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

Area of Science:

• Agricultural diagnostics
• Bioinformatics
• Genomics

Background:

• High-throughput diagnostics in agriculture require speed, accuracy, and multiplexing.
• Bioinformatic analysis of metagenomic data is a bottleneck due to large file sizes.
• Current tools for analyzing high-throughput sequencing (HTS) data often require coding skills and high-performance computing.

Purpose of the Study:

• To develop a user-friendly web application, Microbe Finder (MiFi®), to overcome limitations in HTS data analysis for diagnostics.
• To enable quick detection and identification of known pathogen species/strains in raw, unassembled HTS metagenomic data.
• To outline the rigorous validation process for HTS-based diagnostic tools developed through MiFi®.

Main Methods:

• Development of Microbe Finder (MiFi®) web application for HTS data analysis.
• Utilizing MiProbe™ platform for developing pathogen-specific electronic probes (e-probes).
• Describing the e-probe development, curation, and validation process using grapevine pathogens as a model.

Main Results:

• MiFi® provides a solution for rapid detection and identification of known pathogens from HTS data.
• The MiProbe™ platform facilitates the creation of validated pathogen-specific e-probes.
• Validated e-probes are accessible to diagnosticians via MiDetect™.

Conclusions:

• MiFi® simplifies HTS-based diagnostic assay development and validation.
• The MiFi® platform, coupled with validated e-probes, can be applied to any pathosystem and HTS platform.
• This approach overcomes computational constraints, making HTS diagnostics more accessible in agriculture.