct effects on the composition of the porcine fecal microbiotas with no significant effect on bacterial diversity as measured using the Shannon, Chao1, Observed species and PD whole tree indices. Understanding these effects is a critical step in designing comprehensive health management programs that optimize local immunity to minimize the disease and the need for antibiotics.