Amplicon or target sequencing uses specific primers for marker genes  e.g., 16S, 18S, ITS that targets a specific gene or region in the genome of any species. These marker genes take a step up from qPCR and gives the ability to fingerprint almost all the species in a particular environment. For example, 16S amplicon metagenomics uses primers that is common across all the bacteria and based on the differences between recovered gene-copy numbers. The 16S gene has been studied in great detail for variety of environments, and scientists have mapped which sequence belongs to which bacterial genus or class or phyla. So, we can look at all of the 16S genes in the microbiome to determine which genus is present and in what relative abundances (10% of bacteria A, 5% of bacteria B).  Amplicon sequencing offers the cheapest and easiest method for investigation of entire bacterial community. There is good amount of data to compare the results as there are ample amount of microbiome studies completed using these marker genes.