Illumina sequencing analysis of the ruminal microbiota in high-yield and low-yield lactating dairy cows

Abstract

Abstract In this study, differences in the ruminal bacterial community between high-yield and low-yield lactating dairy cows fed the same diets were investigated. Sixteen lactating dairy cows with similar parity were divided into two groups based on their milk yield: high-yield (HY) and low-yield (LY) groups. On day 21, rumen content samples were collected, and the microbiota composition was determined using Illumina MiSeq sequencing of the 16S rRNA gene. During the study period, dry matter intake (DMI) and milk yield were measured daily, and milk composition was assessed 3 times per week. The results showed that the milk of the LY group tended to have higher fat ( P =0.08), protein ( P =0.01) and total solid ( P =0.04) contents than that of the HY group, though the HY group had higher ruminal acetate ( P =0.05), propionate ( P =0.02) and volatile fatty acid (VFA) ( P =0.02) concentrations. Principal coordinate analysis indicated significant differences in ruminal bacterial community composition and structure between the HY group and LY group. Overall, Bacteroidetes (HY group: 52.91±3.06%; LY group: 61.88±3.03%) was the predominant phylum, followed by Firmicutes (HY group: 41.10±2.74%; LY group: 32.11±2.97%). The abundances of Ruminococcus 2 , Lachnospiraceae and Eubacterium coprostanoligenes were significantly higher in the HY group than in the LY group. In addition, 3 genera— Anaerostipes , Bacteroidales and Anaeroplasma —were identified as biomarker species with the greatest impacts on the ruminal community structure in the LY group. These findings facilitate the understanding of bacterial synthesis within the rumen and reveal an important mechanism underlying differences in milk production in dairy cows.