Comparison of DNA extraction kits for PCR-DGGE analysis of human intestinal microbial communities from fecal specimens

Table 1 Comparison of recommended DNA extraction protocols based on technical booklets included with respective extraction kits.

Extraction kit/Steps	M¹	Q¹	FSp¹	FSo¹
Fecal wt (mg)	250 - 1000	180 - 220	200	500
Beads	Unknown beads	None	Ceramic + garnet	Ceramic + silica
Cell lysis and homogenization	Flat bed vortexer (10 min)	Centrifuge (14,000 rpm, 1 min)	Fast Prep^® Instrument (speed 6.0, 40 s)	Fast Prep^® Instrument (speed 5.5; 30 s)
Adsorption of inhibitors	IRS²solution	InhibitEx tablet	None listed	None listed
Approximate time to completion ³	45 to 60 min	60 to 80 min	45 to 60 min	60 to 80 min
Average cost of kit ⁴	$176.00	$181.00	$344.20	$240.45

¹M, Mobio Ultra Clean^® Fecal DNA Isolation Kit; Q, QIAamp^® DNA Stool Mini Kit; FSp, FastDNA^® SPIN Kit; FSo, FastDNA^® SPIN Kit for Soil
²Abbreviations are not defined by manufacturers due to being proprietary in nature
³Approximate time to complete DNA extraction for 12 samples using kits M, FSp, and FSo, but only 6 to 8 samples for kit Q (due to using table-top vortexer for shaking as listed in the protocol)
⁴Prices as of May 2010 (based on 50 preparations for kits M, Q, and FSo; 100 preparations for kit FSp)

ISSN: 1475-2891