Progress in next-generation sequencing has played a significant role in ecological studies of microbial populations. These advances have led to a rapid evaluation in metagenomics studies (analysis of DNA of microbial communities without the need to culture). Many statistical and computational tools and metagenomics databases have led to the discovery of huge amounts of data. In this research, in addition to a review of the new generation sequencing method, tools and bioinformatics methods used, the case studies about the microbiome of suppressive soils and manipulation of the microbiome to fight off plant diseases are presented and discussed. Suppressive soil is a soil in which the plant diseases incidence occurs at a low rate despite the presence of known pathogens. Attention to the structure and accurate identification of the microbiome of these soils is very interesting to devotees of reducing the use of chemical pesticides.