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Identification of Rare Bacterial Pathogens by 16S rRNA Gene Sequencing and MALDI-TOF MS
Published on: July 11, 2016
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Microbe-ID: an open source toolbox for microbial genotyping and species identification
Javier F Tabima1, Sydney E Everhart2, Meredith M Larsen3
1Department of Botany and Plant Pathology, Oregon State University , Corvallis , OR , United States.
Peerj
|September 8, 2016
Summary
A new web-based tool, Microbe-ID, offers rapid species identification and strain genotyping for invasive organisms using customizable genetic markers. This bioinformatics solution addresses the need for user-friendly, fast analytical tools in organism monitoring and response.
Area of Science:
- Bioinformatics
- Molecular Biology
- Computational Biology
Background:
- Accurate identification of invasive species, genotypes, and strains is crucial for effective monitoring and rapid response.
- Molecular markers are vital for identification but require sophisticated bioinformatic tools for analysis.
- Existing user-friendly analytical tools for rapid identification are limited.
Purpose of the Study:
- To develop a customizable, web-based bioinformatics toolset for rapid species identification and strain genotyping.
- To provide user-friendly applications for analyzing molecular markers of invasive organisms.
- To facilitate custom toolbox creation for diverse genetic marker types.
Main Methods:
- Development of Microbe-ID, a web-based application suite with Sequence-ID and Genotype-ID components.
- Sequence-ID utilizes BLAST for species identification against custom reference databases.
- Genotype-ID employs minimum spanning networks or dendrograms for genotype placement using user-created reference databases.
Main Results:
- Microbe-ID enables rapid identification of organisms using nucleotide sequences or any molecular marker.
- A demonstration website (microbe-id.org) and a specific implementation for *Phytophthora* (phytophthora-id.org) were created.
- The *Phytophthora*-ID implementation uses Sequence-ID for ITS/cox spacer analysis and Genotype-ID for SSR marker-based clonal lineage grouping of *P. infestans* and *P. ramorum*.
Conclusions:
- Microbe-ID provides a flexible and accessible platform for organism identification and genotyping.
- The open-source nature and availability on GitHub and CRAN promote widespread adoption and customization.
- This toolset significantly enhances capabilities for monitoring invasive species and managing plant pathogens.
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