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

Authors: PARK, TANSOL - Chung-Ang University; Li, Wenli; Zanton, Geoffrey

Submitted to: bioRxiv
Publication Type: Other
Publication Acceptance Date: 3/29/2023
Publication Date: N/A
Citation: N/A

Interpretive Summary: The gut microbiome, comprised of bacteria, fungi, protists, and archea living inside of the gut, can impact animal nutrition while its impact on the host health and disease have been a topic of considerable interest. Nutrients that are absorbed from digestion first travel to the liver before going to the rest of the body making the gut-liver axis of considerable interest for investigations into host-microbial interactions. Many studies in human and mouse models have demonstrated the existence of significant microbial community embedded in diverse tissue types, including blood and liver. However, in beef and dairy cattle, the rumen microbiome has been the primary focus while the liver microbiome and its metabolic role in host health and performance remain largely unexplored. Using whole transcriptome sequencing data, we surveyed the liver microbiome in various cattle breeds using whole transcriptome sequencing data. We discovered abundant microbial taxa in the liver that varied by age, species, and developmental stage. We also observed the significant impact of the species and breed on the variation of core-liver taxa and microbial functions. Additionally, several core phyla identified in our study were not previously reported, indicating the difference in sensitivity or ability in detecting microbes between DNA and RNA-based methods.

Technical Abstract: The gut-liver axis is at the forefront of host-microbial interactions given the liver’s close proximity 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 one primary focus. The liver microbiome and its metabolic role in host health and performance remain largely unexplored. Identification of bacteria embedded in the liver will be transformative for delineating molecular mechanisms influenced by the gut microbiome that impact host nutritional and physiological functions. The objective of this study was to evaluate through meta-analysis the liver microbiome in various cattle breeds with different sex, age, and developmental stages using whole transcriptome RNA sequencing data. 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. We discovered abundant microbial taxa in the liver, varying by age, species, and developmental stage. Overall 6, 2, and 2 bacterial phyla were significantly associated with ruminant species, breeds, and ages (Q < 0.05), respectively. Tenericutes and its lower class, Mollicutes were associated with both the ruminant species and breeds, negatively with Bos taurus and Nellore. 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 whole transcriptome sequencing 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, indicating the difference in sensitivity or ability in detecting microbes between DNA and RNA-based methods.