Table 1.

Capabilities of Methods for Measuring the Microbiome

Method	Bacteria	Fungi	Viruses	Relative Abundance	Absolute Abundance	Species Richness	Resistome
Culture	Culturable organisms	Culturable organisms	Culturable organisms	Culturable organisms	Semiquantitative, culturable organisms	Culturable organisms	In vitro phenotypic susceptibility
qPCR	Known targets	Known targets	Known targets	Limited	Limited	Limited	If known resistance sequences exist
16S rRNA sequencing	All bacterial targets	Analogous methods (ITS and 28s)	No	Yes	No	Yes	Possibly inferred from taxonomic information
MGS	Yes	Yes	Yes	Yes	No	Yes	Identifies known resistance sequences
QMP	Yes	Depends on sequencing and quantitation technique	Depends on sequencing and quantitation technique	Yes	Yes	Yes	Depends on sequencing technique (16S or MGS)
Metabolomics	Reflects impact of microbiome composition	Reflects impact of microbiome composition	No	No	No	No	Undefined

Abbreviations: ITS, internal transcribed spacer; MGS, metagenomic sequencing; QMP, quantitative microbiome profiling; qPCR, quantitative polymerase chain reaction; rRNA, ribosomal RNA.