Microbe-ID: An open source toolbox for microbial genotyping and species identification

Authors

Javier F. Tabima, Oregon State University
Sydney E. Everhart, University of Nebraska-LincolnFollow
Meredith M. Larsen, USDA-ARS, Corvallis, OR
Alexaandra J. Weisberg, Oregon State University
Zhian N. Kamvar, Oregon State UniversityFollow
Mathew A. Tancos, Cornell University
Christine D. Smart, Cornell University
Jeff H. Chang, Oregon State University
Niklaus J. GrünwaldFollow

Document Type

Article

Date of this Version

4-28-2016

Citation

Tabima JF, Everhart SE, Larsen MM, Weisberg AJ, Kamvar ZN, Tancos MA, Smart CD, Chang JH, Grünwald NJ. (2016) Microbe-ID: An open source toolbox for microbial genotyping and species identification. PeerJ Preprints 4:e2005v1 https://doi.org/10.7287/peerj.preprints.2005v1

Comments

CC-BY 4.0 Open Access

Abstract

Development of tools to identify species, genotypes, or novel strains of invasive organisms is critical for monitoring emergence and implementing rapid response measures. Molecular markers, although critical to identifying species or genotypes, require bioinformatic tools for analysis. However, user-friendly analytical tools for fast identification are not readily available. To address this need, we created a web-based set of applications called Microbe-ID that allow for customizing a toolbox for rapid species identification and strain genotyping using any genetic markers of choice. Two components of Microbe-ID, named Sequence-ID and Genotype-ID, implement species and genotype identification, respectively. Sequence-ID allows identification of species by using BLAST to query sequences for any locus of interest against a custom reference sequence database. Genotype-ID allows placement of an unknown multilocus marker in either a minimum spanning network or dendrogram with bootstrap support from a user-created reference database. Microbe-ID can be used for identification of any organism based on nucleotide sequences or any molecular marker type and several examples are provided. We created a public website for demonstration purposes called Microbe-ID (www.microbe-id.org) and provided a working implementation for the genus Phytophthora (www.phytophthora-id.org). In Phytophthora-ID, the Sequence-ID application allows identification based on ITS or cox spacer sequences. Genotype-ID groups individuals into clonal lineages based on simple sequence repeat (SSR) markers for the two invasive plant pathogen species P. infestans and P. ramorum. All code is open source and available on github and CRAN. Instructions for installation and use are provided at https://github.com/grunwaldlab/Microbe-ID.