A metagenomic DNA sequencing assay that is robust against environmental DNA contamination
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.
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UpdateIn: Nat Commun. 2022 Jul 21;13(1):4197. - PMID 35864089 |
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| Medienart: |
E-Artikel |
| Erscheinungsjahr: |
2021 |
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| Erschienen: |
2021 |
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Zur Gesamtaufnahme - year:2021 |
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| Enthalten in: |
bioRxiv : the preprint server for biology - (2021) vom: 23. Nov. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Mzava, Omary [VerfasserIn] |
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Date Revised 08.11.2023 published: Electronic UpdateIn: Nat Commun. 2022 Jul 21;13(1):4197. - PMID 35864089 Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1101/2021.11.22.469599 |
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NLM333824865 |
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| 520 | |a 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 | ||
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| 700 | 1 | |a Djomnang Kounatse, Liz-Audrey |e verfasserin |4 aut | |
| 700 | 1 | |a Lenz, Joan |e verfasserin |4 aut | |
| 700 | 1 | |a Longman, Randy |e verfasserin |4 aut | |
| 700 | 1 | |a Steadman, Amy |e verfasserin |4 aut | |
| 700 | 1 | |a Salvatore, Mirella |e verfasserin |4 aut | |
| 700 | 1 | |a Suthanthiran, Manikkam |e verfasserin |4 aut | |
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| 700 | 1 | |a Dadhania, Darshana |e verfasserin |4 aut | |
| 700 | 1 | |a De Vlaminck, Iwijn |e verfasserin |4 aut | |
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