Abstract:Microbial community structure and interspecies interactions are the key factors that determine the function of the community. Although these communities are the major drivers of many biosphere processes, due to the fact that only 1%-10% of natural microbes could be recovered by classical culture-dependent methods, relatively little is known about their structure and function. Some recently emerged novel methods, e.g. metagenomics, single cell analysis and community genetics enable researcher could decipher the ecological properties of microbial communities on the basis of the questions being asked: the composition of the community, the function of individual species, the model of interspecies interaction and predictive modeling at the community level. In the present review, we describe the current concept and application of metagenomics, single cell analysis and community genetics to study microbial ecology and progress toward predictive modeling.