Table 1.

Methods used and/or currently used to measure metagenomes, and significant benefits and limitations for metagenomic analysis

Technique	Benefit	Limitation
Traditional DNA Sequencing	Provide long continuous reads Targeted and specific	Laborious and time consuming Amplification bias Inefficient
Amplicon Sequencing	Characterize target sequences (i.e., 16s rRNA, 18s rRNA genes, OTUs)	Low-throughput method
Shotgun Sequencing	High-throughput Massive parallel sequencing Unbiased microbiome profiling	Require high sequencing depth
RNA Sequencing	High sensitivity and reproducibility Require low sequencing depth	Require biological replicates Accuracy depends on annotation quality of reference genome