MicroFisher: Fungal taxonomic classification for metatranscriptomic and metagenomic data using multiple short hypervariable markers

Journal Article · Thu Jan 23 00:00:00 UTC 2025 · bioRxiv

DOI: https://doi.org/10.1101/2024.01.20.576350 · OSTI ID:2570203

Wang, Haihua; Wu, Steven; Zhang, Kaile; Chen, Ko-Hsuan; Vilgalys, Rytas; Liao, Hui-Ling

AbstractProfiling the taxonomic and functional composition of microbes using metagenomic (MG) and metatranscriptomic (MT) sequencing is advancing our understanding of microbial functions. However, the sensitivity and accuracy of microbial classification using genome– or core protein-based approaches, especially the classification of eukaryotic organisms, is limited by the availability of genomes and the resolution of sequence databases. To address this, we propose the MicroFisher, a novel approach that applies multiple hypervariable marker genes to profile fungal communities from MGs and MTs. This approach utilizes the hypervariable regions of ITS and large subunit (LSU) rRNA genes for fungal identification with high sensitivity and resolution. Simultaneously, we propose a computational pipeline (MicroFisher) to optimize and integrate the results from classifications using multiple hypervariable markers. To test the performance of our method, we applied MicroFisher to the synthetic community profiling and found high performance in fungal prediction and abundance estimation. In addition, we also used MGs from forest soil and MTs of root eukaryotic microbes to test our method and the results showed that MicroFisher provided more accurate profiling of environmental microbiomes compared to other classification tools. Overall, MicroFisher serves as a novel pipeline for classification of fungal communities from MGs and MTs.

• Research Organization: Chicago Office, Argonne, IL (United States)
• Sponsoring Organization: University of Florida
• Grant/Contract Number: SC0020403
• OSTI ID: 2570203
• Journal Information: bioRxiv, Journal Name: bioRxiv
• Publisher: Cold Spring Harbor LaboratoryCopyright Statement
• Country of Publication: United States
• Language: English