Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA.
Division of Gastroenterology and Hepatology, Weill Cornell Medicine, Jill Roberts Center for IBD, New York, NY, USA.
Nat Commun. 2022 Jul 21;13(1):4197. doi: 10.1038/s41467-022-31654-0.
Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present Sample-Intrinsic microbial DNA Found by Tagging and sequencing (SIFT-seq) a metagenomic sequencing assay that is robust against environmental DNA contamination introduced during sample preparation. The core idea of SIFT-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied SIFT-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of sepsis and inflammatory bowel disease in blood.
宏基因组 DNA 测序是一种强大的工具，可用于描述微生物群落，但容易受到环境 DNA 污染的影响，特别是在应用于微生物生物量低的样本时。在这里，我们提出了一种新的方法——通过标记和测序（SIFT-seq）进行样本固有微生物 DNA 发现，这是一种针对样品制备过程中引入的环境 DNA 污染具有稳健性的宏基因组测序检测方法。SIFT-seq 的核心思想是在 DNA 分离和文库制备之前，用标签标记样品中的 DNA，该标签可以通过 DNA 测序记录。任何在标记后引入样品的污染 DNA 都可以通过生物信息学方法识别并去除。我们将 SIFT-seq 应用于血液和尿液中低负荷微生物感染的筛查、识别 COVID-19 合并感染、描述尿液微生物组以及鉴定血液中脓毒症和炎症性肠病的微生物 DNA 特征。
