A metagenomic DNA sequencing assay that is robust against environmental DNA contamination
ABSTRACT 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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Preprint| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
bioRxiv.org - (2022) vom: 28. Okt. Zur Gesamtaufnahme - year:2022 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
Mzava, Omary [VerfasserIn] |
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| doi: |
10.1101/2021.11.22.469599 |
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| PPN (Katalog-ID): |
XBI033073503 |
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| 520 | |a ABSTRACT 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 Chang, Adrienne |e verfasserin |4 aut | |
| 700 | 1 | |a Smalling, Sami |e verfasserin |4 aut | |
| 700 | 1 | |a Kounatse, Liz-Audrey Djomnang |e verfasserin |4 aut | |
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| 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 | |
| 700 | 1 | |a Lee, John R. |e verfasserin |4 aut | |
| 700 | 1 | |a Mason, Christopher E. |e verfasserin |4 aut | |
| 700 | 1 | |a Dadhania, Darshana |e verfasserin |4 aut | |
| 700 | 1 | |a De Vlaminck, Iwijn |e verfasserin |4 aut | |
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