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Article

Microbe Finder (MiFi®): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data

1
Institute of Biosecurity and Microbial Forensics (IBMF), Oklahoma State University, Stillwater, OK 74078, USA
2
Department of Entomology and Plant Pathology, Oklahoma State University, Stillwater, OK 74078, USA
*
Author to whom correspondence should be addressed.
Plants 2021, 10(2), 250; https://doi.org/10.3390/plants10020250
Received: 12 October 2020 / Revised: 18 January 2021 / Accepted: 20 January 2021 / Published: 28 January 2021
Agricultural high throughput diagnostics need to be fast, accurate and have multiplexing capacity. Metagenomic sequencing is being widely evaluated for plant and animal diagnostics. Bioinformatic analysis of metagenomic sequence data has been a bottleneck for diagnostic analysis due to the size of the data files. Most available tools for analyzing high-throughput sequencing (HTS) data require that the user have computer coding skills and access to high-performance computing. To overcome constraints to most sequencing-based diagnostic pipelines today, we have developed Microbe Finder (MiFi®). MiFi® is a web application for quick detection and identification of known pathogen species/strains in raw, unassembled HTS metagenomic data. HTS-based diagnostic tools developed through MiFi® must pass rigorous validation, which is outlined in this manuscript. MiFi® allows researchers to collaborate in the development and validation of HTS-based diagnostic assays using MiProbe™, a platform used for developing pathogen-specific e-probes. Validated e-probes are made available to diagnosticians through MiDetect™. Here we describe the e-probe development, curation and validation process of MiFi® using grapevine pathogens as a model system. MiFi® can be used with any pathosystem and HTS platform after e-probes have been validated. View Full-Text
Keywords: Microbe Finder (MiFi); diagnostics; nucleic acid; metagenomics; pathogens; taxonomy; sequencing; assay validation; sensitivity and specificity Microbe Finder (MiFi); diagnostics; nucleic acid; metagenomics; pathogens; taxonomy; sequencing; assay validation; sensitivity and specificity
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MDPI and ACS Style

Espindola, A.S.; Cardwell, K.F. Microbe Finder (MiFi®): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data. Plants 2021, 10, 250. https://doi.org/10.3390/plants10020250

AMA Style

Espindola AS, Cardwell KF. Microbe Finder (MiFi®): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data. Plants. 2021; 10(2):250. https://doi.org/10.3390/plants10020250

Chicago/Turabian Style

Espindola, Andres S., and Kitty F. Cardwell 2021. "Microbe Finder (MiFi®): Implementation of an Interactive Pathogen Detection Tool in Metagenomic Sequence Data" Plants 10, no. 2: 250. https://doi.org/10.3390/plants10020250

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