Comparing Pyrosequencing Methods for Microbial Community Analysis
Author Information
Author(s): Tamaki Hideyuki, Wright Chris L., Li Xiangzhen, Lin Qiaoyan, Hwang Chiachi, Wang Shiping, Thimmapuram Jyothi, Kamagata Yoichi, Liu Wen-Tso
Primary Institution: University of Illinois at Urbana-Champaign
Hypothesis
How do different pyrosequencing methods affect sequencing throughput and microbial community analysis outcomes?
Conclusion
Different pyrosequencing methods can significantly affect sequencing output but do not alter the outcomes of microbial community analysis.
Supporting Evidence
- Method-2 and Method-3 produced 1.5–1.6 times more usable reads than Method-1 after quality trimming.
- Multidimensional scaling analysis showed that samples from the same environment clustered together regardless of the sequencing method used.
- All methods provided similar numbers of operational taxonomic units (OTUs) and diversity indices across samples.
Takeaway
This study looked at three ways to read tiny pieces of DNA from different environments, and found that while some methods gave more data, they all told a similar story about the tiny living things in those samples.
Methodology
The study compared three pyrosequencing methods using 10 environmental samples to evaluate sequencing output and microbial community analysis.
Potential Biases
Potential biases in microbial community compositions due to differences in primer sets and sequencing methods.
Limitations
The study did not explore the effects of biases associated with DNA extraction and primer selection on the results.
Participant Demographics
Environmental samples included alpine meadow soils, drinking water biofilms, and anaerobic digester sludge from various locations.
Statistical Information
P-Value
0.001
Statistical Significance
p<0.001
Digital Object Identifier (DOI)
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