Human body is a habitat for a large number of microorganisms, called microbiome. Microbiome has been recognized as a key factor in understanding human health and diseases. Bacteria are a major component of most of human body including gut. The study of human microbiome has been accelerated by the invention of next generation sequencing and bioinformatics. Application of the concept and techniques used in microbial ecology to microbiome allows us to understand the role and effects of microbiome, especially gut microbiome to human health and diseases. In this presentation, the principles of human microbiome and related methodology will be explained.