Mzava Omary, Cheng Alexandre Pellan, Chang Adrienne, Smalling Sami, Djomnang Kounatse Liz-Audrey, Lenz Joan, Longman Randy, Steadman Amy, Salvatore Mirella, Suthanthiran Manikkam, Lee John R, Mason Christopher E, Dadhania Darshana, De Vlaminck Iwijn
Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York, USA.
Jill Roberts Center for IBD, Weill Cornell Medicine, Division of Gastroenterology and Hepatology, New York, NY, USA.
bioRxiv. 2021 Nov 23:2021.11.22.469599. doi: 10.1101/2021.11.22.469599.
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 contamination-free metagenomic DNA sequencing (Coffee-seq), a metagenomic sequencing assay that is robust against environmental contamination. The core idea of Coffee-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 Coffee-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 inflammatory bowel disease in blood.
宏基因组DNA测序是表征微生物群落的强大工具，但对环境DNA污染敏感，尤其是应用于微生物生物量较低的样本时。在此，我们展示了无污染宏基因组DNA测序（Coffee-seq），这是一种对环境污染具有抗性的宏基因组测序分析方法。Coffee-seq的核心思想是在DNA分离和文库制备之前，用一种可通过DNA测序记录的标签标记样本中的DNA。然后，可以通过生物信息学方法识别并去除标记后引入样本中的任何污染DNA。我们应用Coffee-seq来筛查血液和尿液中低负荷微生物的感染情况、识别新冠病毒共感染、表征泌尿微生物组以及识别血液中炎症性肠病的微生物DNA特征。
