204 The effect of feeding bacillus subtilis on fecal microbiota and antimicrobial resistance gene composition of weaned pigs

Our previous research observed that dietary supplementation of 500 mg/kg of Bacillus subtilis reduced the frequency of diarrhea and enhanced growth performance of weaned pigs experimentally infected with a pathogenic Escherichia coli (E. coli). This study aimed to further investigate the effects of dietary Bacillus subtilis or carbadox on the functional antimicrobial resistance gene (AMR) composition and abundance of the microbial community in feces collected from weaned pigs in this research project. The four experimental treatments were: 1) negative control, pigs fed with control diet without E. coli challenge, 2) positive control, pigs fed with control diet with E. coli challenge, 3) antibiotic group, pigs fed diet supplemented with 50 mg/kg of carbadox with E. coli challenge, and 4) probiotics group, pig fed diet supplemented with 500 mg/kg of Bacillus subtilis probiotics with E. coli challenge. A total of 32 fecal samples were directly collected from the rectum of pigs on day 21 after the first E. coli inoculation with 8 samples per treatment. Total microbial community DNA was extracted from fecal samples and then submitted to UC Davis Genome Center for Whole Genome- Shotgun Sequencing (NovaSeq S4 PE150) on the Illumina platform. Microbiota data analysis were conducted using Sourmash and R packages. AMR gene analysis was performed with the ATLAS pipeline and AMRFinderPlus. Supplementing Bacillus subtilis or antibiotics did not impact alpha diversity, including Chao1 and Shannon indices. The bacterial community composition in fecal samples collected from pigs in the antibiotics group were more separated (P < 0.05) from those in the other treatments. At the phylum level, supplementation of antibiotics reduced (P < 0.05) the relative abundance of Bacillota but increased (P < 0.10) the relative abundance of Bacteroidota and Eremiobacterota in feces of pigs compared with those in other groups. At the family level, supplementation of antibiotics had the lowest (P < 0.05) relative abundance of Lactobacillaceae, Streptococcaceae, Ruminococcaceae, CAG-239, and Burkholderiaceae among all treatments. However, pigs fed with antibiotics had the highest (P < 0.05) relative abundance of Erysipelotrichaceae, Turicibacteraceae, Clostridiaceae, Oscillospiraceae, Peptostreptococcaceae, and Succinivibrionaceae among all dietary treatments. A total of 77 AMR gene determinants were identified in fecal samples. 38 AMR genes that belong to 8 drug classes were shared by all treatments. The presence of aph(2’’)-lla were lower (P < 0.10) in Bacillus subtilis group compared with other treatments. The presence of tetB(P) were lower (P < 0.05) in the positive control among all treatments. The presence of cfx(A) were higher (P < 0.05) in negative and positive control than Bacillus subtilis treatment. In conclusion, dietary Bacillus subtilis and carbadox have different impacts on microbiota community and the presence of antimicrobial resistance gene in feces of weaned pigs.