Objectives: Gut microorganisms may play a fundamental role in the pathogenesis and worsening of liver disease and pathology [1], where of their composition and the production of toxic compounds are considered as trigger actors [2]. Clinically widely studied, Hepatic Encephalopathy treatment with prebiotic, antibiotic and probiotic, generally evidences a reduction of ammonia production by gut microbial activity and an increase in neurocognitive tests and mental status. Nevertheless from a strictly microbiological point of view, little is known about the dynamics, interaction and metabolite production among the main bacterial groups in liver diseases [3]. Thus we investigated, how lactulose, rifaximin or VSL#3 and their combination affect gut microbial composition, determining changes in ammonia and metabolites levels during cirrhosis treatment,Methodology: Samples in independent batch culture fermentations were used to assess microbial population dynamics using flow cytometry FISH, ammonia concentrations and short chain fatty acid production.Results: Microbial modulation by prebiotic, antibiotic and probiotic treatment differently effect the population dynamics and its metabolism, as revealed by the different short chain fatty acid profiles and the specific increase in beneficial bacteria.Conclusions: The reduction of ammonia and regulation of metabolite production observed emphasize the importance of gut microbiota handling in HE treatment.