Metatranscriptomic Profiling Reveals Linkages between the Active Rumen Microbiome and Feed Efficiency in Beef Cattle

Area of Science:

• Animal Science
• Microbiology
• Genomics

Background:

• Rumen microbiome composition and function are crucial for cattle feed efficiency.
• Understanding the active microbiome provides insights into host metabolic processes.
• Feed efficiency varies significantly among beef cattle, impacting production.

Purpose of the Study:

• To characterize the active rumen microbiome in beef cattle with varying feed efficiencies.
• To identify compositional and functional differences in the rumen microbiome related to feed efficiency.
• To explore the role of microbial metabolic functions, including carbohydrate-active enzymes (CAZymes), in host feed efficiency.

Main Methods:

• Applied total RNA-based metatranscriptomics to analyze active rumen microbiomes.
• Estimated active bacterial and archaeal compositions using 16S rRNA.
• Assessed active microbial metabolic functions and CAZymes using mRNA from metatranscriptomic data.

Main Results:

• Identified core components of the active rumen microbiome, including specific bacterial phyla, families, archaeal clades, metabolic pathways, and CAZymes.
• Found differences in the abundance of certain bacterial families (e.g., Lachnospiraceae) and archaeal taxa (e.g., Methanomassiliicoccales) between efficient and inefficient cattle.
• Observed differential abundance of 32 microbial metabolic pathways and 12 CAZymes, with more diverse activities in inefficient cattle.

Conclusions:

• The active rumen microbiome composition and function are linked to feed efficiency in beef cattle.
• Inefficient cattle exhibit a more diverse active rumen microbiome, suggesting a role in host feed efficiency variation.
• Findings provide a foundation for understanding and potentially manipulating rumen microbial functions to improve cattle feed efficiency and nutrient utilization.