Analysis of host jejunum transcriptome and associated microbial community structure variation in young calves with feed-induced acidosis

Authors: NAREN, GAOWA - China Agricultural University; Li, Wenli; GELSINGER, SONIA - Select Veal Feeds, Inc; MURPHY, BRIANNA - University Of Wisconsin; LI, SHENGLI - China Agricultural University

Submitted to: Metabolites
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/15/2021
Publication Date: 6/23/2021
Citation: Naren, G., Li, W., Gelsinger, S., Murphy, B., Li, S. 2021. Analysis of host jejunum transcriptome and associated microbial community structure variation in young calves with feed-induced acidosis. Metabolites. 11(7). Article 414. https://doi.org/10.3390/metabo11070414.
DOI: https://doi.org/10.3390/metabo11070414

Interpretive Summary: Starch-rich, concentrated starter is common during calf weaning period. However, such diets have been associated with ruminal acidosis. So far, much of the work pertaining ruminal acidosis primarily focused on the starter intake, growth performance and measurement of ruminal pH. Lately, some tissue transcriptome work has been done using rumen epithelial tissue. However, the underlying molecular changes in other parts of the digestive tract as a result of feed-induced acidosis remain largely unexplored. The small intestine functions to absorb nutrients and minerals from food and plays an important role in the host immune defense mechanism. Using our established model of feed-induced acidosis in young calves, we aimed to investigate the changes in jejunum transcriptome, and its associated microbial community structure variations. Using whole transcriptome RNA sequencing, our study captured jejunum transcriptome changes in young calves with feed-induced acidosis. We observed transcriptomic remodeling in the jejunum as shown in the down-regulation of many genes involved in DNA replication. Moreover, genes encoding amino acid and peptide transporters, sodium ion transmembrane transport changed significantly in the jejunum in acidotic calves. The abundance of active jejunal microbes changed significantly and they were correlated with the expression variation of many host genes involved in the immune response. Overall, our study provided transcriptome-level knowledge of jejunum in young calves subjected to acidosis-inducing diet. The significantly changed genes and microbes identified by this work laid the foundation for future functional follow-up in the small intestine of young calves affected by ruminal acidosis.

Technical Abstract: The maximum intake of starch-rich starter is common during the calf weaning period. Such diets may lead to ruminal acidosis. Currently, the underlying molecular mechanisms of feed-induced acidosis remain largely unexplored. Using whole transcriptome RNA-seq, this study aimed to investigate the changes in jejunum transcriptome, and associated microbial community structure variations (MCSR). Using our established model of feed-induced acidosis in young calves, ruminal acidosis was induced by a starch-rich, low-fiber diet (Aci; pelleted, 42.7% starch, 15.1% neutral detergent fiber (NDF)), while texturized starter was fed as a control (Con, 35.3% starch, 25.3% NDF). The trial started at 1 week of age through 16 weeks with 4 calves randomly assigned to each treatment. Jejunum tissue collection was done at 17 weeks. rRNA reads were used for the study of the jejunum MCSR and host mRNA reads were used to investigate the transcriptome profile. Raw read alignment to the cattle genome was done with STAR (2.5.2b). DESeq2 was used for mRNA expression analysis. After genus-level classification using Kraken2, microbial genera abundance difference between Aci and Con was identified (Kruskal-Wallis test, P<0.05). Three gram-negative bacteria (Campylobacter, Burkholderia, and Acidaminococcus) and two gram-positive bacteria (Corynebacterium and Olsenella) were significantly higher in Aci group, while producers of butyrate (Lachnoclostridium and Ruminococcus, whose low abundance was previously associated with gut inflammation) were significantly lower in Aci group. Compared to the control, 402 up-regulated genes (URG) and 451 down-regulated genes (DRG) were identified in the Aci group (P < 0.05, fold-change (FC) > 1.5, mean read counts > 10). The differentially expressed genes (DEGs) were involved in the KEGG pathway of cell cycle (bta04110, 18 genes, z-score=-4.24) and protein digestion and absorption (bta04974, 8 genes, z-score=2.12). Moreover, correlation analysis indicated that two pathogenic genera (Francisella and Moraxella) were negatively correlated with NLRX1 gene (r < -0.7, P < 0.05), which had a reported role in the immune system process. The highest number of genera in jejunum were correlated with AXL (positively related to Campylobacter, Corynebacterium, Acidaminococcus, Sphaerochaeta, and Burkholderia, r > 0.7; negatively related to Moraxella, Francisella, and Ruminococcus, r < -0.7; P < 0.05). All the findings provide a transcriptome level understanding of the molecular mechanisms in host jejunum in young calves in a model of feed-induced acidosis.