Rumen microbiome biogeography and ventral epithelial architecture in three ruminant species

Area of Science:

• Microbiology
• Genomics
• Animal Science

Background:

• Ruminants utilize rumen microbiome for fibrous plant fermentation.
• Spatial biogeography of the rumen microbiome and ventral epithelium's genetic diversity are poorly understood.

Purpose of the Study:

• To investigate the spatial microbiome and ventral rumen epithelium's genetic diversity in roe deer, sika deer, and sheep.
• To understand species-specific microbial and epithelial variations and their impact on ruminant productivity.

Main Methods:

• Multi-omics approach including region-resolved microbiome, metabolome, single-cell RNA sequencing (scRNA-seq), ATAC-seq, and bulk RNA sequencing (RNA-seq).
• Analysis of 11 ruminal sacs and ventral epithelium from three ruminant species.

Main Results:

• Identified species-specific microbial compositions and metabolic capacities influencing short-chain fatty acid and vitamin B production.
• Revealed functional divergence and metabolic changes within the rumen microbiome across different sacs.
• Uncovered immune responses and structural remodeling in the ruminal ventral epithelium via single-cell profiling.
• Demonstrated vitamin B12's role in promoting epithelial growth and identified genes for stem cell differentiation.

Conclusions:

• Rumen microbial ecology and epithelial architecture vary significantly among ruminant species.
• Findings provide insights into improving livestock productivity through understanding rumen function and host-microbe interactions.