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phyloFlash: Rapid Small-Subunit rRNA Profiling and Targeted Assembly from Metagenomes
Harald R Gruber-Vodicka1, Brandon K B Seah2, Elmar Pruesse3
1Max Planck Institute for Marine Microbiology, Bremen, Germany hgruber@mpi-bremen.de.
Msystems
|October 28, 2020
Summary
phyloFlash rapidly classifies and assembles small-subunit rRNA (SSU rRNA) genes from metagenomes, enabling taxonomic profiling and linking to microbial genomes. This tool overcomes the common absence of SSU rRNA in metagenome-assembled genomes (MAGs).
Area of Science:
- Microbial Ecology
- Bioinformatics
- Genomics
Background:
- The small-subunit rRNA (SSU rRNA) gene is crucial for microbial ecology, serving as a universal marker across all life domains.
- Metagenome-assembled genomes (MAGs) are vital for studying environmental microbes but often lack SSU rRNA genes, hindering taxonomic classification and integration with existing data.
- Existing methods for SSU rRNA gene recovery from metagenomic data can be inefficient or produce chimeric sequences.
Purpose of the Study:
- To present phyloFlash, a novel bioinformatics pipeline designed to rapidly recover and analyze SSU rRNA genes from metagenomic data.
- To facilitate taxonomic classification and targeted assembly of SSU rRNA genes, thereby bridging the gap caused by their absence in MAGs.
- To provide a user-friendly tool for high-throughput quality control and analysis of microbial communities.
Main Methods:
- phyloFlash employs a cleaned, curated reference database for SSU rRNA gene-centered taxonomic classification and targeted assembly.
- Utilizes the general-purpose mapper BBmap for efficient extraction of SSU rRNA reads, outperforming specialized tools in speed and selectivity.
- Employs the SPAdes assembler for robust, reference-independent assembly of SSU rRNA genes, minimizing chimera formation.
- Integrates recovered SSU rRNAs with MAGs through graph-based parsing of the assembly graph.
Main Results:
- phyloFlash demonstrates rapid processing of Illumina (meta)genomic data with high efficiency and user-friendly outputs.
- The pipeline achieves satisfactory levels of chimera formation and is independent of reference database composition.
- BBmap shows a fivefold increase in SSU rRNA read extraction speed compared to SortMeRNA with similar sensitivity and higher selectivity.
- phyloFlash successfully links SSU rRNA data to MAGs, enabling comprehensive microbial community analysis.
Conclusions:
- phyloFlash effectively addresses the challenge of missing SSU rRNA genes in MAGs, enhancing microbial taxonomic profiling.
- The software provides a domain-agnostic solution for analyzing bacterial, archaeal, and eukaryotic SSU rRNA genes.
- phyloFlash is a valuable, easy-to-use tool for researchers in microbial ecology and metagenomics, facilitating integration with existing workflows.
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