Dietary Cupplant (Silphium perfoliatum L.) flavonoid supplementation is associated with changes in cecal microbial diversity and community structure in broiler chickens.

Cupplant (Silphium perfoliatum L.) contains flavonoids that may influence the intestinal microbiota, but their effects in broilers remain poorly defined. We examined cecal microbial responses to dietary Cupplant flavonoids. Two hundred forty one-day-old broilers were assigned to four diets containing 0 (CH), 100 (S1), 200 (S2), or 300 (S3) mg/kg flavonoid extract, with five replicate cages per treatment. At day 42, cecal digesta from six birds per treatment were characterized using 16S rRNA gene amplicon sequencing; one cage per treatment contributed two sampled birds. QIIME2/DADA2 processing yielded 1,601,918 retained reads and 2,735 amplicon sequence variants. Observed ASVs, Chao1 richness, and Shannon diversity were higher in S3 than CH (adjusted P < 0.05), although responses were non-monotonic. Global Bray-Curtis PERMANOVA showed treatment-associated differences in community composition (pseudo-F(3,20) = 2.997, R² = 0.310, P = 0.001), while PERMDISP was non-significant (P = 0.168). All pairwise PERMANOVA comparisons remained significant after multiplicity correction. False-discovery-rate (FDR)-controlled metagenomeSeq identified six genera in the CH-S1 comparison and three in CH-S3, with Escherichia-Shigella, Desulfovibrio, and Anaerotignum recurring in both contrasts; CH-S2 had no FDR-significant genera. Reconstructed FDR-controlled networks retained only 6.8-12.0 % of nominal edges, and βNTI, NST, and iCAMP results did not support a monotonic dose-dependent shift in community assembly. Descriptive final body weight and average daily gain values were similar across treatments, but cage-level growth inference was not possible from the archived data. Cupplant flavonoid supplementation was associated with non-linear changes in cecal microbial diversity and composition, warranting confirmation in cage-aware, adequately powered studies.