The Effects of Artificially Dosed Adult Rumen Contents on Abomasum Transcriptome and Associated Microbial Community Structure in Calves

Abstract

This study aimed to investigate the changes in abomasum transcriptome and the associated microbial community structure in young calves with artificially dosed, adult rumen contents. Eight young bull calves were randomly dosed with freshly extracted rumen contents from an adult cow (high efficiency (HE), n = 4), or sterilized rumen content (Con, n = 4). The dosing was administered within 3 days of birth, then at 2, 4, and 6 weeks following the initial dosing. Abomasum tissues were collected immediately after sacrifice at 8 weeks of age. Five genera (Tannerella, Desulfovibrio, Deinococcus, Leptotrichia, and Eubacterium; p < 0.05) showed significant difference in abundance between the treatments. A total of 975 differentially expressed genes were identified (p < 0.05, fold-change > 1.5, mean read-counts > 5). Pathway analysis indicated that up-regulated genes were involved in immune system process and defense response to virus, while the down-regulated genes involved in ion transport, ATP biosynthetic process, and mitochondrial electron transport. Positive correlation (r > 0.7, p < 0.05) was observed between TRPM4 gene and Desulfovibrio, which was significantly higher in the HE group. TRPM4 had a reported role in the immune system process. In conclusion, the dosing of adult rumen contents to calves can alter not only the composition of active microorganisms in the abomasum but also the molecular mechanisms in the abomasum tissue, including reduced protease secretion and decreased hydrochloric acid secretion.

Keywords: abomasum transcriptome; artificial dosing; young calves.

Figure 1

RT-qPCR confirmation of four differentially expressed genes (DEGs) identified by RNA-seq. Log₂FC (high efficiency (HE) vs. sterilized rumen content (Con)) of target genes were calculated for both RNA-seq and RT-qPCR methods.

Figure 2

Heatmap showing top 40 DEGs between treatments. The log2 ratio values of DEG abundance were used for cluster analysis with the R pheatmap package. Red and blue indicate relative over- or under-expression of genes, respectively.

Figure 3

Function annotation-GO analysis of DEGs. FDR: false discovery rate; MF: molecular functions; BP: biological process; CC: cellular component. The x-axis is the richness calculated from the numbers of DEGs in a term divided by all the genes included in that term. As shown on the right side of the figure, the size of the circumference correlates with the number of genes.

Figure 4

A Pearson correlation matrix between significantly changed active bacteria and the genes enriched in immune response. The scale of the colors is denoted as follows: the more positive the correlation (closer to 1), the darker the shade of blue; the more negative the correlation (closer to −1), the darker the shade of red. *: p < 0.05; Abo: abomasum tissue.

Figure 5

Ion transporters involved in hydrochloric acid (HCl) output of the parietal cell. ATP4A, KCND2, SLC26A7, SLC4A2 and CLIC6 were the DEGs in abomasum.