Assessing the impact of diet on microbial succession, growth, and milk production in dairy cow

Cows rely on their gastrointestinal tract (GIT) microbiota for survival on a plant-based diet. The development of these microbial communities is essential and has consequences for agriculturally relevant outcomes like milk production. However, the acquisition and succession of microbes in the calf GIT and how this process is affected by early-life factors, such as diet, are not fully understood. This thesis encompasses work to investigate these questions by determining the GIT-associated microbial communities of dairy cows raised on calf starter grains and/or corn silage and tracking animals from birth to adulthood. Bacterial, archaeal, and fungal communities were determined by Illumina amplicon sequencing of rumen and fecal samples obtained from Holstein dairy cows from 2 weeks of age to the middle of their first lactation cycle (> 2 years). These communities were correlated to animal growth, health, and milk production to determine the long-term effects of calf diet. The succession of microorganisms in the GIT was unique to each animal, and corn silage promoted a more adult-like microbiota by weaning. However, all animals converged on an adult-like composition between weaning (8 weeks) and 1 year of age. Regardless of diet, adults and calves possessed the same taxa but had different specific operational taxonomic units (OTUs), indicating species-level differences in the microbiota. Some diet-driven differences persisted in adult animals but these did not correlate with animal growth, milk production, or overall efficiency. This suggests that calf feed does not have long-term effects on the adult cow, and practices aimed at altering the microbiota for improved production may be most effective between weaning and 1 year of age.