cMicrobes present in the rumen of dairy cows are essential for degradation of cellulosic and nonstructural carbohydrates of plant origin. The prepartum and postpartum diets of high-producing dairy cows are substantially different, but in what ways the rumen microbiome changes in response and how those changes may influence production traits are not well elucidated. Here, we sequenced the 16S and 18S rRNA genes using the MiSeq platform to characterize the prepartum and postpartum rumen fluid microbiomes in 115 high-producing dairy cows, including both primiparous and multiparous animals. Discriminant analysis identified differences between the microbiomes of prepartum and postpartum samples and between primiparous and multiparous cows. 18S rRNA sequencing revealed an overwhelming dominance of the protozoan class Litostomatea, with over 90% of the eukaryotic microbial population belonging to that group. Additionally, fungi were relatively more prevalent and Litostomatea relatively less prevalent in prepartum samples than in postpartum ones. The core rumen microbiome (common to all samples) consisted of 64 bacterial taxa, of which members of the genus Prevotella were the most prevalent. The Chao1 richness index was greater for prepartum multiparous cows than for postpartum multiparous cows. Multivariable models identified bacterial taxa associated with increased or reduced milk production, and general linear models revealed that a metagenomically based prediction of productivity is highly associated with production of actual milk and milk components. In conclusion, the structure of the rumen fluid microbiome shifts between the prepartum and first-week postpartum periods, and its profile within the context of this study could be used to accurately predict production traits.
Rumen microbiology studies in the last 4 to 5 decades have contributed to the advancement of the field of anaerobic microbiology (1, 2) and have explained much regarding the nature of ruminal fermentation, its effect on ruminant nutrition, and the physiological importance of volatile fatty acid production by ruminal microorganisms to the nutrition of the host. Additionally, ruminal microbiology provided vital concepts and quantitative data that are essential for the construction of the mathematical models that allow for precision nutrition of ruminants, which has been adopted throughout the world in modern meat and milk production systems (3). However, direct manipulation of fermentation by biotechnological means has so far been restricted to a few antimicrobial compounds and some microorganisms that can be added to the feed.High-throughput sequencing technologies have opened new frontiers in microbial analysis by allowing cost-effective characterization of complex microbial communities in biological samples, and they have significantly improved our knowledge of bovine rumen microbial diversity. Over 27,000 carbohydrate-active genes, 50 proteins with enzymatic activity against cellulosic substrates, and 15 uncultured microbial genomes were reveal...