Strain-resolved comparison of beef and draft cattle rumen microbiomes using single-microbe genomics

Abstract

Abstract Background Beef and draft cattle have distinct rumen microbiota that can influence their metabolic processes and body composition. However, traditional metagenomic sequencing methods only provide broad surveys of the rumen microbial genomic contents. In this study, we utilized high-throughput single-cell genome sequencing to investigate these differences at the strain level. Results Following quality control and contig assembly, we obtained 97 bacterial genomes, 17 archaeal genomes, and 241 subspecies genomes from the rumen samples of Angus and Wuling cattle. Our analysis revealed a higher bacterial abundance in Angus rumen, characterized by an enrichment of the Succiniclasticum and Limivicinus genera. In contrast, the rumen of Wuling cattle exhibited a higher archaeal abundance. Additionally, we observed variations in the types and abundance of microbial-derived enzymes responsible for plant fiber degradation and volatile fatty acid (VFA) production between the two cattle breeds. The Angus rumen was found to harbor a higher diversity and abundance of cellulases and hemicellulases, particularly from the Ruminococcus unknown_0 genus. Furthermore, genera such as Succiniclasticum, Butyrivibrio, Limivicinus, UBA2868, and Prevotella were identified as key contributors to VFA production. Our findings suggest that the Angus rumen may have a stronger VFA production capacity due to the higher abundance of acidogenic genera. Interestingly, we also observed a greater abundance of Methanobrevibacter_A methanogens, which play a crucial role in energy flow in the rumen ecosystem, in Wuling cattle compared to Angus cattle. Conclusion Our study highlights differences in the rumen microbiome of Angus and Wuling cattle. This difference could, at least partially, account for the variation in fat content that ultimately results in the superior meat quality of Angus cattle and the sustained muscle activity required by draft cattle. Overall, single-cell genome sequencing reveals distinct microbial composition and metabolic pathways between the two breeds, providing insights into their unique physiological and metabolic needs.

Keywords

• High-throughput
• Single-microbe genomics sequencing
• Rumen microbe
• Beef cattle
• Draft cattle