Effects of High Soybean Meal Inclusion on the Gut Microbiome of Finishing Pigs

Soybean meal (SBM), the primary protein source in U.S. Midwest swine diets, is typically supplemented with synthetic amino acids to optimize growth. Variation in SBM inclusion can influence pig performance and gut health due to non-protein components, such as polysaccharides and oligosaccharides; as these can affect microbial metabolism, further investigations are needed to increase our understanding of the effects of SBM on the swine gut environment. As new processing facilities expand SBM availability and lower its costs, understanding how high SBM inclusion impacts the gut microbiome is increasingly important. In this context, this study aimed at characterizing the effect of SBM inclusion levels on swine gut bacterial communities. 546 mixed-sex pigs were used in a 111-day trial to evaluate the effects of diets with 1) low SBM inclusion supplemented with synthetic amino acids (5%; LowSBM) vs 2) high SBM inclusion (28%; HighSBM). All diets met or exceeded NRC requirements, with standardized ileal digestible (SID) lysine and net energy (NE) levels kept constant. To determine fecal bacterial composition and identify candidate gut microbial species, 14 fecal samples per treatment were randomly collected from at least one pig in each pen receiving the respective diet for DNA extraction and 16S rRNA sequencing via PCR amplification of the V1–V3 regions. To further explore how HighSBM diets shaped gut microbiome function, we performed shotgun metagenomic sequencing on selected fecal samples. Reads were assembled with MEGAHIT (v1.2.9), binned using CONCOCT (v1.1.0), MaxBin2 (v2.2.7), and MetaBAT2 (v2.18), then refined with DASTool (v1.1.7). Annotated genomes were obtained using DRAM (v1.5), enabling prediction of the metabolic potential of the most abundant gut bacterial species. A 16S rRNA gene-based analysis of beta diversity, visualized through Principal Coordinate Analysis (PCoA) with Bray-Curtis distances, indicated significant differences in bacterial composition between the two treatments (PERMANOVA, P < 0.05). Notably, we found specific Operational Taxonomic Units (OTUs) that were in higher abundance in the HighSBM samples compared to the LowSBM samples (P < 0.05). These included Ssd-39, closely related to Streptococcus alactolyticus (99.5% identity; 15% vs. 10%); Ssd-1160, related to Treponema brennaborense (88.0% identity; 2% vs. 0.1%); and Ssd-1254, closely related to Treponema bryantii (97.0% identity; 2% vs. 0.03%). Using metagenome-assembled genomes (MAGs; quality assessment: >70% completeness; < 10% contamination), functional annotation revealed metabolic capabilities such as polysaccharide degradation, and butyrate production. Interestingly, MAGs affiliated to the genus Treponema suggest a role in fiber degradation, utilization and lactate production. As SBM becomes more affordable, this study offers insight into optimizing its use as a protein source in swine. These results indicate that HighSBM swine diets can alter gut microbiome composition, influencing short-chain fatty acid and metabolite production that would be driven by the polysaccharides and amino acids present in SBM.