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Guided Protocol for Fecal Microbial Characterization by 16S rRNA-Amplicon Sequencing
Published on: March 19, 2018
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Using 16S rRNA gene as marker to detect unknown bacteria in microbial communities
Quang Tran1, Diem-Trang Pham1, Vinhthuy Phan2
1Department of Computer Science, University of Memphis, Memphis, 38152, TN, USA.
BMC Bioinformatics
|January 4, 2018
Summary
A new method uses short reads from 16S rRNA genes to detect unknown bacteria in environmental samples. This approach reduces costs and maintains accuracy for microbial genome identification.
Area of Science:
- Microbiology
- Genomics
- Bioinformatics
Background:
- Metagenomics faces challenges in identifying and quantifying microbial genomes from next-generation sequencing data.
- Current methods struggle with unknown bacteria or those with unsequenced genomes.
Purpose of the Study:
- To develop a novel method for detecting unknown bacteria in environmental samples.
- To leverage short reads from 16S ribosomal RNA (rRNA) genes for bacterial identification.
Main Methods:
- Utilized short reads exclusively from 16S rRNA genes, bypassing the need for whole genome data.
- Applied the method to bacterial genomes from the Human Oral Microbiome Database.
Main Results:
- Demonstrated that short 16S rRNA gene reads contain sufficient information for detecting unknown bacteria.
- Achieved accurate and robust predictions across varying read coverages and proportions of unknown bacteria.
Conclusions:
- The proposed method offers a cost-effective and computationally efficient approach to metagenomic analysis.
- The strong conservation of the 16S rRNA gene suggests high accuracy potential across diverse environmental samples.
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