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Updated: Jul 3, 2026
11:22
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
The rational exploration of microbial diversity
Christopher Quince1, Thomas P Curtis, William T Sloan
1Department of Civil Engineering, University of Glasgow, Glasgow, UK. quince@civil.gla.ac.uk
The ISME Journal
|July 25, 2008
Summary
Discovering microbial diversity requires significant sequencing effort. While the upper ocean is relatively well-characterized, deep-sea vents and soils harbor vast microbial communities demanding extensive surveys for full exploration.
Area of Science:
- Microbial Ecology
- Bioinformatics
- Genomics
Background:
- Microbial exploration has yielded many discoveries but lacked structured surveys.
- Estimating microbial diversity and required sequencing effort is crucial for future research.
Purpose of the Study:
- To estimate microbial diversity and the sequencing effort needed to describe it across different environments.
- To predict the feasibility of achieving comprehensive metagenome sequencing.
Main Methods:
- Application of a robust statistical method to large gene sequence libraries.
- Analysis of taxa-abundance distributions to estimate diversity and sequencing requirements.
Main Results:
- Upper ocean harbors an estimated 1400 phylotypes; 90% metagenome coverage achievable with a fivefold increase in shotgun reads.
- Deep ocean, hydrothermal vents, and soils exhibit significantly higher diversity, requiring hundreds of times more samples and tens of thousands of times more sequencing effort for 90% taxonomic and metagenomic coverage.
Conclusions:
- Comprehensive sequencing of hyperdiverse microbial environments is currently challenging.
- Taxa-abundance distributions can guide strategies for future microbial exploration and method development.
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