Bacillus- and Lactobacillus-Based Dietary Synbiotics Are Associated with Shifts in the Oropharyngeal, Proximal Colonic, and Vaginal Microbiomes of Korean Native Black Pigs

Abstract

In this study, we evaluated the modulatory effect of synbiotics (probiotics + prebiotics) on the oropharyngeal, proximal colonic, and vaginal microbiomes of Korean native pigs using 16S rRNA gene sequencing. We found increased abundances of an unclassified deltaproteobacterial genus in oropharyngeal communities of pigs supplemented with a Lactobacillus-based synbiotic. These pigs also had increased abundances of unclassified genera of Tremblayales and Lactobacillales in their proximal colons. In another group, pigs supplemented with a Bacillus-based synbiotic had increased Megasphaera and reduced Campylobacter within their oropharyngeal microbiota. In addition, their vaginal microbiota had increased Clostridium and Halalkalibacillus, as well as reduced Filifactor and Veillonella. We then explored changes in the predicted microbial functionality, associated with the synbiotics. Our analysis showed a reduction in the abundance of a fatty acid and lipid biosynthesis pathway among proximal colonic microbiomes of the Lactobacillus-fed pigs. In pigs supplemented with a Bacillus-based synbiotic, the analysis showed reduced pathway abundances for the biosynthesis of carbohydrates, as well as vitamins, cofactors, and carrier molecules within their oropharyngeal microbiomes. Meanwhile, their vaginal microbiomes had higher pathway abundances for aromatic compound degradation and secondary metabolite biosynthesis, but lower abundances for amino acid degradation. The results confirmed our hypothesis that dietary synbiotics modulate the microbiome, not only in the proximal colon, but also the oropharyngeal cavity and vaginal tract of these pigs.