Caecum transcriptome and associated microbial community in young calves with artificial dosing of rumen content obtained from an adult cow

The nutritional studies in the cattle typically focus on the rumen and its microbial environment, leaving other parts of the gastrointestinal (GI) tract largely unexplored. Thus, underlying molecular mechanisms and the responses to dietary treatment in the lower gut is poorly understood. In this study, we investigated the caecum transcriptome changes and its associated microbial communities in calves with or without artificially dosed rumen content extracted from an adult cow. Eight calves were included in the study, four received artificially dosed adult rumen content (Treated) and the rest received autoclaved rumen content as a control. We observed significant transcriptome changes in the caecum between treatments, with 1,836 differentially expressed genes (DEGs) identified. A predominant portion of the DEGs were down-regulated in the treated group, which showed significant enrichment for molecular pathways related to immune response, host response to pathogens, and inflammatory responses. For the DEGs correlated with the highest number of microbes, gene ontology analysis indicated an enrichment in pathways associated with inflammation and immune response.  By comparing the microbial taxa abundance among different GI tissues collected from the same study, we observed the same dosing strategy may lead to differential retention of the microbial community in different GI tract locations. Our work indicated the hind gut showed robust response to artificial dosing and the caecum microbial community may interact extensively with the host to shape the development and maturity of the host immune system in early life. Furthermore, our analysis suggested that tissue-specific analysis is required to fully understand the impact of early dosing on animal performance and physiology.