Spatial multi-omics reveals the coadaptation between microbial ecology and epithelial morphology in the rumen

Regional variation in ruminal epithelial morphology has been recognized in ruminants; however, the underlying microbial, metabolic and transcriptomic profiles, remain poorly understood. Here, we compared morphological profiles of 14 ruminal regions and identified four representative regions including Atrium ruminis 4 (fluid layer), Atrium ruminis 2 (fiber mat), Saccus ventralis 3 (sludge layer), and Saccus dorsalis 1 (gas dome). Across these regions, the epithelial surface area progressively decreased from the fluid- and fiber-associated regions toward the gas dome, revealing a size-density trade-off in ruminal papillae. Transcriptomic profiling indicated that the regions with large papillae were enriched in epithelial differentiation, keratinization, and nutrient transport, whereas the regions with dense, small papillae specialized in mechanical motility. Microbial composition analysis showed that regions with high epithelial surface area were enriched in fibrolytic taxa and associated phospholipid metabolism. Specifically, Oscillospira and Treponema positively correlated with epithelial surface area, whereas Acetitomaculum exhibited a negative correlation. Metabolic changes were coupled with epithelial morphology, characterized by the accumulation of lysophosphatidylcholines, acylcarnitines, taurine, and bile acids in regions with larger surface area. Using epithelial organoid, we demonstrated that 1- O -octadecyl-2-hydroxy-sn-glycero-3-phosphocholine promoted epithelial differentiation and growth. Our findings reveal that functional complementarity shapes regional morphological heterogeneity in the rumen.