A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.
Journal
bioRxiv : the preprint server for biology
Titre abrégé: bioRxiv
Pays: United States
ID NLM: 101680187
Informations de publication
Date de publication:
23 Nov 2021
23 Nov 2021
Historique:
entrez:
30
11
2021
pubmed:
1
12
2021
medline:
1
12
2021
Statut:
epublish
Résumé
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.
Identifiants
pubmed: 34845444
doi: 10.1101/2021.11.22.469599
pmc: PMC8629186
pii:
doi:
Types de publication
Preprint
Langues
eng
Subventions
Organisme : NIAID NIH HHS
ID : R37 AI051652
Pays : United States
Organisme : NIAID NIH HHS
ID : DP2 AI138242
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008267
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI124237
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI146165
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI133331
Pays : United States
Organisme : Bill & Melinda Gates Foundation
ID : INV-003145
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI151059
Pays : United States
Commentaires et corrections
Type : UpdateIn
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