Effect Of Early-Life Management Practices On The Rumen Metagenome Of Beef Cattle

Abstract

Although the rumen microbiome plays a critical role in beef cattle health and productivity, the effect of early-life management practices on the rumen metagenome of beef calves has been scarcely studied. Through two research studies, this thesis investigated the effect of four castration time windows and two weaning strategies on the rumen metagenome of beef calves through a comprehensive metagenomic sequencing approach that included a technical comparison of shotgun metagenomic sequencing and 16S rRNA gene sequencing to study the rumen microbiome. We found that castration timing had limited long-term effects on the rumen microbiome, while weaning strategy showed short-term effects on the microbiome composition and methanogenic gene content of the rumen, but not on the rumen resistome. In addition, our results showed that despite technical discrepancies, 16S rRNA gene sequencing and shotgun metagenomic sequencing methods led to similar ecological inferences about the effect of weaning strategy on the rumen microbiome of beef calves. These studies highlight the importance of considering early-life interventions in beef cattle management and provide insights into the comparability of rumen microbiome sequencing methods. Understanding rumen microbiome dynamics and choosing appropriate sequencing approaches are crucial for advancing rumen microbiome research in beef cattle.