Microbe-ID: An open source toolbox for microbial genotyping and species identification
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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.
Cite this as
2016. Microbe-ID: An open source toolbox for microbial genotyping and species identification. PeerJ Preprints 4:e2005v1 https://doi.org/10.7287/peerj.preprints.2005v1note This preprint is not peer-reviewed. You may wish to reference the subsequent peer-reviewed version of this article.
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This is a preprint submission to PeerJ Preprints.
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Supplemental Information
Supplementary Figure 1
UPGMA dendrogram of sub-module MLST-ID of Genotype-ID. The tree was constructed using 100 bootstrap replicates and MLST analysis of 8 genes (5 housekeeping genes and 3 virulence genes) of Clavibacter michiganensis. The query used is a concatenation of a WASH sample using all 8 genes. Queries are represented in blue. Note that all queries are correctly placed amongst samples of its presumptive clonal lineage while also representing relationships between lineages in the reference dataset.
Supplemental figure 2
UPGMA dendrogram of sub-module Binary-ID of Genotype-ID using 100 bootstrap replicates for Aphanomyces euteiches. The queries used for this iteration of Binary-ID are two samples from a presumptive “Athena” origin. Queries are represented in red. Note that all queries were correctly placed amongst samples of its presumptive clonal lineage while also representing relationships between lineages in the reference dataset, indicating both queries are more closely related to the “Athena” population than the “Mt. Vernon” population.
Additional Information
Competing Interests
NJ Grünwald and JH Chang are academic editors for PeerJ.
Author Contributions
Javier F Tabima conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.
Sydney E Everhart conceived and designed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.
Meredith M Larsen performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Alexandra J Weisberg performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Zhian N Kamvar performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Matthew A Tancos performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.
Christine D Smart wrote the paper, reviewed drafts of the paper.
Jeff H Chang wrote the paper, reviewed drafts of the paper.
Niklaus J Grünwald conceived and designed the experiments, wrote the paper, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
https://github.com/grunwaldlab/Microbe-ID
Funding
This research is supported in part by US Department of Agriculture (USDA) Agricultural Research Service Grant 5358-22000-039-00D (NJG), USDA National Institute of Food and Agriculture (NIFA) Grant 2011-68004-30154 (NJG), the USDA ARS Floriculture Nursery Research Initiative (NJG), USDA NIFA Grant 2014-51181-22384 (JHC and NJG), and USDA NIFA 2012-67012-19844 (SEE). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
