Seed microbiota are very diverse and variable, however, it’s possible to identify a stable (core) fraction across samples. Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing to its role for plant health and productivity. Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea sp., Pseudomonas sp., Bacillus sp., Paenibacillus sp., or Stenotrophomonas sp. are dominant seed taxa. Phenotypes variability in the same population may be partially explained by the original load of inherited microbiota. Not only beneficial, but pathogens can pass to the next generation. Adaptability and epigenetic processes, as well as biopriming processes, could be conditioned by the inherited microbiota. We decided to analyze seed culturable microbiota from different populations (wild, stress adapted, local and commercial varieties) of Fabaceae and Solanaceae. Population changes were considered to elucidate relevance in the performance under stress. They were referred as well to other traits as epigenetic marks or metabolomic changes. Due to variability, we need to prepare sets above 50-100 seed per replica to ensure reliability. Mutant lines of plants for specific compounds or epigenetic marks may help to elucidate adaptation traits. Culturable microbiota was helpful validating those traits and metagenomics as in vivo models of the community. With this approach, we can control pathogen dispersion and enhance some breeding models, as well as to provide with new inoculants.