Effect of divergent feeding during early life on the rumen microbiota in calves

The present study determined whether divergent feeding regimens during the first 41 weeks of a calf's life, are related with long-term changes in the rumen microbiota, and the associated fermentation end-products. Twenty-four calves were arranged in a 2x2 factorial design with two divergent treatments across 3 periods. In period 1 (P01, 0-14 weeks), calves were offered a low-milk volume/concentrate starter diet with early weaning (CO) or high-milk volume/pasture diet and late weaning (FO). In period 2 (P02, 15-30 weeks), calves from both groups were randomly allocated to either high-quality (HQ) or low-quality (LQ) pasture grazing groups. In period 3 (P03, 31-41 weeks), calves were randomly allocated to one of two grazing groups and offered the same pasture-only diet. At weeks 9, 19 and 41, methane (CH4) and hydrogen (H2) emissions, and dry matter intake (DMI) were measured in respiration chambers and rumen samples for evaluation of microbiota and short-chain fatty acids (SCFA) characterizations were collected. Microbial 16s rRNA from ruminal samples was extracted using the phenol-chloroform, bead beating with filtration kit for purification II protocol and sequenced using the Illumina MiSeq system. Sequence reads were provided in fastq format.