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用于验证rRNA基因扩增子测序的海洋微生物模拟群落

Marine microbial mock communities for validating rRNA gene amplicon sequencing.

作者信息

Lampe Robert H, Rabines Ariel J, Ellman Bryce A, Zheng Hong, Allen Andrew E

机构信息

Integrative Oceanography Division, Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, USA.

Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, California, USA.

出版信息

Microbiol Resour Announc. 2025 Jul 10;14(7):e0029825. doi: 10.1128/mra.00298-25. Epub 2025 May 30.

DOI:10.1128/mra.00298-25
PMID:40444952
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC12243523/
Abstract

Mock communities are defined mixtures of cells or DNA for methods development, testing, or validation. Here, we present mock communities based on previously used 16S and 18S rRNA gene sequences from diverse marine microorganisms. Their use as controls for amplicon sequencing enables the detection of biased or aberrant runs.

摘要

模拟群落是为方法开发、测试或验证而定义的细胞或DNA混合物。在此,我们基于先前使用的来自不同海洋微生物的16S和18S rRNA基因序列呈现模拟群落。将它们用作扩增子测序的对照能够检测有偏差或异常的测序运行。

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本文引用的文献

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A blueprint for contemporary studies of microbiomes.微生物群落当代研究的蓝图。
Microbiome. 2025 Apr 8;13(1):95. doi: 10.1186/s40168-025-02091-0.
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Diversity and ecology of protists revealed by metabarcoding.通过宏条形码技术揭示的原生生物多样性与生态学。
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Comprehensive single-PCR 16S and 18S rRNA community analysis validated with mock communities, and estimation of sequencing bias against 18S.综合单-PCR 16S 和 18S rRNA 社区分析与模拟群落验证,以及对 18S 测序偏差的估计。
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Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.使用QIIME 2进行可重复、交互式、可扩展和可延伸的微生物组数据科学研究。
Nat Biotechnol. 2019 Aug;37(8):852-857. doi: 10.1038/s41587-019-0209-9.
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Best practices for analysing microbiomes.微生物组分析的最佳实践。
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Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run.微生物组分析中分类单元的消失强化了模拟群落作为每次测序运行标准的价值。
mSystems. 2018 Apr 3;3(3). doi: 10.1128/mSystems.00023-18. eCollection 2018 May-Jun.
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Primer selection impacts specific population abundances but not community dynamics in a monthly time-series 16S rRNA gene amplicon analysis of coastal marine bacterioplankton.引物选择会影响特定种群的丰度,但不会影响沿海海洋细菌浮游生物的每月时间序列 16S rRNA 基因扩增子分析中的群落动态。
Environ Microbiol. 2018 Aug;20(8):2709-2726. doi: 10.1111/1462-2920.14091. Epub 2018 Apr 6.
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DADA2: High-resolution sample inference from Illumina amplicon data.DADA2:从Illumina扩增子数据进行高分辨率样本推断。
Nat Methods. 2016 Jul;13(7):581-3. doi: 10.1038/nmeth.3869. Epub 2016 May 23.
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Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples.每个碱基都很重要:使用模拟群落、时间序列和全球野外样本评估海洋微生物群落的小亚基rRNA引物。
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10
Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform.开发一种双索引测序策略和策管管道,用于分析 MiSeq Illumina 测序平台上的扩增子序列数据。
Appl Environ Microbiol. 2013 Sep;79(17):5112-20. doi: 10.1128/AEM.01043-13. Epub 2013 Jun 21.