sequencing, computational biology, bioinformatics, microbial ecology, and systems biology in translational medicine. We have defined and developed “metabiomics” as a systems biology approach to biomarker discovery and molecular diagnostics based on multi-functional knowledge of the human microbiome, metagenomic, transcriptomic, proteomic, and metabolomic networks and pathways associated with human health and disease. Demonstrating the effectiveness of our patent-pending MultiTag™ Sequencing (MTS™) analysis platform, we have developed non-invasive molecular diagnostic methods for several gastrointestinal and autoimmune diseases, including human microbiome association studies of colon polyps, colorectal cancer, irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), and hepatic encephalopathy (HE) in chronic liver disease (CLD). Our metabiomic diagnostic methods are based on multi-functional biomarkers associated with the molecular pathways of GI dysbiosis and autoimmune diseases that provide earliest possible detection, unprecedented sensitivity and accuracy, and lower costs as compared to traditional testing methods.