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. 2025 Jul 16.
doi: 10.1038/s41587-025-02738-1. Online ahead of print.

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper

Ben J Woodcroft  1 , Samuel T N Aroney  2 , Rossen Zhao  2 , Mitchell Cunningham  3 , Joshua A M Mitchell  2 , Rizky Nurdiansyah  2 , Linda Blackall  3 , Gene W Tyson  2
Affiliations

Comprehensive taxonomic identification of microbial species in metagenomic data using SingleM and Sandpiper

Ben J Woodcroft et al. Nat Biotechnol. .

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.

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Conflict of interest statement

Competing interests: The authors declare no competing interests.

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