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Status of the microbial census.
Patrick D Schloss1, Jo Handelsman
1Department of Plant Pathology, University of Wisconsin-Madison, 1630 Linden Dr., Madison, WI 53706, USA.
Microbiology and Molecular Biology Reviews : MMBR
|December 14, 2004
Summary
The 16S rRNA gene is widely used for bacterial phylogeny, but current sequencing efforts reveal we are far from a complete bacterial census. Further exploration of diverse environments and phylogenetic groups is needed to discover novel bacterial diversity.
Area of Science:
- Microbiology
- Bioinformatics
- Evolutionary Biology
Background:
- The 16S ribosomal RNA (rRNA) gene is the most extensively utilized marker for bacterial phylogenetic studies, with over 78,000 sequences in public databases.
- Despite widespread use, a quantitative assessment of sequencing efforts and their effectiveness in capturing bacterial diversity has been lacking.
Purpose of the Study:
- To quantitatively assess the current state of bacterial sampling using 16S rRNA gene sequences.
- To evaluate the relative taxonomic richness of different bacterial phyla and identify under-sampled groups.
- To inform future strategies for microbial diversity surveys.
Main Methods:
- Construction of rarefaction curves for individual bacterial phyla and the entire bacterial domain.
- Analysis of publicly available 16S rRNA gene sequences from GenBank and the Ribosomal Database Project.
- Quantitative assessment of sequencing depth and taxonomic coverage.
Main Results:
- Current sequencing efforts have not achieved a comprehensive census of bacterial diversity, with a minimum estimated species richness of 35,498.
- Numerous globally distributed bacterial phyla remain significantly under-sampled.
- Existing sampling strategies may not be optimal for discovering novel bacterial diversity.
Conclusions:
- A vast amount of bacterial diversity remains undiscovered, highlighting the need for more extensive sequencing.
- Targeted surveys of chemically diverse environments and under-sampled phylogenetic groups are crucial for accelerating the discovery of bacterial species.
- Future research should focus on optimizing sampling strategies to maximize the capture of novel microbial life.