goat rumen metagenome

The aim of our study is to elucidate the mechanisms by which rumen microbiota regulate milk fat yield (MFY) in dairy goats. By investigating the milk yield and milk composition of a cohort of mid-lactation Saanen dairy goats, we selected 10 high MFY (HFY) and 10 low MFY (LFY) goats based on the product of milk yield and milk fat percentage. Using multi-omics approaches, we aimed to uncover the mechanisms by which rumen microbiota regulate MFY, providing scientific evidence for improving milk production and milk fat synthesis in dairy goats and for the breeding of high-quality dairy goats. In this experiment, we constructed a high-quality reference geneset and assembled genome database of goat rumen microbiome by integrating metagenomic sequencing data of rumen digesta and utilizing gene prediction and genome binning techniques. Using these data resources, combined with rumen metabolomics, we analyzed the mechanisms by which microbiome regulate MFY and identified key functional strains. HFY goats exhibited superior lactation phenotypes, with higher concentrations of propionate, acetate, butyrate, and beta-hydroxybutyrate in the rumen and serum, which are biomarkers of milk yield and milk fat percentage, compared to LFY goats. Additionally, the rumen of HFY goats was enriched with various Prevotella species, which were positively correlated with key metabolic phenotypes. Functionally, the highly expressed functional enzyme genes in the rumen of HFY goats showed stronger synthesis capabilities for acetate, propionate, butyrate, thiamine, pantothenic acid, and niacin, and these enzyme genes were mainly phylogenetically attributed to Prevotella. Conversely, the highly expressed enzyme genes in the LFY group were involved in methane metabolism. At the genomic level, we found that Prevotella in the goat rumen are independent and efficient synthesizers of thiamine, pantothenic acid, and niacin, and have the ability to convert them into downstream active forms. Importantly, the Prevotella MAGs enriched in the HFY and LFY groups showed a transition from strong to poor synthesis capabilities for thiamine, propionate, and niacin, with MAG 4742, annotated as Prevotella bryantii, capable of independently synthesizing all three vitamins and their corresponding active forms.