SingleM

SingleM profiles microbial community composition from metagenomic data by targeting conserved regions within universal marker genes to estimate taxonomy and relative abundance.

Key Features:

• Novelty Detection: Detects species that lack genomic representation in existing databases, including novel phyla and previously uncharacterized microorganisms prevalent in environmental samples.
• Comprehensive Profiling: Profiles known microbial species with high accuracy while concurrently identifying novel species within metagenomic datasets.
• Computational Efficiency: Processes large-scale metagenomic datasets efficiently, demonstrated by application to 248,559 publicly available metagenomes from environments such as marine, freshwater, sediment, and soil.
• Enhanced Resolution: Incorporates user-recovered genomes into its reference database to refine profiling resolution.
• Identification for Genome Recovery: Identifies metagenomes suitable for recovery of novel metagenome-assembled genomes, particularly from lineages of interest.

Scientific Applications:

• Microbial ecology research: Reveals novel species across diverse environments and informs community composition analyses.
• Genome discovery and MAG recovery: Guides selection of metagenomes for recovery of metagenome-assembled genomes.
• Environmental microbiology and biogeochemistry: Informs studies of microbial roles and diversity in marine, freshwater, sediment, and soil ecosystems.
• Evolutionary biology: Supports discovery of new Bacteria and Archaea lineages and assessment of genomic database coverage.

Methodology:

Leverages conserved regions within universal marker genes for profiling and supports incorporation of user-recovered genomes into its reference database; applied to 248,559 publicly available metagenomes.