Abstract
Variation exists in milk protein concentration of dairy cows of the same breed that are fed and managed in the same environment, and little information was available on this variation which might be attributed to differences in rumen microbial composition as well as their fermentation metabolites. This study is aimed at investigating the difference in the composition and functions of rumen microbiota as well as fermentation metabolites in Holstein cows with high and low milk protein concentrations. In this study, 20 lactating Holstein cows on the same diet were divided into two groups (10 cows each), high degree of milk protein group (HD), and low degree of milk protein (LD) concentrations based on previous milk composition history. Rumen content samples were obtained to explore the rumen fermentation parameters and rumen microbial composition. Shotgun metagenomics sequencing was employed to investigate the rumen microbial composition and sequences were assembled via the metagenomics binning technique. Metagenomics revealed that 6 Archaea genera, 5 Bacteria genera, 7 Eukaryota genera, and 7 virus genera differed significantly between the HD and LD group. The analysis of metagenome-assembled genomes (MAGs) showed that 2 genera (g__Eubacterium_H and g__Dialister) were significantly enriched (P < 0.05, linear discriminant analysis (LDA) > 2) in the HD group. However, the LD group recorded an increased abundance (P < 0.05, LDA > 2) of 8 genera (g__CAG-603, g__UBA2922, g__Ga6A1, g__RUG13091, g__Bradyrhizobium, g__Sediminibacterium, g__UBA6382, and g__Succinivibrio) when compared to the HD group. Furthermore, investigation of the KEGG genes revealed an upregulation in a higher number of genes associated with nitrogen metabolism and lysine biosynthesis pathways in the HD group as compared to the LD group. Therefore, the high milk protein concentration in the HD group could be explained by an increased ammonia synthesis by ruminal microbes which were converted to microbial amino acids and microbial protein (MCP) in presence of an increased energy source made possible by higher activities of carbohydrate-active enzymes (CAZymes). This MCP gets absorbed in the small intestine as amino acids and might be utilized for the synthesis of milk protein.
Key points
• Rumen microbiota and their functions differed between cows with high milk protein % and those with low milk protein %.
• The rumen microbiome of cows with high milk protein recorded a higher number of enriched genes linked to the nitrogen metabolism pathway and lysine biosynthesis pathway.
• The activities of carbohydrate-active enzymes were found to be higher in the rumen of cows with high milk protein %.
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Data availability
The raw sequences of rumen bacterial genes were uploaded to the Sequence Read Archive (SRA) of the National Centre for Biotechnology Institute (NCBI) with the BioProject accession number (PRJNA907195) https://www.ncbi.nlm.nih.gov/sra/?term=PRJNA907195
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This research was funded by grants from the National Key Research and Development Program of China (2021YFF1000703-01). Our project was also supported by the High-Performance Computing Platform of Bioinformatics Center, Nanjing Agricultural University.
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SM acquired the funding, conceived the idea, supervised the project, supplied the resources and software, and edited the draft. AB participated in data curation, performed the laboratory and bioinformatics analysis, wrote the original draft, and edited the manuscript. LZ participated in data curation, and performed the laboratory analysis. JZ participated in data curation, and performed the laboratory analysis.
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Amin, A.B., Zhang, L., Zhang, J. et al. Metagenomics analysis reveals differences in rumen microbiota in cows with low and high milk protein percentage. Appl Microbiol Biotechnol 107, 4887–4902 (2023). https://doi.org/10.1007/s00253-023-12620-2
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DOI: https://doi.org/10.1007/s00253-023-12620-2