MIrROR

MIrROR provides a curated database and mapping-based analysis pipeline for high-resolution metataxonomic profiling of bacterial 16S-ITS-23S rRNA operons (~4,300 bp) using long-read sequencing.

Key Features:

• Extensive Database: Contains 97,781 curated 16S-ITS-23S rRNA operon sequences extracted from 43,653 bacterial genomes in NCBI GenBank, representing 9,485 species.
• Target Region: Focuses on the full-length 16S-ITS-23S rRNA operon (~4,300 bp) to provide higher species-level taxonomic resolution than short-read regions.
• Mapping-based Taxonomic Profiling: Implements a mapping strategy for taxonomic assignment of long-read sequences against the MIrROR database.
• Benchmarking and Validation: Evaluated against publicly available databases and tools using mock communities and simulated datasets to assess species classification and coverage.
• Integration with Public Data: Provides BLAST functionality and integrates taxonomic profiling results from 16S-ITS-23S rRNA operon BioProjects on NCBI.
• Compatibility with Long-Read Sequencers: Designed for application with long-read sequencing platforms such as Oxford Nanopore Technologies MinION.

Scientific Applications:

• Species-level Bacterial Community Profiling: Enables precise species-level characterization of bacterial communities using full-length operon sequences.
• Environmental Microbiology: Supports analysis of microbial diversity and community structure in environmental samples.
• Clinical Diagnostics: Facilitates species-resolved profiling relevant to clinical microbiology and diagnostics.
• Ecological Monitoring: Allows high-resolution tracking of microbial community changes for ecological monitoring.

Methodology:

16S-ITS-23S rRNA operon sequences were extracted from NCBI GenBank; taxonomic profiling is performed via a mapping-based analysis against the MIrROR database; BLAST is provided for sequence search; benchmarking used mock communities and simulated datasets and integrated 16S-ITS-23S BioProject results from NCBI.