Evaluating the Impact of High- and Low-Starch Diets on the Ruminal Microbiota of Dairy Cows

Ruminants harbor a ruminal microbiome that converts their host-indigestible diet into nutrients. This microbiome contains three distinct communities: liquid, solid, and epithelial (or epimural). Currently, there is limited research examining the diet-dependent responses of all three microbiomes within the same animal. Here, we used next-generation 16S rRNA sequencing to characterize the ruminal solid (RS), liquid (RL), and epimural (RE) microbiotas of 13 lactating and cannulated Holstein dairy cows fed either a high- or low-starch diet in a crossover experimental design. Independent of diet, we found that all sample types were dominated by the phyla Firmicutes and Bacteroidetes. Proteobacteria and Epsilonbacteraeota were also highly abundant but only in the RE. Although the total VFA molar abundance did not differ between diets, propionate and valerate were found to increase with the high-starch diet, while acetate was increased with the low-starch diet. Overall, we found that the RE microbiota was more diverse than the RS and RL communities, with diet impacting community diversity in the RS. We found that sample type, diet treatment, and their interaction significantly impacted community structure and composition. Notably, Prevotella was most abundant in the RL and RS, particularly on the low-starch diet. We also found that Lachnospiraceae were significantly enriched in the RS and RL with a high-starch diet, whereas Succiniclasticum was highly abundant in the RE with a low-starch diet. These data suggest that diet influences all three ruminal microbiomes and provides a useful framework for understanding the role of these microbiomes in mediating host production.