The most common used method for metagenome sequencing is an amplicon based method. The 16S ribosomal gene has regions more or less conserved across many species, and also variable regions that are species/strain specific. Extensive databases with these species/strain specific 16S sequences are available and allow an easy way to classify the species/strains present in the population studied.
Although this method has quite some drawbacks, it has the advantage that it is relatively cheap and permit to analyze fast many samples. The major drawback comes from the biases that will be introduced during PCR amplification (PCR primers used) and from biases by the choice of the region of the 16S gene used. The latter can eventually be overcome using long read technologies as available from Oxford Nanopore, but this technology is still being prone to a higher sequencing error rate than Illumina sequencing
