Table 2.

Comparison of Different Sequencing Approaches for Evaluation of Microbiome

Technique	Accuracy	Fungus/Virus detection	Resistance mutation detection	Metabolic activity	Limitations of technique
Metataxonomic (e.g., 16S or ITS)	Genus	Fungus with ITS	No	No	Differences in variable regions (V1–V9) used for sequencing
Metagenomic (e.g., shotgun)	Species or Strain	Yes	Yes	No	Need deep sequencing for adequate coverage
RNA-seq	Species	Yes	Yes	Yes	RNA less stable than DNA and requires careful processing