Effects of different dry period managements on rumen microbiome composition

Abstract Text: The effects of two different dry period managements on rumen bacterial population were examined during pre- and postpartum periods. Twenty-four Holstein dairy cows were paired according to their expected calving date, and randomly assigned to one of the two treatments. Treatments included a 60-d dry period (60-d trt) with separate far-off and close-up diets and a 40-d dry period (40-d trt) during which only the close-up diet was fed. The far-off diet contained 1.28 Mcal/kg NE_l, 14.7% CP, and 50% NDF on a DM basis. The close-up diet contained 1.43 Mcal/kg NE_l, 14.6% CP, and 38% NDF. A common lactation diet was fed to all cows after calving, which contained 1.69 Mcal/kg, 17.6% CP, and 31% NDF. The forage portion of ration consisted of timothy hay, barley and corn silage and the concentration portion consisted of soybean, canola, barley and wheat. Rumen fluid was sampled using stomach tube at wks -2, -1, +1, +2 and +7, relative to calving. DNA was extracted, normalized and used for amplification of the V4 region of bacterial 16S rRNA, and subjected to Illumina sequencing. The QIIME pipeline was used for downstream data analyzing. After removing all chimeric reads, sequences were assigned to operational taxonomic units and aligned to Greengenes database. The α- and β-diversity of rumen microbiota were calculated using Chao1 and Unifrac distance matrices, respectively. PERMANOVA procedure was used to compare differences in bacterial communities between treatments and sampling time points. Partial least square discriminant analysis (PLS-DA) of SIMCA was performed to identify taxa associated with each treatment and time point. PERMANOVA analysis revealed significant differences in rumen bacterial composition between pre- and postpartum in the 60-d trt (P<0.01), however, no difference was observed between pre- and postpartum in the 40-d trt (P<0.2). At the genus level, Bulleidia, Coprococcus and Ruminococcus increased in 40-d trt compared with 60-d trt prepartum (P<0.05). After calving, Olsenella increased and Coprococcus, Bifidobacterium and Treponema decreased (P<0.05) in the 40-d trt compared with the 60-d trt. At the phylum level, no significant difference was observed between treatments prepartum (P<0.9). However, after calving, Spirochaetes and Chloroflexi populations decreased (P<0.05) while Proteobacteria and Firmicutes increased (P<0.05) in 40-d trt compared with 60-d trt. Differences between treatments, at the phylum and genus levels during pre- and postpartum were likely due to longer consumption of close-up diet in the 40-d trt compared to the 60-trt.

Keywords: Dairy cow, Dry period management, Rumen microbiome, Illumina sequencing