Analysis of artifacts suggests DGGE should not be used for quantitative diversity analysis

► PCR-DGGE artifacts bias quantitative analysis of microbial community diversity. ► Multiple bands from a single isolate profile contained identical sequences. ► Multiband isolate profiles cause overestimation of species richness. ► DGGE band intensity did not consistently represent initial template concentration. ► Preferential amplification attributed to early cycle inhibition and primer mismatch.