Integrated meta-omics reveals new ruminal microbial features associated with feed efficiency in dairy cattle

Abstract

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, Selenomonas and members of the Succinivibrionaceae family 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.

Characterization of rumen, fecal, and milk microbiota in lactating dairy cows

“…Despite the volume of information on the GIT microbial population, little remains known about how milk yield and milk quality can be impacted by manipulation of the gut microbiota in dairy cattle. Aside from limited assessments of feed efficiency and milk production variables such as lactation stage and milk composition ( Schären et al, 2018 ; Xue et al, 2018 , 2022 ; Buitenhuis et al, 2019 ; Hagey et al, 2019 ), much of the dairy cattle microbiome research has focused on mitigating GIT inflammation or reducing greenhouse gas emissions ( Sanz-Fernandez et al, 2020 ; John et al, 2022 ). Few studies have evaluated the associations between the rumen microbiome and milk yield or quality ( Xue et al, 2018 ; Buitenhuis et al, 2019 ; Hagey et al, 2019 ).…”

Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep

“…Methane not only increases the global greenhouse effect but can also cause animals to lose more than 10% of their energy [ 3 ]. Recent studies have shown that Methanobrevibacter is enriched in the rumens of low-efficiency cows, and the methanogens pathway is also upregulated in low-efficiency cows [ 46 ]. These results demonstrate the negative impact of methanogenic bacteria on ruminants.…”

Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages

“…The rich microorganisms contained in the rumen are an indispensable link in the digestion of animal nutrients and play a key role in the conversion of plants into milk by dairy cows 12 . Numerous studies have shown that the interactions between rumen microorganisms and the host affect host metabolic processes 13 , 14 . The connection between rumen microbial community composition and change and host production performance is an important breakthrough for heat stress affecting dairy farming technology.…”