Table 1.

Comparison of 16S rRNA gene sequencing (16S), metagenomic shotgun sequencing (MSS), and bacterial group quantitative polymerase chain reaction (qPCR).

	Time required for data production	Potential PCR bias	Microbial populations analyzed	Method of quantification	Functional analysis	Computing requirements	Data storage (per sample)	Estimated cost (excluding labor)
16S	Days to weeks	Yes	Bacteria only	Relative abundance	No	Open-source software that can be run on desktop computers	Megabytes	$10-$50/sample (if batched with a large number of samples)
MSS	Weeks to months	No	Bacteria, viruses, fungi	Relative abundance	Yes	Bioinformatic analysis is CPU intensive (requiring computer clusters)	Gigabytes	$200-$800/sample (depending on depth of coverage desired)
qPCR	Hours to days	Yes	Bacteria, viruses, fungi	Gene copies	No	Spreadsheet program (e.g., Excel) that can be run on a desktop computer	Bytes to kilobytes	<$1/sample