From the point of view of systems biology, the plant is considered a super organism that consists of the plant per se and numerous populations of pro- and eukaryotic microbial organisms. Each plant species hosts a genotype-specific core microbiome, dynamically responding to environmental cues, such as soil quality. In the plant endosphere, microbial organisms are an indispensable part of the information processing system, and the plant-endophyte interrelationships result in mutual adjustments through this system. Within the plant tissue, part of the microbiota resides in state called "viable but nonculturable". Pathogen attack or environmental stress can provoke the dormant forms. The link between reviving of endophytic bacterial populations and plant disease resistance in the endosphere is discussed in this paper. The innate endophytic communities possess resistance-competent members, which can be in a latent state. The latent populations can be revived by an incoming microbial organism (e.g. a biocontrol agent or a pathogen), or other environmental factors. Reviving endophytic bacterial populations can be a putative mechanism of the endophyte-mediated plant resistance. Based on the published results, we suggest that the endophyte-mediated stress tolerance or disease resistance can develop, if the plant hosts a sufficient diversity of 'protective' endophytes. Alternatively, the plant can become susceptible upon loss of strategic members from endophytic microbial cohorts. Resident endophytes can be envisaged as a hidden reserve of plant protection to be used in green plant biotechnology. Selection of plant genotypes and soil type hosting beneficial microbiomes should become a common practice for improving plant resistance to complement advanced genetic technologies applied in plant biotechnology.