Comparative Analysis of Bacterial Composition in the Ileum of Weaned Pigs Fed Microbially Enhanced Soybean Meal As a Potential Ingredient Replacement in Conventional Weaning Diets

Simple diets, containing microbially enhanced soybean meal (MESBM), have elicited favorable performance outcomes, which may pertain to either increased beneficial bacteria or competitively-exclusive bacteria that prevent pathogens from colonizing the intestinal tract of early post-weaned pigs. The objective of this research was to assess the effects of MESBM in complex nursery pig diets containing fish meal (FM) and/or spray dried plasma (SDP) on bacterial populations. Pens of weaned pigs (21 d of age, 6.56 ± 0.87 kg; n=5 pens/diet; 7 pigs/pen) were fed one of 4 experimental diets: 1) positive control, containing corn, soybean, SDP, and FM (CON), 2) SDP and MESBM (MESBM_+SDP), 3) FM and MESBM (MESBM_+FM), and 4) MESBM in both Phase I (d1-7 post-wean; 0, 12.75, 20.40, 34% MESBM inclusion, respectively) and II (d8-21; 0, 5, 8, 15% MESBM inclusion, respectively). Ileal digesta was collected from 5 pigs/diet at d21 (1 pig/pen). Digesta microbial gDNA was used for PCR amplification of the 16SrRNA gene (V1-V3 region) and amplicons sequenced via the Illumina Miseq 2x300 platform. The data produced approximately 380,000 high quality sequences that ranged from 5,844 to 70,555 sequences/animal. Data was analyzed using Proc Mixed in SAS with pig as the experimental unit and pig (treatment) as the random effect according to a completely random design. There was no effect of treatment (P > 0.05) on relative abundance of genera. Lactobacillus appeared to be the dominant genus, and pigs were assigned to either high (≥ 50%) or low (≤ 50%) relative abundance categories. Within each treatment, 50% or more of the animals were classified within the high relative abundance group for Lactobacillus. Seventeen OTU (Operational Taxonomic Unit) comprised the Lactobacillus genus, and 2 OTU appeared to be dominant. These, L. amylovorus and L. johnsonii, contributed 33, 39.5, 43.9, and 40.3% of the CON, MESMB+SDP, MESBM+FM, and MESBM, respectively. Animals not characterized by low relative abundance for Lactobacillus were colonized by genera commonly associated with pathogenic bacteria, specifically Terrisporobacter, Clostridium, and Streptococcus. This evidence suggests that strategies to increase intestinal Lactobacillus populations may contribute to competitive exclusion of potential pathogenic bacteria. Production based diets that utilize MESBM as an alternative protein source can potentially induce beneficial microbial composition shifts in the ileum of weaned pigs.