Microbiota profiles and antimicrobial resistance genes in sow fecal samples from farms with and without antibiotic use

Abstract

Objective: Antibiotics have been used in swine production, and they are known to be associated with the gut microbiota and antimicrobial resistance (AMR). This study aimed to evaluate the dynamics of the microbiota and AMR among fecal bacteria in sowsby 16S rRNA gene sequencing and TaqMan array card assays. Methods: A total of 40 healthy multiparous sows were tested in a completely randomized design. Sows were randomly divided into two groups: one was fed a commercial diet with antibiotics for 3 weeks from mating to day 21 of gestation, before the farrowing stage (amoxycillin 300 mg/kg and tiamulin 150 mg/kg: control group, ABO), and the other was fed the same diet without antibiotics (treatment group, NOABO). Results: The ABO group had a higher alpha diversity than the NOABO group (p<0.05). The results re-vealed the highest bacterial abundance in the phylum Firmicutes in sow fe-ces in the ABO group at an average level of 92.01% and 92.32% in the NOABO group. Erysipelotrichaceae, Clostridiaceae, and Terrisporobacter in the ABO group had enriched proportions. On the other hand, Lactobacillales, Bacilli, and Streptococcus were enriched in the NOABO group (p<0.05). In terms of AMR, a comparison of the normal log of resistance gene copies between the ABO and NOABO groups displays that the gene copy number was significantly higher (p<0.05) in the ABO group (59%) than in the NOABO group (41%) especially those of β-lactam, aminoglycosides, quinolones, and macrolides. Conclusion: Our investigations discovered that the core microbiota of withdrawal antibiotics may be related to the gut microbiota and AMR. Therefore, understanding the gut mi-crobiota composition and function in animals could enable strategies for its modulation to improve sows’ gut microbiota and minimize the negative impact of antibiotics.