Endophytes are beneficial microorganisms that reside in different plant tissues. The culturable endophytes are limited so that the knowledge about the microbial communities inside plant tissue is confined. In this study, we concentrated on the metagenomic studies of endophytes that opened a vast knowledge about them. The study of endophytes through the genetic level contributes detailed knowledge about microbial diversity, their composition, functions, and metabolic pathways. This will help to understand their role in plant growth and development. Through metagenomic studies, we can build more information about how endophytes promote plant growth promotion and the different aspects like biofertilization, plant growth hormone production, and stress tolerance. The use of metagenomics gives the importance of plant microbiota to the sustainable use of agriculture and ecological functions.
