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Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
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PhyloToAST: Bioinformatics tools for species-level analysis and visualization of complex microbial datasets
Shareef M Dabdoub1, Megan L Fellows1, Akshay D Paropkari1
1Division of Periodontology, College of Dentistry, The Ohio State University, Columbus, Ohio, USA.
Scientific Reports
|July 1, 2016
Summary
New software, PhyloToAST, enhances microbial microbiome analysis using 16S rRNA gene sequencing. It improves speed, reduces primer bias, and boosts species-level resolution for complex ecosystems.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- The 16S rRNA gene is a standard marker for microbial taxonomic profiling.
- Advances in sequencing generate vast datasets from minimal biological samples.
- Efficient analysis of large-scale microbiome data, especially at the species level, is crucial.
Purpose of the Study:
- To introduce new software, Phylogenetic Tools for Analysis of Species-level Taxa (PhyloToAST).
- To improve the speed and resolution of 16S rRNA gene sequencing data analysis.
- To reduce primer bias and enhance species-level taxonomic profiling within the QIIME pipeline.
Main Methods:
- Development of the PhyloToAST software package.
- Integration of PhyloToAST with the QIIME bioinformatics pipeline.
- Utilizing dual sequencing primers to mitigate primer bias.
Main Results:
- PhyloToAST significantly enhances analysis speed for large microbiome datasets.
- The software improves resolution to the species level.
- Primer bias is reduced, leading to more accurate taxonomic profiling.
- New visualization tools are incorporated.
Conclusions:
- PhyloToAST offers a substantial improvement for 16S rRNA gene-based microbiome analysis.
- The software addresses key challenges in speed, resolution, and bias in microbiome research.
- PhyloToAST is freely available open-source software, promoting wider adoption in the scientific community.
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