A comprehensive understanding of the dynamics between the microbiome and the liver is still poorly understood. Combined omics-based studies are much needed to provide descriptive data on how gut microbes are associated with particular clinical settings of liver disease. Microbiome research in liver diseases have suggested that liver damage can result from interactions with the gut microbiota at various stages of liver diseases. In this study, we will analyze the relationship between the microbiome and its transcriptome, with liver-related diseases. We hypothesize that microbial communities and their functions differ according to liver disease stage and that gene expression profiles differ according to liver disease stage. To test these hypotheses, we will use a combined metagenomics and metatranscriptomics approach, using Oxford’s Nanopore ultra-long sequencing to characterize the genomic structural stability and the highly mutable transcriptomes. Data generated from this study will provide a basis for understanding the functional dynamics of the gut microbiome in association with liver disease. Advances in understanding the gut-liver axis could pave the way to microbiome-based, diagnostic, prognostic and therapeutic applications to improve management of liver diseases.