Here, we report a versatile metagenome purification method to identify uncultivable species from sediments and soils by nested-PCR-DGGE according to 16S rDNA.This combination of methods uses enzymatic lysis in situ, polyvinylpyrrolidone (PVP), Chelex 100, glass bead-silica gel and chaotropic salts, with the advantage that it can be applied to different soils.