Table 1.

Commonly used metagenomic techniques in microbiome analysis.

Technique	Role	Advantage	Limitations
Target amplification (16S rRNA gene Sequencing) (10, 11)	Identifying taxa	▪ Offer taxonomical information ▪ Quick analysis Cheaper than metagenomics	▪ Resolution limited to genus level ▪ PCR and primer biases ▪ False positive in low biomass samples
Shotgun metagenomics (62)	Presents all genome sequences found in a given sample	▪ Permit functional studies ▪ Taxonomic resolution ▪ to species or strain level	▪ Required more Bioinformatical analysis ▪ Functional analysis does not identify active genes ▪ Expensive
Metatranscriptomics (62)	Identifies and measures gut microbial mRNA, reveals which genes and pathways are active	▪ Gene expression and Viability data provided.	▪ Expensive and complex in sequencing Experimental issues (instability of RNA)
Metabolomics (62, 63)	Profiles the metabolites generated by the gut microbiome, defines biochemical pathways	▪ Great amount of data generated. ▪ Functional information	▪ Expensive techniques Complex analysis
Metaproteomics (62, 63)	identifies and quantifies proteins from microbial communities	▪ Provides more precise functional information	▪ Expensive techniques Complex analysis