Benchmarking MicrobIEM - a user-friendly tool for decontamination of microbiome sequencing data.
16S rRNA gene sequencing
Bioinformatic decontamination
Decontam
Low-biomass microbiome
Negative control
SourceTracker
Youden’s index
Journal
BMC biology
ISSN: 1741-7007
Titre abrégé: BMC Biol
Pays: England
ID NLM: 101190720
Informations de publication
Date de publication:
23 Nov 2023
23 Nov 2023
Historique:
received:
01
02
2023
accepted:
16
10
2023
medline:
27
11
2023
pubmed:
24
11
2023
entrez:
23
11
2023
Statut:
epublish
Résumé
Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls. We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (10 MicrobIEM's ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.
Sections du résumé
BACKGROUND
BACKGROUND
Microbiome analysis is becoming a standard component in many scientific studies, but also requires extensive quality control of the 16S rRNA gene sequencing data prior to analysis. In particular, when investigating low-biomass microbial environments such as human skin, contaminants distort the true microbiome sample composition and need to be removed bioinformatically. We introduce MicrobIEM, a novel tool to bioinformatically remove contaminants using negative controls.
RESULTS
RESULTS
We benchmarked MicrobIEM against five established decontamination approaches in four 16S rRNA amplicon sequencing datasets: three serially diluted mock communities (10
CONCLUSIONS
CONCLUSIONS
MicrobIEM's ratio filter for decontamination performs better or as good as established bioinformatic decontamination tools. In contrast to established tools, MicrobIEM additionally provides interactive plots and supports selecting appropriate filtering parameters via a user-friendly graphical user interface. Therefore, MicrobIEM is the first quality control tool for microbiome experts without coding experience.
Identifiants
pubmed: 37996810
doi: 10.1186/s12915-023-01737-5
pii: 10.1186/s12915-023-01737-5
pmc: PMC10666409
doi:
Substances chimiques
RNA, Ribosomal, 16S
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
269Informations de copyright
© 2023. The Author(s).
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