A meta-analysis of liver microbiome in beef and dairy cattle using metatranscriptome sequencing reads

The gut-liver axis is at the forefront of host-microbial interactions given the proximity of liver to the gut and connection via portal circulation. In recent years, many studies in human and mouse models have demonstrated the existence of a significant microbial community embedded in diverse tissue types, including blood and liver. Yet, in cattle, the rumen microbiome has been the primary focus. The liver microbiome and its metabolic role in host health and performance remain largely unexplored. While there has been considerable work focusing on the liver of diseased cattle, the objective of this study was to evaluate, through meta-analysis, the commensal liver microbiome in various cattle breeds. To our knowledge, this is the first study in which a core liver microbiome has been described in cattle without overt liver disease. We discovered abundant microbial taxa in the liver, varying by host age, species, and developmental stage. Eight bacterial phyla (Actinobacteria, Bacteroidetes, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Fusobacteria, Proteobacteria, and Tenericutes) were found to be the core microbial taxa, representing almost half of the total liver bacterial population. Additionally, we identified several KEGG pathways with significant association with cattle age. This study provides a baseline knowledge of the liver microbiome as identified by metatranscriptome sequencing in cattle. Besides finding the microbial taxa previously reported by studies using DNA-based, 16S rRNA amplicon sequencing methods, this study identified several core phyla that have not been reported in cattle liver, highlighting the improved sensitivity or ability in detecting microbes by RNA-over DNA-based methods.