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<p>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.</p>

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

  • 期刊论文

  • 发表日期：

    2025年7月16日

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  • Ben J. Woodcroft,
  • Samuel T. N. Aroney,
  • Rossen Zhao,
  • Mitchell Cunningham,
  • Joshua A. M. Mitchell,
  • Rizky Nurdiansyah,
  • Linda Blackall,
  • Gene W. Tyson

摘要

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.