Changes in the Rumen Epithelial Microbiota of Cattle and Host Gene Expression in Response to Alterations in Dietary Carbohydrate Composition.

The inclusion of high-quality hay (HQH), in place of concentrates, shifts dietary carbohydrate intake, and the extent to which these shifts effect epimural microbiota and epithelial gene expression of the rumen has not yet been evaluated. Eight ruminally cannulated nonlactating Holstein cows were used in a replicated 4 by 4 Latin square design with four dietary treatments containing HQH, with either 0% concentrate/100% HQH (100HQH), 25% concentrate/75% HQH (75HQH), or 40% concentrate/60% HQH (60HQH). The fourth group (control [CON]) was fed 60% normal fiber-rich hay and 40% concentrate. The data showed that measures of diversity for the rumen epimural population, specifically the Shannon (P = 0.004) and Simpson (P = 0.003) indices, decreased with increasing levels of HQH in the diet. The feeding of HQH shifted the epimural population from predominantly Firmicutes to Proteobacteria Phylogenetic analysis revealed that HQH feeding markedly shifted the abundance of Campylobacter spp. from 7.8 up to 33.5% (P < 0.001), with greater ingestion of protein (r = 0.63) and sugars (r = 0.65) in HQH diet being responsible for this shift. The expression of genes targeting intracellular pH regulation, barrier function, and nutrient uptake of rumen epithelium remained stable regardless of the carbohydrate source. In conclusion, the data suggest strong alterations of the ruminal epimural microbiota in response to changes in the nutritive patterns of the diet. Further research is warranted to evaluate the long-term effects of these significant microbial changes on rumen health and food safety aspects in cattle at a transcriptional level.IMPORTANCE Feeding of forages versus starchy concentrates is a highly debated topic. Hay is believed to be healthier and more ecological sustainable for cattle than are concentrates, although the effects of feeding hay with enhanced sugar and protein content on epimural microbiota and host gene expression have not yet been evaluated. This research provides a report of the role of feeding hay with increased sugar and protein content in place of starchy concentrates in altering epimural microbiota and in generating a host response. Our research shows that the addition of high-quality hay to dairy rations shifted nutrient intake, resulting in strong alterations in the epimural microbiota in cattle. This work provides a background for further long-term research regarding the effects of feeding practices on the host-microbiome interaction and its role in rumen health and food safety in cattle.