Instability of the rumen microbiota in pre-ruminant calves

The temporal sequence of microbial establishment in the pre-ruminant rumen has important ecological and pathophysiological implications. In this study, we characterized the rumen microbiota of pre-ruminant calves fed milk replacer using metagenomic tools. Contrast to a relatively stable microbiota of 42-day-old calves, the microbial communities of 14-day-old calves displayed a large variation in phylogenetic composition. The sequences from greater than 24 prokaryotic phyla and 22 eukaryotic phyla were identified in microbial communities of pre-ruminant calves. Bacteroidetes was the most dominant phylum in the rumen microbiota of 42-day-old calves, represented by up to 80% of the total sequences, followed by Proteobacteria and Firmicutes. However, the phylum-level composition of the rumen microbiota of 14-day-old calves was distinctly different from that of older pre-ruminant calves as well as that of post-weaning cattle. A total of 441 prokaryotic genera, including 217 genera that existed in all samples tested, were identified. The functional diversity of the rumen microbiota was reflected by a sum of 8,298 Pfam protein families identified. One of the most salient features of the rumen microbiota of pre-ruminant calves was its instability during early rumen development. Some protein families, including peptidases and glycoside hydrolases, were more abundant in the rumen microbial ecosystem of older pre-ruminant calves. It appeared that microbial establishment in the pre-ruminant calves preceded the development of ruminal papillae. Our results provided insight into understanding dynamics of the rumen microbiota and facilitated our efforts in the formulation of optimal early-weaning strategies.