The soil microbiome represents a soil microbial community associated with many functional activities of the terrestrial system. The culturable techniques are not sufficient to give a holistic picture of the soil microbiome, therefore, than non-culturable techniques, the metagenomic approach gives better insight into the detection of microbial diversity, community structure and functional potential, and moreover overcomes the limitations of traditional culturable Approach. This article covers the basics from sample collection, sequencing and data analysis to deciphering applications, challenges and future directions in soil microbiome research.