A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.
Journal
Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555
Informations de publication
Date de publication:
21 07 2022
21 07 2022
Historique:
received:
22
02
2022
accepted:
28
06
2022
entrez:
21
7
2022
pubmed:
22
7
2022
medline:
26
7
2022
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 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.
Identifiants
pubmed: 35864089
doi: 10.1038/s41467-022-31654-0
pii: 10.1038/s41467-022-31654-0
pmc: PMC9304412
doi:
Substances chimiques
DNA, Bacterial
0
DNA, Environmental
0
DNA
9007-49-2
Types de publication
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4197Subventions
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 : NHLBI NIH HHS
ID : K23 HL151876
Pays : United States
Organisme : NIAID NIH HHS
ID : R37 AI051652
Pays : United States
Organisme : NIDA NIH HHS
ID : U01 DA053941
Pays : United States
Organisme : NIAID NIH HHS
ID : R21 AI133331
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI151059
Pays : United States
Commentaires et corrections
Type : UpdateOf
Informations de copyright
© 2022. The Author(s).
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