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

Wenli Li,Christina Riehle,Daniel Koch,Sonia Gelsinger,Andrea Edwards

doi:10.1038/s41598-019-40375-2

Wenli Li, Christina Riehle + Show 3 more

Open Access

https://doi.org/10.1038/s41598-019-40375-2

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Abstract

Many common management practices used to raise dairy calves while on milk and during weaning can cause rumen acidosis. Ruminal pH has long been used to identify ruminal acidosis. However, few attempts were undertaken to understand the role of prolonged ruminal acidosis on rumen microbial community or host health in young calves long after weaning. Thus, the molecular changes associated with prolonged rumen acidosis in post weaning young calves are largely unknown. In this study, we induced ruminal acidosis by feeding a highly processed, starch-rich diet to calves starting from one week of age through 16 weeks. Rumen epithelial tissues were collected at necropsy at 17 weeks of age. Transcriptome analyses on the rumen epithelium and meta-transcriptome analysis of rumen epimural microbial communities were carried out. Calves with induced ruminal acidosis showed significantly less weight gain over the course of the experiment, in addition to substantially lower ruminal pH in comparison to the control group. For rumen epithelial transcriptome, a total of 672 genes (fold-change, FC ≥ 1.5; adjusted-p ≤ 0.05) showed significant differential expression in comparison to control. Biological pathways impacted by these differentially expressed genes included cell signaling and morphogenesis, indicating the impact of ruminal acidosis on rumen epithelium development. rRNA read-based microbial classification indicated significant increase in 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 and artificial manipulation. Such knowledge provides a foundation for future more precise diagnosis and preventative management of rumen acidosis in dairy calves.

Highlights

Ruminal acidosis is a well-recognized digestive disorder found in dairy cattle[1]
Reduced ruminal pH has been reported in both goats[44] and lactating dairy cattle[45] consuming feeds high in dietary-starch content
Ruminal epithelium is critical for nutrient absorption and transportation[47,48], in addition to short-chain fatty acid (SCFA) metabolism[49]

Summary

Introduction

In order to maintain high milk yield, dairy cattle diets have become more nutrient-dense, containing highly fermentable carbohydrates In some cases, this can lead to an accumulation of volatile fatty acids (VFAs) and reduced buffering capacity in the rumen[2,3], lowering ruminal pH. Recent studies that measured ruminal pH in young calves with acidosis reported mean pH values between 5.5 and 4.1 across various dietary treatments in the weeks surrounding weaning[21,22,23,24] Such a range of variation in ruminal pH used to determine ruminal acidosis suggest a need to develop other tools/biomarkers that will facilitate the precise diagnosis and preventative management. Young calves that have not been adapted to high grain diets are susceptible to acute ruminal acidosis[32] This is most likely due to the lack of a well-developed, viable population of rumen bacteria that can efficiently utilize lactic acid.

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