Soybean meal (SBM) accounts for the second most abundant feed ingredient in poultry feed and derives from a variety of sources with varying quality levels. SBM quality has the potential to impact the gut microbiome due to the altered nutrient levels and bioavailability of nutrients. The microbiome is well established to be beneficial in maintaining homeostasis and contributing to the overall health in broiler chickens. The objective of the present study was to compare the effects of dietary SBM quality and live coccidiosis vaccine cycling on the broiler chicken cecal microbiome. At day of hatch (DOH), n=480 chicks (n=12 pens/group, 20 chicks per pen) were randomly assigned to either: Group 1) high-quality (HQ) SBM formulated to meet or exceed requirements or Group 2) low-quality (LQ) SBM designed to induce inflammation. The LQ SBM was produced using a 1:1:1 mixture of uncooked SBM, normal SBM, and over-processed SBM (autoclaved ~125C for 60 minutes). Chicks were orally gavaged with a 1X dose (0.25mL/chick) of a commercial live coccidiosis vaccine containing E. acervulina, E. maxima, and E. tenella oocysts at DOH. On d15, 28 and 42, n=8 chickens from each treatment were culled to obtain cecal content samples for microbiome evaluation. Genomic DNA was extracted and 16S rRNA V4 regions were amplified for sequencing. Alpha diversity was discerned at amplicon sequence variant (ASV) level by leveraging observed richness, Shannon diversity, Pielou’s evenness, and Faith’s phylogenetic diversity (Faith’s PD). For alpha diversity, normality was assessed using the Shapiro-Wilk test and homogeneity of variance using Levene’s test. For beta diversity, reads were normalized using cumulative sum scaling (CSS) prior to all downstream analyses. Beta diversity was assessed at ASV level using the Bray-Curtis dissimilarity, Weighted UniFrac, and Unweighted UniFrac distance metrics. To evaluate community-level differences attributed to treatment, time, and treatment-time interaction, PERMANOVA was performed with 9,999 permutations, followed by beta dispersion analysis to assess homogeneity of variances. There was a significant increase in alpha diversity within each treatment group between d15 and d42 according to Faith’s PD (P=0.00) and Observed Richness. Consistent with alpha diversity, time had the greatest effect on compositional dissimilarity (Bray-Curtis and Unweighted UniFrac P=0.0004), with treatment also demonstrating a significant effect (Bray-Curtis, P=0.009). Interestingly, Clostridiaceae was enriched in the HQ SBM group at d15 compared to the LQ SBM group. Further investigation is needed to evaluate the relationship between SBM quality and the intestinal microbiome in broiler chickens.

Coles, M., K. Teague, R. Wolfenden, J. Liu, B. Hale, C. Vuong, B. Hargis and D. Graham. 2025. Impact of low-quality soybean meal and live coccidiosis vaccination on the cecal microbiome composition of broiler chickens. 2025 Poultry Science Association Annual Meeting, Abstract 411P