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Title: Quantification of transcriptome responses of the rumen epithelium to butyrate infusion

Author
item Baldwin, Ransom - Randy
item WU, SITAO - University Of San Diego
item LI, WEIZHONG - University Of California
item Li, Congjun - Cj
item BEQUETTE, BRIAN - University Of Maryland
item Li, Robert

Submitted to: Gene Regulation and Systems Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/1/2012
Publication Date: 6/20/2012
Citation: Baldwin, R.L., Wu, S., Li, W., Li, C., Bequette, B.J., Li, R.W. 2012. Quantification of transcriptome responses of the rumen epithelium to butyrate infusion. Gene Regulation and Systems Biology. 6:67–80.

Interpretive Summary: Butyrate is an important nutrient produced by gut microbes. Butyrate has a broad range of biological function and plays a critical role in energy metabolism and physiology in cattle as well as in human health due to its anti-tumor and anti-inflammatory properties. However, its regulatory effect on the rumen wall has not been examined. This report identified pathways and global gene networks influenced by butyrate. Cattle farmers will benefit from this study because extensive animal production and maintenance of animal health can be properly balanced via selectively enhancing butyrate synthesis. Customers in general may benefit from this study by having a better therapeutic use of butyrate in treating diseases.

Technical Abstract: Short-chain fatty acids (SCFAs), such as butyrate, produced by gut microorganisms play an important role in energy metabolism and physiology in ruminants as well as in human health. Butyrate is a preferred substrate in the rumen epithelium where approximately 90% of butyrate is metabolized. Additionally, butyrate serves as a signaling molecule and exerts its impact on multiple signaling pathways. In this study, the temporal effects of elevated butyrate concentrations on the transcriptome of the rumen epithelium was quantified via serial biopsy sampling using high-throughput RNA-seq technology and bioinformatic tools. The mean number of genes transcribed in the rumen epithelial transcriptome was 17,323.63 ± 277.20 (± sd; N =24) while the core transcriptome consisted of 15,025 genes. Collectively, a total of 80 genes were identified as being significantly impacted by direct ruminal butyrate infusion across all time points sampled relative to initiation of butyrate infusion. Maximal transcriptional effect of butyrate on the rumen epithelium was observed at the 72-h post initiation of infusion when the abundance of 58 genes was altered. The initial reaction of the rumen epithelium to elevated exogenous butyrate may represent a stress response as Gene Ontology (GO) terms identified as enriched were predominantly related to biological processes such as response to bacteria and biotic stimuli. An algorithm for the reconstruction of accurate cellular networks (ARACNE) was used to infer global gene networks impacted by treatment. ARACNE inferred regulatory gene networks with 113,738 direct interactions in the butyrate-epithelium interactome using a combined cutoff of an error tolerance (e =0.10) and a stringent P-value threshold of mutual information (5.0 x 10-11). Several regulatory networks controlled by transcription factors, such as CREBBBP and TTF2, which were regulated by butyrate, were involved in distinct functions. Our findings provide insight into the regulation of butyrate transport and metabolism in the rumen epithelium and transcriptome dynamics, which will guide our future efforts in exploiting potential beneficial effect of butyrate in animal well-being and human health.