Prepartum and Postpartum Rumen Fluid Microbiomes: Characterization and Correlation with Production Traits in Dairy Cows

Abstract

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...

Ruminal Bacterial Community Composition in Dairy Cows Is Dynamic over the Course of Two Lactations and Correlates with Feed Efficiency

“…Moreover, research focused on the development of the ruminal community over time has relied primarily on calves (3-6, 23, 37) or a limited number of time points with adult animals (20, 23) and thus could not include data on the efficiency of downstream milk production. To date, studies on the ruminal microbiota of dairy cows in relation to their milk production metrics have been limited by restricted sampling periods (12,20), making it difficult to address issues of long-term community stability with host metrics. In this study, we tracked the ruminal bacterial community, feed consumption, and milk production over the course of 2 years, including three stages within each lactation cycle.…”

“…Feed efficiency in dairy cattle is known to be affected by a variety of factors, including host genetics, environmental conditions such as ambient temperature, the various metabolic contributions and demands of pregnancy, tissue mobilization, and immune response. Moreover, recent studies have reported that the composition of the ruminal microbial community is associated with differences in several drivers of feed efficiency (2, 12-15), milk yield and composition (12,(16)(17)(18)(19), and alterations in pregnancy stage (20).Recent work using high-throughput sequencing technology has revealed correlations between the abundance of particular ruminal bacterial genera with milk composition and RFI, although these determinations did not consider changes over entire lactation cycles (12,20). Given that milk production is altered by major physiological shifts associated with stage of lactation and pregnancy (6, 21), it is necessary to consider that time may be a significant variable in the composition of the ruminal microbial community.…”

“…Recent work using high-throughput sequencing technology has revealed correlations between the abundance of particular ruminal bacterial genera with milk composition and RFI, although these determinations did not consider changes over entire lactation cycles (12,20). Given that milk production is altered by major physiological shifts associated with stage of lactation and pregnancy (6, 21), it is necessary to consider that time may be a significant variable in the composition of the ruminal microbial community.…”

“…Feed efficiency in dairy cattle is known to be affected by a variety of factors, including host genetics, environmental conditions such as ambient temperature, the various metabolic contributions and demands of pregnancy, tissue mobilization, and immune response. Moreover, recent studies have reported that the composition of the ruminal microbial community is associated with differences in several drivers of feed efficiency (2,(12)(13)(14)(15), milk yield and composition (12,(16)(17)(18)(19), and alterations in pregnancy stage (20).…”

Modulation of the rumen microbiome

“…Addressing the gaps in current understanding of the rumen microbial ecosystem 41 is therefore key to the development of new strategies to control the microbial populations. The rumen contains a very dense microbial ecosystem, endproducts of microbial digestion, salts and plant material including partially digested fibre, carbohydrate, and phenolic compounds and as such, samples of rumen material often present unique technical challenges.…”