Metagenomic analysis of the rumen microbiome of dairy cows during the transition period
In the current study we characterized the rumen microbiome of dairy cows belonging to different lactations which were grouped as first lactation (L1; n=5), second lactation (L2; n=2) and third lactation (L3; n=2). The rumen samples were collected using stomach tube method at four time points i.e., three weeks prior to the anticipated freshening date (S1), soon after the animal freshened (S2), four weeks (S3) and eight weeks (S4) into lactation. We pooled the genomic DNA by lactation number (3 lactation groups x 4 sampling times) to yield 12 samples. All animals received the same dry cow ration (CP-14.65%; NDF-43.66%; Starch-21.9%) prior to calving and the same lactating cow rations (CP-17.21%; NDF-33.14%; Starch-27.19%) post calving. The pooled genomic DNA was subjected to shotgun sequencing on Ion-torrent platform, aligned for contigs using Nextgene and uploaded to MG-Rast server for further analysis. On average 17,000 contigs per sample were obtained and subsequently used for phylogenetic and functional assignments in MG-Rast. Based on the phylogenetic data, both study group and study day tended to have an effect on the community compositions (P<0.12; Permanova test) while study groups differed in their functional profiles (P<0.05; Permanova test). The most abundant bacterial phyla observed were Bacteroidetes(60%), Firmicutes(20%) and Proteobacteria(7%) across all communities. As the cows transitioned into lactation, the abundance of Bacteroidetes decreased while that of Firmicutes increased. The phylum Proteobacteria increased in abundance with the onset of lactation and also with increased parity. The abundance of archaeal communities were found to be higher in the dry period but reduced at the onset of lactation. Both carbohydrate and protein metabolism were the most predominant functional activities with a progressive increase (P<0.1) in protein utilization from L1 to L3 dairy cows. Differences also occurred in the carbohydrate and protein metabolism before and after the onset of lactation (P<0.05). This study is the first report to demonstrate distinct shifts in both phylogenetic and the associated metabolic activity in both primiparous and multiparous dairy cows in their transition period.
Dairy cows, transition period, rumen microbiome, Ion-torrent, Metabolic potential