Project description:The structure and function of the microbiome inhabiting the rumen are, amongst other factors, mainly shaped by the animal’s feed intake. Describing the influence of different diets on the inherent community arrangement and associated metabolic activities of the most active ruminal fractions (bacteria and archaea) is of great interest for animal nutrition, biotechnology and climatology. Samples were obtained from three fistulated Jersey cows rotationally fed with corn silage, grass silage or hay, each supplemented with a concentrate mixture. Samples were fractionated into ruminal fluid, squeezed solid and solid matter. DNA, proteins and metabolites were analyzed subsequently. DNA extracts were used for Illumina sequencing of the 16S rRNA gene and the metabolomes of rumen fluids were determined by 500MHz-NMR spectroscopy. Tryptic peptides derived from protein extracts were measured by LC-ESI-MS/MS and spectra were processed by a two-step database search for quantitative metaproteome characterization. Protein- and DNA-based datasets revealed significant differences between sample fractions and diets and affirmed similar trends concerning shifts in phylogenetic composition. Ribosomal genes and proteins belonging to the phylum of Proteobacteria, particularly Succinivibrionaceae, exhibited a higher abundance in corn silage-based samples while fiber-degraders of the Lachnospiraceae family emerged in great quantities throughout the solid phase fractions. The analysis of 8163 quantified bacterial proteins revealed the presence of 166 carbohydrate active enzymes in varying abundance. Cellulosome affiliated proteins were less expressed in the grass silage, glycoside hydrolases appeared in slightest numbers in the corn silage. Most expressed glycoside hydrolases belonged to families 57 and 2. Enzymes analogous to ABC transporters for amino acids and monosaccharides were more abundant in the corn silage whereas oligosaccharide transporters showed a higher abundance in the fiber-rich diets. Proteins involved in carbon metabolism were detected in high numbers and identification of metabolites like short-chain fatty acids, methylamines and phenylpropionate by NMR enabled linkage between producers and products. This study forms a solid basis to retrieve deeper insight into the complex network of gut microbial adaptation.

Project description:Inoculation with homofermentative lactic acid bacteria (LAB) effectively enhances the silage quality of forages. Moreover, feeding such LAB-inoculated silage modulates rumen microbiota composition and metabolites, thereby improving ruminant production performance. Nevertheless, the specific mechanism through which LAB inoculants regulate the silage–rumen–mammary gland axis remains unclear.Inoculation with homofermentative Lactiplantibacillus plantarum BX62 improved the alfalfa silage quality. Dairy goats fed the BX62 group silage showed significantly higher milk fat content compared to the control group (no inoculation) (P < 0.05). Integrated analysis of silage microbial metabolomics and experimental validation revealed a significant increase in flavonoid content in the BX62 silage. This was attributed to microbial community restructuring and secretion of carbohydrate-active enzymes (CAZymes), which facilitated plant cell wall degradation and flavonoid release. Rumen metagenomic assembly and binning indicated that feeding flavonoid-rich BX62 silage induced the proliferation of flavonoid-degrading microbes and reshaped the rumen microbiota, which resulted in the upregulation of CAZymes and energy metabolic pathways (e.g., ko00620 Pyruvate metabolism), and enhanced fiber degradation and volatile fatty acid (VFA) production in the rumen. Consequently, acetate-dependent milk fat synthesis was promoted in BX62 group goats as showed by the elevated expressions of acetyl-CoA carboxylase 1 (ACC1), fatty acid synthase (FASN) and acyl-CoA synthetase short-chain family member 2 (ACSS2) in mammary gland. Moreover, four milk fat-positively correlated bacteria species (Eggerthellaceae bacterium, Clostridioides difficile, Candidatus Limivicinus sp., and Collinsella aerofaciens) harboring flavonoid-degrading genes proliferated with elevated flavonoid concentrations in the rumen. In vitro trial further confirmed flavonoid degradation capability in both C. difficile and A. equolifaciens (family Eggerthellaceae), and dose-dependent growth promotion in A. equolifaciens. These results demonstrate that silage-derived flavonoids drive rumen microbiome remodeling and promote mammary lipogenesis through a silage-rumen microbiota-mammary gland triad mechanism.

Project description:Inoculation with homofermentative lactic acid bacteria (LAB) effectively enhances the silage quality of forages. Moreover, feeding such LAB-inoculated silage modulates rumen microbiota composition and metabolites, thereby improving ruminant production performance. Nevertheless, the specific mechanism through which LAB inoculants regulate the silage–rumen–mammary gland axis remains unclear.Inoculation with homofermentative Lactiplantibacillus plantarum BX62 improved the alfalfa silage quality. Dairy goats fed the BX62 group silage showed significantly higher milk fat content compared to the control group (no inoculation) (P < 0.05). Integrated analysis of silage microbial metabolomics and experimental validation revealed a significant increase in flavonoid content in the BX62 silage. This was attributed to microbial community restructuring and secretion of carbohydrate-active enzymes (CAZymes), which facilitated plant cell wall degradation and flavonoid release. Rumen metagenomic assembly and binning indicated that feeding flavonoid-rich BX62 silage induced the proliferation of flavonoid-degrading microbes and reshaped the rumen microbiota, which resulted in the upregulation of CAZymes and energy metabolic pathways (e.g., ko00620 Pyruvate metabolism), and enhanced fiber degradation and volatile fatty acid (VFA) production in the rumen. Consequently, acetate-dependent milk fat synthesis was promoted in BX62 group goats as showed by the elevated expressions of acetyl-CoA carboxylase 1 (ACC1), fatty acid synthase (FASN) and acyl-CoA synthetase short-chain family member 2 (ACSS2) in mammary gland. Moreover, four milk fat-positively correlated bacteria species (Eggerthellaceae bacterium, Clostridioides difficile, Candidatus Limivicinus sp., and Collinsella aerofaciens) harboring flavonoid-degrading genes proliferated with elevated flavonoid concentrations in the rumen. In vitro trial further confirmed flavonoid degradation capability in both C. difficile and A. equolifaciens (family Eggerthellaceae), and dose-dependent growth promotion in A. equolifaciens. These results demonstrate that silage-derived flavonoids drive rumen microbiome remodeling and promote mammary lipogenesis through a silage-rumen microbiota-mammary gland triad mechanism.

			Action	DRS
	SRR9832140.fastq.gz	Fastqsanger.gz
	SRR9832150.fastq.gz	Fastqsanger.gz
	SRR9832160.fastq.gz	Fastqsanger.gz
	SRR9832170.fastq.gz	Fastqsanger.gz
	SRR9832180.fastq.gz	Fastqsanger.gz

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