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Pyrosequencing for Microbial Identification and Characterization
Published on: August 22, 2013
Rapid phylogenetic dissection of prokaryotic community structure in tidal flat using pyrosequencing
Bong-Soo Kim1, Byung Kwon Kim, Jae-Hak Lee
1School of Biological Sciences and Institute of Microbiology, Seoul National University, Seoul, 151-742, Republic of Korea.
Journal of Microbiology (Seoul, Korea)
|September 2, 2008
Summary
Pyrosequencing and bioinformatics reveal greater prokaryotic diversity in tidal flats than previously known. This automated method offers a faster, more in-depth analysis of bacterial and archaeal communities without cloning.
Area of Science:
- Microbiology
- Environmental Science
- Bioinformatics
Background:
- Understanding prokaryotic community structure is crucial for ecological role assessment.
- 16S rRNA gene amplification and sequencing are popular methods.
- Conventional Sanger sequencing with cloning is costly and labor-intensive.
Purpose of the Study:
- To investigate prokaryotic community structure in Korean tidal flat sediments.
- To implement pyrosequencing and an automated bioinformatic pipeline for rapid and accurate taxonomic assignment.
- To compare the diversity revealed by pyrosequencing with previous clone library studies.
Main Methods:
- Utilized pyrosequencing for 16S rRNA gene amplification and sequencing.
- Employed an automated bioinformatic pipeline for taxonomic assignment.
- Analyzed prokaryotic community structure in tidal flat sediments.
Main Results:
- Pyrosequencing revealed higher bacterial and archaeal diversity than clone library studies.
- Identified 21 bacterial divisions and 37 candidate divisions; Proteobacteria (Gamma- and Delta-subclasses) was most abundant.
- Found 4 archaeal divisions; Euryarchaeota was most abundant, with 8 classes and 11 unclassified groups.
Conclusions:
- The combined pyrosequencing and bioinformatics approach provides a simple, in-depth, and automated method for dissecting prokaryotic communities.
- This method bypasses the need for extensive pretreatment like cloning.
- Revealed a more comprehensive view of prokaryotic diversity in tidal flat ecosystems.
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