Comparison of practical factors of the DNA extraction and direct PCR methods for gut microbiome studies

MethodExtraction timecNo. of protocol stepsKit cost/sample (US$)Storage of extracted DNA
DNA extractiona~8 h (1–2 days)326.90dLong-term
Direct PCRb45 min32.30eShort-term
  • a Information is shown for DNA extraction with the PowerSoil-htp 96-Well Soil DNA kit, 384 extractions (Mo Bio Laboratories, Inc.).

  • b Information is shown for direct PCR with the Extract-N-Amp Plant PCR kit, 100 extractions (Sigma-Aldrich).

  • c Time is estimated for parallel extraction of 96 to 192 samples.

  • d Price includes PCR reagents (Phusion High-Fidelity PCR master mix with HF buffer [Thermo Scientific]) that are not part of the DNA extraction kit.

  • e Price includes PCR reagents that are part of the kit.