Direct comparison of single-strand conformation polymorphism (SSCP) and denaturing gradient gel electrophoresis (DGGE) to characterize a microbial community on the basis of 16S rRNA gene fragments.
Characterization of microbial communities using single-strand conformation polymorphism (SSCP) was compared with that using denaturing gradient gel electrophoresis (DGGE). This comparison was based on the V3-4 region (Escherichia coli positions: 341-806) of 16S rRNA gene of bacterial or archaeal communities obtained from a methanogenic bioreactor. Significant differences in the bacterial banding profiles were observed while attempting to detect the diversity of the community and its succession during the reactor operation. The SSCP produced a number of sharp bands and differentiated the bacterial community structures to which the DGGE gave an identical pattern. On the other hand, the SSCP and DGGE provided similar succession patterns for archaeal community.
Hori
Tomoyuki
T
Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo 113-8657, Japan.
Haruta
Shin
S
Ueno
Yoshiyuki
Y
Ishii
Masaharu
M
Igarashi
Yasuo
Y
D001419:Bacteria / Q000235:genetics* / Q000302:isolation & purification; D019149:Bioreactors / Q000382:microbiology*; D016172:DNA Fingerprinting / Q000379:methods; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel / Q000379:methods*; D016133:Polymerase Chain Reaction; D018807:Polymorphism, Single-Stranded Conformational; D012336:RNA, Ribosomal, 16S / Q000737:chemistry / Q000235:genetics*; D012722:Sewage / Q000382:microbiology
D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S; D012722:Sewage