PSXIII-2 The effect of feeding Bacillus subtilis on gut microbiome functional pathways of weaned pigs.

Abstract Our previous research observed that dietary supplementation of Bacillus subtilis reduced the frequency of diarrhea and enhanced growth performance of weaned pigs experimentally infected with a pathogenic Escherichia coli (E. coli). The aim of this study was to further investigate the effects of dietary Bacillus subtilis or carbadox on the microbiome functional pathways 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 2.56 x 109 CFU/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. 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. Quality-checked reads were input into Humann3 for functional annotation. A total of 451 pathways were detected in fecal samples. The most abundant pathways were related to energy production, nucleotide metabolism, and protein synthesis. Pathways with significant (P < 0.05) differences in relative abundance across treatments were selected and categorized by functional role. In major carbon metabolism, antibiotic supplementation reduced (P < 0.05) the relative abundance of pathways like glycogen degradation, D-galactose degradation, and starch biosynthesis, likely due to decreased contributions from Bifidobacterium boum and Lactobacillus amylovorus. Overall, fermentation pathways involving acetylene, acetyl-CoA, and homolactic fermentation had lower (P < 0.05) relative abundance in the antibiotic-treated group compared to other treatments, likely due to key contributions from Coprococcus, Lactobacillus spp., and E. coli. For essential amino acid biosynthesis, the antibiotic-treated group showed lower (P < 0.05) L-methionine and L-lysine biosynthesis among all groups but increased (P < 0.05) L-valine biosynthesis compared to probiotic group and negative control. Bacillus subtilis supplementation reduced (P < 0.05) pathways for branched-chain amino acids, L-histidine, and L-valine biosynthesis compared to the positive control. Antibiotic treatment increased (P < 0.05) L-histidine degradation to the highest level while reducing (P < 0.05) tryptophan degradation to the lowest level. Additionally, antibiotics downregulated (P < 0.05) biosynthesis pathways for non-essential amino acids, including L-glutamine, L-alanine, L-cysteine, and L-asparagine, likely due to differences in Bifidobacterium spp. and Prevotella spp. abundance. In conclusion, dietary Bacillus subtilis and carbadox have distinct impacts on the functional pathway profiles in the feces of weaned pigs.