利用SingleM和矶鹞对宏基因组数据中的微生物种类进行综合分类鉴定

IF 33.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Nature biotechnology Pub Date : 2025-07-16 DOI:10.1038/s41587-025-02738-1

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

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引用次数: 0

摘要

确定宏基因组数据中微生物的分类和相对丰度在技术上仍然具有挑战性。在这里，我们提出了“SingleM”，它使用通用标记基因中的保守区域来估计群落组成。通过准确地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“矶鹞”整理了248,559个公开可用的宏基因组的微生物群落概况。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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

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

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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来源期刊

Nature biotechnology 工程技术-生物工程与应用微生物

CiteScore

63.00

自引率

1.70%

发文量

382

审稿时长

3 months

期刊介绍： Nature Biotechnology is a monthly journal that focuses on the science and business of biotechnology. It covers a wide range of topics including technology/methodology advancements in the biological, biomedical, agricultural, and environmental sciences. The journal also explores the commercial, political, ethical, legal, and societal aspects of this research. The journal serves researchers by providing peer-reviewed research papers in the field of biotechnology. It also serves the business community by delivering news about research developments. This approach ensures that both the scientific and business communities are well-informed and able to stay up-to-date on the latest advancements and opportunities in the field. Some key areas of interest in which the journal actively seeks research papers include molecular engineering of nucleic acids and proteins, molecular therapy, large-scale biology, computational biology, regenerative medicine, imaging technology, analytical biotechnology, applied immunology, food and agricultural biotechnology, and environmental biotechnology. In summary, Nature Biotechnology is a comprehensive journal that covers both the scientific and business aspects of biotechnology. It strives to provide researchers with valuable research papers and news while also delivering important scientific advancements to the business community.