Abstract: Microbiome is a novel research field related with a variety of chronic inflamatory diseases. Technically, there are two
major approaches to analysis of microbiome: metataxonome by sequencing the 16S rRNA variable tags, and metagenome by
shot-gun sequencing of the total microbial (mainly bacterial) genome mixture. The 16S rRNA sequencing analyses pipeline
includes sequence quality control, diversity analyses, taxonomy and statistics; metagenome analyses further includes gene
annotation and functional analyses. With the development of the sequencing techniques, the cost of sequencing will decrease,
and big data analyses will become the central task. Data standardization, accumulation, modeling and disease prediction are
crucial for future exploit of these data. Meanwhile, the information property in these data, and the functional verification with
culture-dependent and culture-independent experiments remain the focus in future research. Studies of human microbiome
will bring a better understanding of the relations between the human body and the microbiome, especially in the context of
disease diagnosis and therapy, which promise rich research opportunities.