Caecum transcriptome changes upon artificial dosing of rumen content obtained from an adult cow

Authors: Li, Wenli; LARSEN, ANNA - Oak Ridge Institute For Science And Education (ORISE); MURPHY, BRIANNA - Oak Ridge Institute For Science And Education (ORISE)

Submitted to: Journal of Animal Science and Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/24/2024
Publication Date: N/A
Citation: N/A

Interpretive Summary: Born without a functional rumen and almost devoid of microbes, ruminants are thought to acquire the functional ruminal microbes from the environment as the rumen develops. Few attempts have been undertaken to understand the role of early rumen microbial colonization on gut development or host health in neonatal ruminants. The molecular changes associated with ruminal bacterial colonization in the lower gut remain largely unknown. In our previous work, we investigated if an artificial dosing regimen of adult rumen content can manipulate the rumen microbial communities, we dosed the newborn calves with the rumen content extracted from an adult cow beginning at birth and every other week after that until eight weeks of age. We observed significant transcriptome changes in the rumen and its associated microbial communities. As a follow up study, we focus on the caecum and its microbial communities from the same set of calves. Additionally, we compared the microbial community profiles among several gastrointestinal (GI) tissues, including the liver, rumen, abomasum, ileum and caecum. Our findings indicate that the impact of artificial early dosing is persistent in the non-rumen GI tissues. Most importantly, we observed differential retention of the microbial communities amongst different GI tissue types, indicating the need of systematic analysis of all the GI tissues to assess the impact of early dosing on the calf’s development and health. Our study provides a foundation for the development of probiotic treatments aimed at improving rumen development and lower gut health.

Technical Abstract: In this study, we examined caecum transcriptome changes in response to dosing with exogenous rumen fluid in the early life of the calf, starting at birth, and repeated every other week. Eight calves were included in this study; four of them receiving artificial dosing and the remaining four as the control group. At age of eight weeks, calf caecum tissues were collected and subjected to host transcriptome and microbial meta-transcriptome analysis using RNA-sequencing. Additionally, we compared the microbial community profiles among several digestive tract tissues (including the liver, rumen, abomasum and ileum) collected from the same set of animals. A total of 1836 genes showed significantly differential expression (DE) between the dosed and control calves (fold-change>=2; padj<0.005, mean read-count >=10). For the up-regulated genes in treated samples, gene ontology analysis indicated that they were predominantly enriched in cell proliferation (p-value <0.0001). In comparison, down-regulated genes had significant enrichment in immune and inflammatory response (p-value <0.001). The association analysis between the differentially expressed genes and the microbial genus-level abundance identified 57 genes with significant correlation with the caecum microbial genera (Pearson’r >0.8 p-value <0.001). The function annotation of these genes included cell proliferation, immune response, and lipid metabolism. At the genus level, the microbial profile for the liver is clearly separated from the rest of the tissue types. Though the treated samples, this study’s findings shed light on the molecular processes in the caecum due to early introduction of an adult rumen microbial community into young calves. Further, this study provides a foundation for the development of probiotic treatments aimed at improving rumen development and lower gut health.