Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases

• Our research aimed to investigate the extent of errors caused by the use of PCR-DGGE and sequencing its excised bands.
• Our results highlight concerns about the use of the PCR-DGGE to profile 16S rRNA genes.
• The sequencing of DGGE excised bands should be avoided to prevent errors in species identification.

Controversy surrounding bacterial phylogenies has become one of the most important challenges for microbial ecology. Comparative analyses with nucleotide databases and phylogenetic reconstruction of the amplified 16S rRNA genes from DGGE (Denaturing Gradient Gel Electrophoresis) excised bands have been used by several researchers for the identification of organisms in complex samples. Here, we individually analyzed DGGE-excised 16S rRNA gene bands from 10 certified bacterial strains of different species, and demonstrated that this kind of approach can deliver erroneous outcomes to researchers, besides causing/emphasizing errors in public databases.