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

IRS2 solution

InhibitEx tablet

None listed

None listed


Approximate time to completion3

45 to 60 min

60 to 80 min

45 to 60 min

60 to 80 min


Average cost of kit4

$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)

Ariefdjohan et al. Nutrition Journal 2010 9:23   doi:10.1186/1475-2891-9-23

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