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Significance test for comparing complex microbial community fingerprints using pairwise similarity measures
Siegfried Kropf1, Holger Heuer, Martin Grüning
1Institute for Biometry and Medical Informatics, Otto von Guericke University, Leipziger Str. 44, Magdeburg 39120, Germany. Siegfried.Kropf@medizin.uni-madgeburg.de
Journal of Microbiological Methods
|April 6, 2004
Summary
This study introduces permutation tests for analyzing microbial communities using electrophoresis data. The new method enhances comparisons of bacterial soil communities affected by different crop plants.
Area of Science:
- Microbiology
- Bioinformatics
- Molecular Biology
Background:
- Electrophoresis is crucial for studying complex microbial communities.
- Analysis systems convert electrophoresis patterns into data for similarity calculations.
- These measures are typically used in cluster analyses.
Purpose of the Study:
- To apply permutation tests for comparing groups of electrophoresis lanes.
- To extend these methods for combined analysis across multiple gels.
- To provide a computer program for these procedures.
Main Methods:
- Utilized pairwise measures of difference/similarity from electrophoresis lane patterns.
- Applied permutation tests to compare groups of lanes.
- Integrated extensions for multi-gel analysis.
Main Results:
- Successfully applied permutation tests to compare bacterial soil communities.
- Demonstrated the method's utility in assessing the effect of different crop plants.
- The procedures are available as a computer program.
Conclusions:
- Permutation tests offer a robust statistical framework for analyzing electrophoresis data from microbial communities.
- The developed methods and software facilitate more comprehensive comparisons of complex samples.
- This approach is effective for ecological studies, such as evaluating crop plant impacts on soil bacteria.