Microbial species in natural habitat has extremely high abundance and diversity,their activity and interactions play an important role in maintaining ecosystem stability.Microbiota in human and other hosts affects host disease and health.Next generation sequencing technology makes possible to quickly obtain data of microbial community composition and function.Research focus in microbial community and ecosystem ecology has shifted from describing observational patterns to understanding microbial inter-specific interactions,and to predicting dynamic changes in community structure and function.Numerous algorithm and modeling techniques have been developed to infer microbial network from sequencing data.However,such top-down approach has intrinsic limitations.The bottom-up approach,that is,direct investigation of microbial interactions through in vitro and in vivo experiments,could help to understand higher level ecological patterns.In addition,analytical modeling and simulations can reveal how microbial interactions affect community dynamics and function.Future studies could benefit from integrating these observational,experimental,and theoretical approaches,to improve understanding and prediction of microbial interactions,and to meet the challenges of rapid climate change,pathogen infection,and antibiotic resistance evolution.