Increase in Dietary Energy of Milk Replacer Increases Rumen Microbiome Diversity in Heifer Calves

The diversity of the rumen microbiome of a calf can affect their ability to convert feed into energy. The objectives of this study were to 1) characterize the rumen microbiome of pre-weaned and post-weaned Holstein heifer calves and 2) determine the effect of differing energy levels on rumen microbial composition. Holstein heifer calves (n = 12) were randomly assigned to 1 of 2 milk replacer diets: a restricted (R; 20% CP, 20% Fat; n = 6) or enhanced diet (E; 28% CP, 25% Fat; n = 6). Calves were euthanized and rumen fluid samples were collected at pre-weaning (8 wks; n = 6) or post-weaning (10 wks; n = 6). Libraries were constructed from extracted DNA and DNASeq was conducted using a paired-end analysis at 100 bp using Illumina HiSeq 2500. Operational taxonomic unit (OTU) clustering analysis was conducted using the 16s rRNA Greengenes reference. A PERMANOVA analysis was conducted in R to determine OTU populations for age and treatment. There was no difference in microbiome composition between pre-weaning and post-weaning calves (P = 0.761). Microbiome composition differed between E and R calves (P < 0.001). Bacteroidetes and Firmicutes represented the most abundant phyla for both E and R calves. Enhanced calves had 49.4% Bacteriodetes and 36.4% Firmicutes; whereas, R calves had 31.6% Bacteriodetes and 41.1% Firmicutes. Overall, change in dietary energy of milk replacer influences calf rumen microbial profiles.