Recent advances in DNA sequencing technologies have enhanced our understanding of the diversity of microbes associated with plants in the field. Nonetheless, we have not yet developed frameworks for predicting and managing plant microbiomes, partly due to the complexity of host-symbiont and symbiont-symbiont interactions in natural conditions. Here, I discuss how we can gain the “bird’s-eye” view of interaction networks involving hundreds or thousands of microbial species and then explore “core microbes”, which have great impacts on whole microbiome dynamics and host plant physiology.