Random Sampling Process Leads to Overestimation of β-Diversity of Microbial Communities
| Autor: | Yi-Huei Jiang, Jizhong Zhou, Benjamin Yamin Zhou, Zhili He, Liyou Wu, Kai Xue, Ye Deng, Zhou Shi, Yunfeng Yang |
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| Jazyk: | angličtina |
| Rok vydání: | 2013 |
| Předmět: |
Jaccard index
Biology Poisson distribution Microbiology 03 medical and health sciences symbols.namesake Microbial ecology Virology Statistics Environmental Microbiology Molecular Biology Relative abundance distribution Selection Bias 030304 developmental biology 0303 health sciences 030306 microbiology Ecology Sampling (statistics) Reproducibility of Results Replicate Models Theoretical Biota QR1-502 Metagenomics Poisson sampling symbols Research Article |
| Zdroj: | mBio mBio, Vol 4, Iss 3 (2013) |
| ISSN: | 2150-7511 |
| Popis: | The site-to-site variability in species composition, known as β-diversity, is crucial to understanding spatiotemporal patterns of species diversity and the mechanisms controlling community composition and structure. However, quantifying β-diversity in microbial ecology using sequencing-based technologies is a great challenge because of a high number of sequencing errors, bias, and poor reproducibility and quantification. Herein, based on general sampling theory, a mathematical framework is first developed for simulating the effects of random sampling processes on quantifying β-diversity when the community size is known or unknown. Also, using an analogous ball example under Poisson sampling with limited sampling efforts, the developed mathematical framework can exactly predict the low reproducibility among technically replicate samples from the same community of a certain species abundance distribution, which provides explicit evidences of random sampling processes as the main factor causing high percentages of technical variations. In addition, the predicted values under Poisson random sampling were highly consistent with the observed low percentages of operational taxonomic unit (OTU) overlap ( IMPORTANCE Due to the vast diversity and uncultivated status of the majority of microorganisms, microbial detection, characterization, and quantitation are of great challenge. Although large-scale metagenome sequencing technology such as PCR-based amplicon sequencing has revolutionized the studies of microbial communities, it suffers from several inherent drawbacks, such as a high number of sequencing errors, biases, poor quantitation, and very high percentages of technical variations, which could greatly overestimate microbial biodiversity. Based on general sampling theory, this study provided the first explicit evidence to demonstrate the importance of random sampling processes in estimating microbial β-diversity, which has not been adequately recognized and addressed in microbial ecology. Since most ecological studies are involved in random sampling, the conclusions learned from this study should also be applicable to other ecological studies in general. In summary, the results presented in this study should have important implications for examining microbial biodiversity to address both basic theoretical and applied management questions. |
| Databáze: | OpenAIRE |
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