使用SingleM和矶鹬对宏基因组数据中的微生物物种进行全面的分类鉴定。

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

作者信息

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

机构信息

Centre for Microbiome Research, School of Biomedical Sciences, Queensland University of Technology (QUT), Translational Research Institute, Woolloongabba, Queensland, Australia.

School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia.

出版信息

Nat Biotechnol. 2025 Jul 16. doi: 10.1038/s41587-025-02738-1.

DOI:10.1038/s41587-025-02738-1

PMID:40670710

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.

摘要

确定宏基因组数据中微生物的分类学和相对丰度在技术上仍然具有挑战性。在这里，我们展示了“SingleM”，它利用通用标记基因内的保守区域来估计群落组成。通过准确纳入缺乏基因组代表性的物种，我们表明未知物种在大多数环境微生物群落中占主导地位。我们的网站“矶鹬”整理了来自248,559个公开可用宏基因组的微生物群落概况。