DNA Extraction from Stool or Luminal Aspirate

There are two different protocols that are useful for extracting DNA for 16S RNA sequencing. The Mo-Bio soil kit listed is typically used for large scale sample preparation. The only exception from the manufacturer instructions is that we use a GenoGrinder (or colleagues at Argonne use the MoBio 96-well Plate Shaker) to physically lyse the samples in the MoBio provided Bead Plates and Bead Solution for 5-10 minutes, depending on the sample type. For your samples, presumably an aspirate or biopsy collected during colonscopy, 6 minutes of beadbeating will suffice. For tougher samples like firm stool or mouse fecal pellets, 10 minutes are required.

Be sure to keep all samples in a sterile tube on dry ice upon collection and at -80C (if possible) until processing.