Misguided phylogenetic comparisons using DGGE excised bands may contaminate public sequence databases.
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.
Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR, Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte, Minas Gerais, Brazil. Electronic address: victor.pylro@brmicrobiome.org.
Victor Satler
VS
Pylro
Genomics and Computational Biology Group, René Rachou Research Centre - CPqRR, Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte, Minas Gerais, Brazil.
Daniel Kumazawa
DK
Morais
Microbiology Department, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
Karlos Henrique Martins
KH
Kalks
Universidade Federal do Pampa, São Gabriel, RS 97300-000, Brazil.
Luiz Fernando Wurdig
LF
Roesch
AgroEcology Department, Rothamsted Research, Harpenden, Herts AL52JQ, United Kingdom.
Penny R
PR
Hirsch
Microbiology Department, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil.
Marcos Rogério
MR
Tótola
Biology Department, Universidade Federal de Viçosa, Viçosa, MG, 36570-900, Brazil.
Karla
K
Yotoko
D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D030561:Databases, Nucleic Acid / Q000592:standards*; D058645:Denaturing Gradient Gel Electrophoresis / Q000379:methods; D020459:Genes, rRNA; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
D012336:RNA, Ribosomal, 16S
16S rRNA gene; PCR-DGGE bacteria phylogeny; Public databases