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ARS Home » Pacific West Area » Corvallis, Oregon » Horticultural Crops Research Unit » Research » Publications at this Location » Publication #328779
Title: Microbe-ID: An open source toolbox for microbial genotyping and species identification

Author
item TABIMA, JAVIER - Oregon State University
item EVERHART, SYDNEY - University Of Nebraska
item Larsen, Meredith
item WEISBERG, ALEXANDRA - Oregon State University
item KAMVAR, ZHIAN - Oregon State University
item TANCOS, MATT - Cornell University
item SMART, CHRISTINE - Cornell University
item CHANG, JEFF - Oregon State University
item Grunwald, Niklaus - Nik

Submitted to: PeerJ
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2016
Publication Date: 8/18/2016
Citation: Tabima, J.F., Everhart, S.E., Larsen, M.M., Weisberg, A.J., Kamvar, Z.N., Tancos, M.A., Smart, C.D., Chang, J.H., Grunwald, N.J. 2016. Microbe-ID: An open source toolbox for microbial genotyping and species identification. PeerJ. 4:e2279. doi: 10.7717/peerj.2279.

Interpretive Summary: 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 computational 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. We created a public website for demonstration purposes called Microbe-ID (www.microbe-id.org) and provided a working implementation for the group of plant pathogens in the genus Phytophthora (www.phytophthora-id.org). All code is open source and available on public repositories and code instructions for implementation are provided.

Technical 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.