Microbiota/microbiome has been one of the lead topics in science these years, and its impact on host health and disease became a frontier scientific issue. Albeit a large number of laboratories around the world are focusing on this task, most of the researches are lack of detailed mechanisms. In this review, we clarify and illustrate the concepts of microbiota/microbiome. We sketch the interaction mode of human microbiota with the host, and list the diseases which have been reported in the past. In addition, six critical issues are put forward, and the direction of this field is prospected.