Transcriptome analysis of rumen epithelium and metatranscriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis

Authors: Li, Wenli; ARNOLD, SONIA - University Of Wisconsin; EDWARDS, ANDREA - University Of Wisconsin; RIEHLE, CHRISTINA - University Of Wisconsin

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/4/2019
Publication Date: 3/18/2019
Citation: Li, W., Arnold, S., Edwards, A., Riehle, C. 2019. Transcriptome analysis of rumen epithelium and metatranscriptome analysis of rumen epimural microbial community in young calves with feed induced acidosis. Scientific Reports. 9. Article 4744. https://doi.org/10.1038/s41598-019-40375-2.
DOI: https://doi.org/10.1038/s41598-019-40375-2

Interpretive Summary: Ruminal acidosis is a well-recognized digestive disorder found in well-managed dairy herds. Many of the common management practices used to raise dairy calves while on milk and during weaning can cause rumen acidosis. Rumen pH has long been used to diagnose sub-clinical ruminal acidosis. However, little is known how prolonged sub-clinical ruminal acidosis affects calf rumen physiology and overall development. Additionally, the long-term effect of ruminal acidosis on the calf rumen microbial community is not known. With feed induced rumen acidosis, we hope to gain knowledge about the genetic changes in the calf rumen and its associated microbial species in post weaning calves at 16 weeks of age. Such knowledge will allow more precise development of biomarkers either based on host rumen gene expression or rumen microbial gene expression. Developed biomarkers are likely to facilitate improved diagnosis and management of ruminal acidosis in dairy calves.

Technical Abstract: In dairy calves, many of the common management practices used to raise dairy calves while on milk and during weaning can cause rumen acidosis. Rumen pH has long been used to identify ruminal acidosis. However, few attempts have been undertaken to understand the role of prolonged ruminal acidosis on rumen microbial community or health in neonatal calves. Thus, the molecular changes associated with prolonged rumen acidosis in post weaning young calves are largely unknown. In this study, we induced ruminal acidosis through starch concentrated feed in young calves starting from 6 weeks (preweaning) of age up to 16 weeks (post-weaning). Rumen epithelial tissues were collected at necropsy at 17 weeks of age and subjected to transcriptome analysis both on the rumen epithelium and on the associated microbial communities. Calves with induced ruminal acidosis showed significantly less weight gain in addition to substantially lower rumen pH 8 hours after feeding. Rumen transcriptome changes included enrichment in mRNAs corresponding to genes involved in cell signaling and morphogenesis, indicating the impact of ruminal acidosis on rumen papilla development. rRNA reads based microbial classification indicated increased abundance of several genera in calves with induced acidosis. Our study provides insight into host rumen transcriptome changes associated with prolonged acidosis in post weaning calves. Shifts in microbial species abundance are promising for microbial species based biomarker development. Such knowledge provides a foundation for future more precise diagnosis and preventative management of rumen acidosis in dairy calves.