Comparative assessment of next-generation sequencing, denaturing gradient gel electrophoresis, clonal restriction fragment length polymorphism and cloning-sequencing as methods for characterizing commercial microbial consortia

2015 ◽  
Vol 108 ◽  
pp. 103-111 ◽  
Author(s):  
A.D. Samarajeewa ◽  
A. Hammad ◽  
L. Masson ◽  
I.U.H. Khan ◽  
R. Scroggins ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Restriction Fragment Length Polymorphism ◽  
Gel Electrophoresis ◽  
Fragment Length Polymorphism ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Comparative Assessment ◽  
Microbial Consortia ◽  
Gradient Gel Electrophoresis ◽  
Generation Sequencing ◽  
Restriction Fragment Length

scholarly journals Optimization of Terminal-Restriction Fragment Length Polymorphism Analysis for Complex Marine Bacterioplankton Communities and Comparison with Denaturing Gradient Gel Electrophoresis

1999 ◽  
Vol 65 (8) ◽  
pp. 3518-3525 ◽  
Author(s):  
Markus M. Moeseneder ◽  
Jesús M. Arrieta ◽  
Gerard Muyzer ◽  
Christian Winter ◽  
Gerhard J. Herndl
Keyword(s):  
Restriction Fragment Length Polymorphism ◽  
16S Rrna ◽  
Length Polymorphism ◽  
Gel Electrophoresis ◽  
Fragment Length Polymorphism ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Marine Bacterioplankton ◽  
Gradient Gel Electrophoresis ◽  
Restriction Fragment Length ◽  
Bacterioplankton Communities

ABSTRACT The potential of terminal-restriction fragment length polymorphism (T-RFLP) and the detection of operational taxonomic units (OTUs) by capillary electrophoresis (CE) to characterize marine bacterioplankton communities was compared with that of denaturing gradient gel electrophoresis (DGGE). A protocol has been developed to optimize the separation and detection of OTUs between 20 and 1,632 bp by using CE and laser-induced fluorescence detection. Additionally, we compared T-RFLP fingerprinting to DGGE optimized for detection of less abundant OTUs. Similar results were obtained with both fingerprinting techniques, although the T-RFLP approach and CE detection of OTUs was more sensitive, as indicated by the higher number of OTUs detected. We tested the T-RFLP fingerprinting technique on complex marine bacterial communities by using the 16S rRNA gene and 16S rRNA as templates for PCR. Samples from the Northern and Middle Adriatic Sea and from the South and North Aegean Sea were compared. Distinct clusters were identifiable for different sampling sites. Thus, this technique is useful for rapid evaluation of the biogeographical distribution and relationships of bacterioplankton communities.

Sign in / Sign up

Export Citation Format

Share Document