Background: Recently, we reported that some dairy cows could produce high amounts of milk with high amounts of protein (defined as milk protein yield [MPY]) when a population was raised under the same nutritional and management condition, a potential new trait that can be used to increase high-quality milk production. It is unknown to what extent the rumen microbiome and its metabolites, as well as the host metabolism, contribute to MPY. Here, analysis of rumen metagenomics and metabolomics, together with serum metabolomics was performed to identify potential regulatory mechanisms of MPY at both the rumen microbiome and host levels. Results: Metagenomics analysis revealed that several Prevotella species were significantly more abundant in the rumen of high-MPY cows, contributing to improved functions related to branched-chain amino acid biosynthesis. In addition, the rumen microbiome of high-MPY cows had lower relative abundances of organisms with methanogen and methanogenesis functions, suggesting that these cows may produce less methane. Metabolomics analysis revealed that the relative concentrations of rumen microbial metabolites (mainly amino acids, carboxylic acids, and fatty acids) and the absolute concentrations of volatile fatty acids were higher in the high-MPY cows. By associating the rumen microbiome with the rumen metabolome, we found that specific microbial taxa (mainly Prevotella species) were positively correlated with ruminal microbial metabolites, including the amino acids and carbohydrates involved in glutathione, phenylalanine, starch, sucrose, and galactose metabolism. To detect the interactions between the rumen microbiome and host metabolism, we associated the rumen microbiome with the host serum metabolome and found that Prevotella species may affect the host’s metabolism of amino acids (including glycine, serine, threonine, alanine, aspartate, glutamate, cysteine, and methionine). Further analysis using the linear mixed effect model estimated contributions to the variation in MPY based on different omics and revealed that the rumen microbial composition, functions, and metabolites, and the serum metabolites contributed 17.81, 21.56, 29.76, and 26.78%, respectively, to the host MPY. Conclusions: These findings provide a fundamental understanding of how the microbiome-dependent and host-dependent mechanisms contribute to varied individualized performance in the milk production quality of dairy cows under the same management condition. This fundamental information is vital for the development of potential manipulation strategies to improve milk quality and production through precision feeding.

Background: As the global population continues to grow, competition for resources between humans and livestock has been intensifying. Increasing milk protein production and improving feed efficiency are becoming increasingly important to meet the demand for high-quality dairy protein. In a previous study, we found that milk protein yield in dairy cows was associated with the rumen microbiome. The objective of this study was to elucidate the potential microbial features that underpins feed efficiency in dairy cows using metagenomics, metatranscriptomics, and metabolomics.Results: Comparison of metagenomic and metatranscriptomic data revealed that the latter was a better approach to uncover the associations between rumen microbial functions and host performance. Co-occurrence network analysis of the rumen microbiome revealed differential microbial interaction patterns between the animals with different feed efficiency, with high-efficiency animals having more and stronger associations than low-efficiency animals. In the rumen of high-efficiency animals,Selenomonasand members of theSuccinivibrionaceaefamily positively interacted with each other, functioning as keystone members due to their essential ecological functions and active carbohydrate metabolic functions. At the metabolic level, analysis using random forest machine learning suggested that six ruminal metabolites (all derived from carbohydrates) could be used as metabolic markers that can potentially differentiate efficient and inefficient microbiomes, with an accuracy of prediction of 95.06%.Conclusions: The results of the current study provided new insights into the new ruminal microbial features associated with feed efficiency in dairy cows, which may improve the ability to select animals for better performance in the dairy industry. The fundamental knowledge will also inform future interventions to improve feed efficiency in dairy cows.

Aims: To determine the in-vitro effect and mode of action of tea saponin on the rumen microbial community and methane production. Methods and Results: Saponin extracted from tea seeds was added to (1) an in-vitro fermentation inoculated with rumen fluid and (2) a pure culture of Methanobrevibacter ruminantium. Methane production and expression of the methyl coenzyme-M reductase subunit A (mcrA) were monitored in both cultures. Abundance of methanogens, protozoa, rumen fungi and cellulolytic bacteria were quantified using real-time PCR, and bacterial diversity was observed using denaturing gradient gel electrophoresis. Addition of tea saponin significantly reduced methane production and mcrA gene expression in the ruminal fermentation but not with the pure culture of M. ruminantium. The abundance of protozoa and fungi were significantly decreased 50% and 79% respectively but methanogen numbers were not affected, and Fibrobacter succinogenes increased by 41%. Bacterial diversity was similar in cultures with or without tea saponin. Conclusions: Tea saponin appeared to reduce methane production by inhibiting protozoa and presumably lowering methanogenic activity of protozoal-associated methanogens. Significance and Impact of the Study: Tea saponin may be useful as a supplement to indirectly inhibit methane production in ruminants without a deleterious effect on rumen function.

This study revealed the rumen bacteriome from a large dairy cattle cohort ( n = 334) raised under the same management and showed the linkages among the rumen core and pan bacteriomes, rumen short-chain fatty acids, and milk production phenotypes. The findings from this study suggest that the pan rumen bacteriome, together with the core bacteriome, potentially contributes to variations in host milk production traits. Fundamental knowledge on the rumen core and pan microbiomes and their roles in contributing to lactation performance provides novel insights into future strategies for manipulating rumen microbiota to enhance milk production in dairy cattle.