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Multiple hypervariable markers improve mycobiome classification in metatranscriptome and metagenome data.

Haihua Wang1,2, Steven H Wu3, Kaile Zhang1,2

  • 1North Florida Research and Education Center, University of Florida, Quincy, FL, USA.

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|April 8, 2026
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Summary
This summary is machine-generated.

MicroFisher enhances fungal community profiling from metagenomic and metatranscriptomic data. This novel tool improves taxonomic identification and abundance estimation, outperforming existing methods for environmental microbiome analysis.

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Area of Science:

  • Environmental microbiology
  • Bioinformatics
  • Fungal ecology

Background:

  • Metagenomic and metatranscriptomic sequencing advance understanding of fungal functions in ecosystems.
  • Current mycobiome classification methods face limitations due to reference genome availability and database resolution.

Purpose of the Study:

  • To develop a novel computational tool, MicroFisher, for accurate taxonomic identification of fungal communities.
  • To improve the sensitivity and accuracy of mycobiome profiling from sequencing data.

Main Methods:

  • Developed MicroFisher, a tool identifying taxonomically useful reads using multiple hypervariable markers.
  • Applied MicroFisher to simulated fungal communities, forest soil metagenomes, and root eukaryotic metatranscriptomes.
  • Utilized high-resolution hypervariable marker gene databases and weighted integration algorithms.

Main Results:

  • MicroFisher demonstrated higher performance in fungal prediction and abundance estimation compared to existing tools.
  • The tool provided more accurate profiling of environmental microbiomes, including rare taxa detection.
  • Outperformed current state-of-the-art tools in fungal community classification.

Conclusions:

  • MicroFisher offers a novel and accurate pipeline for classifying fungal communities from metagenomic and metatranscriptomic data.
  • The tool addresses limitations of genome- or core protein-based approaches.
  • Enables more comprehensive analysis of environmental mycobiomes, including rare species.