Changes in meta-transcriptome of rumen epimural microbial community and liver transcriptome in young calves with feed induced acidosis

Abstract

The common management practices of dairy calves leads to increased starch concentration in feed, which subsequently may cause rumen acidosis while on milk and during weaning. Until recently, few attempts were undertaken to understand the health risks of prolonged ruminal acidosis in post weaning calves. Resultantly, the molecular changes in the digestive tracts in post-weaning calves with ruminal acidosis remain largely unexplored. In this study, we investigated the liver transcriptome changes along with its correlation with the rumen microbial rRNA expression changes in young calves using our model of feed induced ruminal acidosis. In this model, new born calves were fed a highly processed, starch-rich diet starting from one week of age through 16 weeks. A total of eight calves were involved in this study. Four of them were fed the acidosis-inducing diet (Treated) and the rest of the four were fed a standard starter diet (Control). Liver and rumen epithelial tissues were collected at necropsy at 17 weeks of age. Transcriptome analyses were carried out in the liver tissues and rRNA meta-transcriptome analysis were done using the rumen epithelial tissues. The correlation analysis was performed by comparing the liver mRNA expression with the rumen epithelial rRNA abundance at genus level. Calves with induced ruminal acidosis had significantly lower ruminal pH in comparison to the control group, in addition to significantly less weight-gain over the course of the experiment. In liver tissues, a total of 428 differentially expressed genes (DEGs) (fold-change, FC ≥ 1.5; adjusted P ≤ 0.1) were identified in treated group in comparison to control. Biological pathways enriched by these DEGs included cellular component organization, indicating the impact of ruminal acidosis on liver development in young calves. Specifically, the up-regulated genes were enriched in acute phase response (P < 0.01), pyruvate metabolic process (P < 0.01) and proton-acceptors (P ≪ 0.001), indicating the liver’s response to feed induced acidosis at the transcriptome level. Twelve transferase activity related genes had significant correlation with rumen microbial rRNA expression changes. Among these genes, two up-regulated genes were reported with involvement in lipid metabolism in the liver, implying the direct effect of feed-induced acidosis on both the rumen microbial community and liver metabolism. Our study provides insight into the physiological remodeling in the liver resultant from the prolonged acidosis in post weaning calves, which may facilitate future RNA-seq based diagnosis and precision management of rumen acidosis in dairy calves.

Investigating the impact of feed-induced, subacute ruminal acidosis on rumen epimural transcriptome and metatranscriptome in young calves at 8- and 17-week of age

“…Differential abundance analysis of microbial taxa at genus level was done using DEseq2 (with Benjamini and Hochberg method for multiple testing) using the raw read counts mapped to the given taxa ( p < 0.05; mean read count ≥10 and fold-change ≥2). For the RE tissues collected at 17 weeks of age, we used genus-level reads counts from our previously published work ( 19 ). It is known that rumen development is accompanied by microbial colonization ( 30 ).…”

The rumen liquid metatranscriptome of post-weaned dairy calves differed by pre-weaning ruminal administration of differentially-enriched, rumen-derived inocula

“…Sequences classified as chloroplast and mitochondria were excluded before downstream analysis. Raw-read counts at each taxonomic level (i.e., phylum and genus) were normalized per sample with the per million factor as described in [ 25 ]. Major classified taxa, defined as occupying over 0.01% average relative abundance in at least one of the treatments, were discussed in this study.…”

Integration of Multiplied Omics, a Step Forward in Systematic Dairy Research

“…increased ( p < 0.05) and anti-inflammatory(IL-6) ones decreased( p < 0.05), in addition, SARA will increase milk somatic cell count (SCC) with a dropped milk protein and lipid component ( p < 0.05). Li et al [ 28 , 29 ] found that young calves with high starch induced rumen acidosis performs a different rumen epithelial transcriptome and meta-trascriptome profile with correlated rumen microbiome, liver transcriptome pattern also involved in this process, the abundance of Olsenella , Desulfovibri , and Fusobacterium necrophorum increased significantly in the rumen fluid, and 95 genes in the liver changed with differed microbiome rRNA expression, among them, 77 genes are enriched in the pathways of membrane-bounded organelle and transferase activity. Six-hundred-and-seventy-two epithelial genes related to cell signaling and morphogenesis showed significantly altered expression, in which, 12 genes ( COX5B , KRT78 , KRT15 , ATP5I , ATP5L , ATP5G2 , COX8B , COX8A , UBC , DSP , ITM2B , and C10H15orf48 ) related to hydrogen ion transmembrane transport only exists in the acidosis group; other differentially expressed genes are mostly involved in cell division and growth, like membrane-bounded organelle, cytoplasm, cellular component organization or biogenesis.…”