Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper.
basic_science · Level V
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- Record sourced from PubMed, PMID 40670710.
- Also identified by DOI 10.1038/s41587-025-02738-1.
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Abstract
Determining the taxonomy and relative abundance of microorganisms in metagenomic data remains technically challenging. Here we present 'SingleM', which estimates community composition using conserved regions within universal marker genes. By accurately incorporating species lacking genomic representation, we show that unknown species dominate in most environmental microbial communities. Our website 'Sandpiper' collates microbial community profiles from 248,559 publicly available metagenomes.