Transcriptome profiling revealed that key rumen epithelium functions change in relation to short-chain fatty acids and rumen epithelium-attached microbiota during the weaning transition. Bos taurus

The rumen is a major site of short-chain fatty acid (SCFA) production and absorption, promoting its functional and histological development during the weaning transition. However, it remains unclear how the rumen epithelium links to ruminal SCFA concentration and epithelium-attached microbes at the molecular level. This study aims to characterize the functional changes of the rumen epithelium associated with ruminal SCFA concentration and epithelium-attached microbes during the weaning transition. Six ruminally cannulated Holstein bull calves were weaned from milk at week 6. Rumen papillae were collected by biopsy at week 5 (W5), week 7 (W7), and week 12 (W12) and subjected to transcriptome analysis using RNA-Sequencing (RNA-Seq), papillae histology (surface area, length, and width) analysis, and microbiota profiling using amplicon seq. Rumen fluid was collected at the same time to determine the extent of rumen fermentation (total SCFA, acetate, propionate, and butyrate concentration). The expression of genes related to SCFA metabolism was commonly detected during the weaning transition. Bioconductor edgeR package was used to identify differentially expressed (DE) genes based on the pairwise comparison between each week, and the number of DE genes was 87 (W5 vs W7), 56 (W7 vs W12), and 457 (W5 vs W12), respectively. Metabolic pathway analysis using the list of significant DE genes showed that LXR/RXR Activation and p38 MAPK Signaling related to SCFA metabolism and cell apoptosis were up- and down-regulated in W12 compared to W5, respectively. Functional analysis, including the weighted correlation network analysis (WGCNA) and gene ontology, and metabolic pathway analysis using Database for Annotation, Visualization, and Integrated Discovery (DAVID) showed that a gene module, consisting of 498 genes that are related to ketogenesis, adenosine triphosphate generation, reactive oxygen species generation, and protective roles against oxidative stress, was positively correlated with ruminal total SCFA concentration and rumen papillae histology . The relative abundance of epithelium-attached Rikenellaceae RC9 gut group and Campylobacter was positively correlated with genes involved in SCFA absorption and metabolism. These findings suggest that SCFA absorption, metabolism and protective roles against oxidative stress-induced apoptosis are the key responses to ruminal SCFA during the weaning transition, and some epithelium-attached bacteria can cooperatively affect host functions with genes involved in SCFA absorption and metabolism. Future research should examine the contribution of attenuated apoptosis on rumen epithelial functional shifts during the weaning transition in dairy calves.