Evaluating The Impact Of A High-Starch And High-Forage Diet On The Ruminal Solid, Liquid, And Epimural Microbiota Of Dairy Cows

Abstract Ruminants harbor a rumen microbial community that convert their host-indigestible diet into nutrients. This rumen microbiome is known to contain three distinct communities: luminal solids, luminal liquids, and the epithelial, or epimural, communities. Currently, there is little research examining the diet-dependent responses of all three microbial communities within the same animals. To address this, we used next-generation 16S rRNA sequencing to characterize the bacterial communities associated with the ruminal solids, liquids, and epimural tissue of 13 lactating and cannulated Holstein dairy cows fed high-starch (diet A) and high-forage (diet B) diets in a crossover experimental design. This crossover design consisted of two groups, two diets, and two sampling periods, with animals receiving a single diet for 8 weeks. Ruminal solids and liquids were collected by separating whole rumen contents through cheesecloth, while rumen epithelial tissue was collected from the ventral-sac via biopsy. Samples were collected at the end of each diet-treatment period. Independent of diet, all sample-types were dominated by bacteria in the phyla Firmicutes and Bacteroidetes. Proteobacteria and Epsilonbacteraeota were also highly abundant, but only in epimural samples. Overall, the epimural microbiota was more diverse, relative to both luminal communities, and diet was found to impact community diversity in solids only. We also found that sample-type, diet-treatment, and their interactions, significantly impacted community structure (Bray-Curtis; PERMANOVA P < 0.05) and composition (Jaccard; PERMANOVA P < 0.05). Of the genera which differed in abundance according to diet and sample-type, Succiniclasticum was highly abundant in epimural samples only, and increased in abundance under a high-forage diet (P < 0.05). In contrast, Saccharofermentans was highly abundant in luminal samples only, but also increased in abundance under a high-forage diet (P < 0.05). These sample-type and diet-dependent differences in specific bacteria likely reflect the overall dietary and environmental factors shaping the heterogeneity of all three ruminal communities.