16S/18S/ITS Amplicon Sequencing
16S/18S/ITS amplicon sequencing is used to identify microbial abundance and phylogeny. 16S rRNA enables identification of bacteria and archaea in a microbiota sample. The 16S rRNA gene is preferred in taxonomic studies since it is known to be highly evolutionarily conserved. 18S rRNA is a component of eukaryotic ribosomal small subunit. Therefore, its sequencing is used to identify eukaryotic microbes in microbiota. 18S/ITS sequencing is preferred to detect fungal organisms in the sample.

Shotgun Metagenomic Sequencing
Shotgun metagenomic sequencing is defined as untargeted sequencing of all microbial genomic DNA from a sample. The library preparation is similar to whole genome sequencing. The major differences between shotgun metagenomics and amplicon sequencing are (i) shotgun metagenomics sequences all genomic materials while amplicon sequences a small region in the genomes, (ii) shotgun metagenomics captures sequences of all organisms in the microbiota sample while eg. 16S amplicon sequencing only captures microbiota, and (iii) raw shotgun metagenomics data is much more complex, and requires more advanced data processing tools.