Human gut is a habitat for a large number of microorganisms and their genomes, called gut microbiome. In particular, bacteria are major components of most of human gut These days, gut microbiome has been recognized as a key factor in understanding many human diseases. The study of gut microbiome has been accelerated by toe invention of next-generation sequencing (NGS) technology and biomformatics. Basic concepts and techniques used in gut microbiome studies allow US to understand the role and effects of microbiome on health and diseases. Here, I will explain updated technologies and analysis methods and important points to consider when conducting gut microbiome study. In addition, I will provide guidelines of microbiome studies for practical application with some example studies about relationship between microbiome and human diseases, particularly liver disease.