The microbiome composition of the rumen is altered during the peripartal period in dairy cattle
Alterations in ruminal microbiota composition during the peripartal period were studied using eight multiparous fistulated Holstein dairy cows. Cows were fed a typical TMR to meet NRC (2001) requirements during the dry period and early lactation. Ruminal digesta samples were collected on days -14, -7, +10, +20 and +28 relative to calving. DNA was extracted after physical homogenization and utilized for PCR amplification of the V4 region of the 16S rRNA gene using barcoded universal primers to allow for multiplexing. Amplicons were purified, quantified and subjected to Illumina paired-end sequencing. The PANDAseq assembler was used to merge the paired-end sequences for further analyses using QIIME pipelines. After filtration and removing chimeric reads, assembled sequences were assigned to operational taxonomic units and aligned to Greengenes database. The Chao1 estimator of species richness and Unifrac distance matrices were used to calculate α-diversity and β-diversity of microbial communities, respectively. Differences in bacterial composition across time were tested using the PERMANOVA procedure in PRIMER v6 software. Partial least square discriminant analysis (PLS-DA) of SIMCA was performed to identify taxa that were most characteristic of each time point. A total of 1,393,235 sequences were generated and an average of 35,990 high-quality sequences per sample were obtained after quality filtering steps, which resulted in identification of 16 phyla and 303 taxa of which 145 were classified at the genus level. The microbial profile of ruminal digesta differed across time points with highest differences observed when comparing day -14 to day +28 (P = 0.03), and day -7 to day +28 (P = 0.05). At the phylum level, the abundance of Actinobacteria increased while Armatimonadetes, Cloriflexi, Tenericutes, Verrucomicrobia, and WPS-2 decreased in the postpartum compared with prepartum. At the genus level, the abundance of Atopobium, Clostridium, Coprococcus, Lactobacillus, Moryella, Olsenella, Pediococcus, Shuttleworthia Streptococcus, and Weissella increased postpartum compared with prepartum. Variation in the ruminal microbiota among cows was smaller before calving but gradually increased after calving. This may have been associated with the normal decline in voluntary dry matter intake (DMI) before parturition. The greater dissimilarity postpartum in microbial communities among cows may be due to individual differences in physiological responses. Factors such as DMI, the degree of negative energy balance around parturition, and the occurrence of metabolic disorders during this period could affect the ruminal ecosystem and, thus, alter its microbial composition.
Keywords: Dairy cows, rumen microbiota, transition period, illumina sequencing