Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities

@article{Mhling2008ImprovedGP,
  title={Improved group-specific PCR primers for denaturing gradient gel electrophoresis analysis of the genetic diversity of complex microbial communities},
  author={Martin M{\"u}hling and John Woolven-Allen and John Colin Murrell and Ian R. Joint},
  journal={The ISME Journal},
  year={2008},
  volume={2},
  pages={379-392}
}
Key MethodPhylum- and class-specific PCR primers were tested for the production of clone libraries and for denaturing gradient gel electrophoresis (DGGE) analysis of complex bacterial communities.
Improved group-specific primers based on the full SILVA 16S rRNA gene reference database.
TLDR
As observed through theoretical and practical evaluation, the primers developed in this study showed a higher level of precision than previously published primers, thus allowing a deeper insight into microbial community dynamics.
Comparison of 16S rRNA and protein-coding genes as molecular markers for assessing microbial diversity (Bacteria and Archaea) in ecosystems.
TLDR
Analysis of the major groups found in these ecosystems, such as Actinob bacteria, Bacteroides, Proteobacteria and Cyanobacteria, showed good agreement between the protein markers and the results given by 16S rRNA genes from metagenomic reads.
Comparison of primer sets for the study of Planctomycetes communities in lentic freshwater ecosystems.
TLDR
It is suggested that the primer set PLA352F/PLA920R provides good estimates of Planctomycetes richness and diversity compared with other, and can thus be used to study Planctomers dynamics in lentic freshwater ecosystems.
Agarose Gel Purification of PCR Products for Denaturing Gradient Gel Electrophoresis Results in GC-Clamp Deletion
TLDR
It is concluded that the gel purification method is not suitable for DGGE PCR products or even other GC-rich DNA samples.
Capabilities and limitations of DGGE for the analysis of hydrocarbonoclastic prokaryotic communities directly in environmental samples
TLDR
Prokaryotic communities in pristine and oil‐contaminated desert soil, seawater, and hypersaline coastal soil were analyzed using culture‐dependent and culture‐independent approaches and the subdivision primers exhibited satisfactory specificity, but they failed to capture all the available taxa.
An investigation into the potential impacts of ocean acidification and ocean fertilisation on the genetic diversity of marine bacterial assemblages
TLDR
The aim was to investigate bacterioplankton diversity and reveal greater fingerprint diversity within these groups than is possible using primers specific for the entire domain Bacteria, and also to reduce clone library redundancy.
16S rRNA Gene Primer Validation for Bacterial Diversity Analysis of Vegetable Products.
  • M. Nakano
  • Biology
    Journal of food protection
  • 2018
TLDR
These primer pairs were validated for microbial community structure analysis with complex food matrices by using next-generation sequencing and revealed that the primer pair 335f/769r successfully resulted in fewer chloroplast and mitochondrial sequence reads than generated by the universal primer pair SD and therefore is comparatively suitable for metagenomic analyses of complexFood matrices, particularly those that are rich in plant DNA.
Exploring the diversity of Acinetobacter populations in river water with genus-specific primers and probes.
TLDR
The results indicated that culture-independent methods provide more detailed information on the diversity of Acinetobacter populations than that based on culture-dependent methods.
Evaluation of Marine Bacteroidetes-Specific Primers for Microbial Diversity and Dynamics Studies
TLDR
The satisfactory DGGE banding patterns and the wide diversity of sequences retrieved from DGGE bands with primer CF418 prove it to be a valuable alternative for the study of Bacteroidetes communities, recovering a wide range of phylotypes within the group.
...
...

References

SHOWING 1-10 OF 48 REFERENCES
Phylum- and Class-Specific PCR Primers for General Microbial Community Analysis
TLDR
The purpose of the present study was to develop several primer sets targeting commonly occurring and important groups, demonstrating the specificity of the primers under field conditions.
Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA
TLDR
Analysis of the genomic DNA from a bacterial biofilm grown under aerobic conditions suggests that sulfate-reducing bacteria, despite their anaerobicity, were present in this environment.
Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester.
TLDR
A culture-independent molecular phylogenetic approach was used to study prokaryotic diversity in an anaerobic sludge digester, detecting a novel monophyletic group of 164 clones representing 66.6% of the archaeal library and indicating that this group grows better under formate or H2-CO2.
Nested PCR-Denaturing Gradient Gel Electrophoresis Approach To Determine the Diversity of Sulfate-Reducing Bacteria in Complex Microbial Communities
TLDR
A three-step nested-PCR-denaturing gradient gel electrophoresis (DGGE) strategy to detect sulfate-reducing bacteria (SRB) in complex microbial communities from industrial bioreactors and revealed the identity of the community members.
A Highly Selective PCR Protocol for Detecting 16S rRNA Genes of the Genus Pseudomonas (Sensu Stricto) in Environmental Samples
TLDR
The results indicated that the Pseudomonas-selective PCR primers were highly specific and may represent a powerful tool for pseudomonas population structure analyses and taxonomic confirmations.
16S ribosomal DNA amplification for phylogenetic study
TLDR
By use of this method, the phylogenetic study of extremely fastidious or highly pathogenic bacterial species can be carried out without the need to culture them.
PCR primers to amplify 16S rRNA genes from cyanobacteria
TLDR
The use of this specific PCR in combination with denaturing gradient gel electrophoresis to probe the diversity of oxygenic phototrophic microorganisms in cultures, lichens, and complex microbial communities is demonstrated.
Application of a Novel rpoC1-RFLP Approach Reveals that Marine Prochlorococcus Populations in the Atlantic Gyres are Composed of Greater Microdiversity than Previously Described
TLDR
RFLP analysis of the clone libraries from the two gyre sites revealed that the two Prochlorococcus populations had a high degree of microdiversity with 40 and 52 different RFLP-type clones among the 143 clones tested for both the northern and southern gyres, respectively.
Review and re-analysis of domain-specific 16S primers.
Actively Growing Bacteria in the Inland Sea of Japan, Identified by Combined Bromodeoxyuridine Immunocapture and Denaturing Gradient Gel Electrophoresis
ABSTRACT A fundamental question in microbial oceanography concerns the relationship between prokaryote diversity and biogeochemical function in an ecosystem context. We combined bromodeoxyuridine
...
...