Direct examination of the genome’s genetic material included in an environmental sample is known as metagenomics. Cloning environmental DNA was the first step in the field, which was swiftly followed by functional expression screening followed by a direct random shotgun sequencing of environmental DNA. The massively parallel sequencing technique known as next-generation sequencing (NGS) provides incredibly high throughput, scalability, and speed. Using this approach, the nucleotide order of whole genomes or specific DNA or RNA portions may be ascertained. NGS allows researchers to quantify mRNAs for gene expression studies or use RNA sequencing (RNA-Seq) to find new RNA variations and splicing sites, examine epigenetic variables such as DNA–protein interactions and genome-wide DNA methylation, analyze unusual somatic variations, tumor subclones, and other phenomena by sequencing cancer samples, examine the microbiota of humans, and determine new pathogens.