Transcriptomic Analysis Reveals That Perilla frutescens Seeds Enhance Sheep Ruminal Epithelial Homeostasis

The ruminal epithelium plays a central role in nutrient absorption, epithelial barrier function, and mucosal immune defense. However, the molecular mechanisms by which dietary Perilla frutescens seeds (PFS) regulate ruminal epithelial immunity remain poorly understood. This study investigated the transcriptomic responses of the sheep ruminal papilla to dietary PFS supplementation. Forty-five male Tan sheep were assigned to three dietary treatments (n = 15 per group): a low-concentrate diet (LC), a high-concentrate diet (HC), and the LC diet supplemented with 3% PFS (LC + PFS). After an 84-day feeding trial, ruminal papilla tissues from six animals per group were randomly subjected to RNA sequencing and integrated bioinformatic analyses, covering all three pairwise comparisons (LC vs. HC, HC vs. LC + PFS, and LC vs. LC + PFS). The LC vs. LC + PFS comparison served as the direct assessment of PFS effects under the same basal diet, whereas HC vs. LC + PFS was treated as a cross-dietary comparison. LC vs. HC yielded 387 differentially expressed genes (DEGs), HC vs. LC + PFS yielded 104 DEGs, and LC vs. LC + PFS yielded 33 DEGs, with predominant enrichment in metabolic and stress-adaptive pathways (AMPK, MAPK, PI3K-Akt). The latter were mainly associated with metabolic and structural pathways. Propionate and valerate were negatively correlated with several interferon-signaling and antigen-presentation genes. Collectively, the direct LC vs. LC + PFS comparison demonstrates that PFS supplementation under physiological conditions is associated with targeted metabolic modulation. Meanwhile, the cross-dietary HC vs. LC + PFS comparison reveals that, relative to high-concentrate feeding, the PFS-supplemented low-concentrate feeding regimen is transcriptionally associated with enhanced immune surveillance capacity in a non-inflammatory manner. These findings provide transcriptomic evidence supporting the potential of PFS as a modulator of ruminal epithelial homeostasis and offer a foundation for further investigation into its application as a functional feed ingredient.