Forskning
Udskriv Udskriv
Switch language
Region Hovedstaden - en del af Københavns Universitetshospital
Udgivet

Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis

Publikation: Bidrag til tidsskriftTidsskriftartikelForskningpeer review

Harvard

APA

CBE

MLA

Vancouver

Author

Barnes, Christopher J ; Rasmussen, Linett ; Asplund, Maria ; Knudsen, Steen Wilhelm ; Clausen, Maja-Lisa ; Agner, Tove ; Hansen, Anders J. / Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis. I: Journal of Medical Microbiology. 2020 ; Bind 69, Nr. 11. s. 1293-1302.

Bibtex

@article{8a44f304d1a2465dbc537a8f72cd90e8,
title = "Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis",
abstract = "Introduction. The pathogenesis of atopic dermatitis (AD) is not yet fully understood, but the bacterial composition of AD patients' skin has been shown to have an increased abundance of Staphylococcus aureus. More recently, coagulase-negative Staphylococcus (CoNS) species were shown to be able to inhibit S. aureus, but further studies are required to determine the effects of Staphylococcus community variation in AD.Aim. Here we investigated whether analysing metabarcoding data with the more recently developed DADA2 approach improves metabarcoding analyses compared to the previously used operational taxonomic unit (OTU) clustering, and can be used to study Staphylococcus community dynamics.Methods. The bacterial 16S rRNA region from tape strip samples of the stratum corneum of AD patients (non-lesional skin) and non-AD controls was metabarcoded. We processed metabarcoding data with two different bioinformatic pipelines (an OTU clustering method and DADA2), which were analysed with and without technical replication (sampling strategy).Results. We found that OTU clustering and DADA2 performed well for community-level studies, as demonstrated by the identification of significant differences in the skin bacterial communities associated with AD. However, the OTU clustering approach inflated bacterial richness, which was worsened by not having technical replication. Data processed with DADA2 likely handled sequencing errors more effectively and thereby did not inflate molecular richness.Conclusion. We believe that DADA2 represents an improvement over an OTU clustering approach, and that biological replication rather than technical replication is a more effective use of resources. However, neither OTU clustering nor DADA2 gave insights into Staphylococcus community dynamics, and caution should remain in not overinterpreting the taxonomic assignments at lower taxonomic ranks.",
keywords = "Adult, Aged, Cluster Analysis, Computational Biology, DNA Barcoding, Taxonomic, Dermatitis, Atopic/microbiology, Female, Humans, Male, Microbiota, Middle Aged, RNA, Ribosomal, 16S/genetics, Skin/microbiology, Staphylococcus aureus/classification, Young Adult",
author = "Barnes, {Christopher J} and Linett Rasmussen and Maria Asplund and Knudsen, {Steen Wilhelm} and Maja-Lisa Clausen and Tove Agner and Hansen, {Anders J}",
year = "2020",
month = nov,
doi = "10.1099/jmm.0.001256",
language = "English",
volume = "69",
pages = "1293--1302",
journal = "Journal of Medical Microbiology",
issn = "0022-2615",
publisher = "Society for General Microbiology",
number = "11",

}

RIS

TY - JOUR

T1 - Comparing DADA2 and OTU clustering approaches in studying the bacterial communities of atopic dermatitis

AU - Barnes, Christopher J

AU - Rasmussen, Linett

AU - Asplund, Maria

AU - Knudsen, Steen Wilhelm

AU - Clausen, Maja-Lisa

AU - Agner, Tove

AU - Hansen, Anders J

PY - 2020/11

Y1 - 2020/11

N2 - Introduction. The pathogenesis of atopic dermatitis (AD) is not yet fully understood, but the bacterial composition of AD patients' skin has been shown to have an increased abundance of Staphylococcus aureus. More recently, coagulase-negative Staphylococcus (CoNS) species were shown to be able to inhibit S. aureus, but further studies are required to determine the effects of Staphylococcus community variation in AD.Aim. Here we investigated whether analysing metabarcoding data with the more recently developed DADA2 approach improves metabarcoding analyses compared to the previously used operational taxonomic unit (OTU) clustering, and can be used to study Staphylococcus community dynamics.Methods. The bacterial 16S rRNA region from tape strip samples of the stratum corneum of AD patients (non-lesional skin) and non-AD controls was metabarcoded. We processed metabarcoding data with two different bioinformatic pipelines (an OTU clustering method and DADA2), which were analysed with and without technical replication (sampling strategy).Results. We found that OTU clustering and DADA2 performed well for community-level studies, as demonstrated by the identification of significant differences in the skin bacterial communities associated with AD. However, the OTU clustering approach inflated bacterial richness, which was worsened by not having technical replication. Data processed with DADA2 likely handled sequencing errors more effectively and thereby did not inflate molecular richness.Conclusion. We believe that DADA2 represents an improvement over an OTU clustering approach, and that biological replication rather than technical replication is a more effective use of resources. However, neither OTU clustering nor DADA2 gave insights into Staphylococcus community dynamics, and caution should remain in not overinterpreting the taxonomic assignments at lower taxonomic ranks.

AB - Introduction. The pathogenesis of atopic dermatitis (AD) is not yet fully understood, but the bacterial composition of AD patients' skin has been shown to have an increased abundance of Staphylococcus aureus. More recently, coagulase-negative Staphylococcus (CoNS) species were shown to be able to inhibit S. aureus, but further studies are required to determine the effects of Staphylococcus community variation in AD.Aim. Here we investigated whether analysing metabarcoding data with the more recently developed DADA2 approach improves metabarcoding analyses compared to the previously used operational taxonomic unit (OTU) clustering, and can be used to study Staphylococcus community dynamics.Methods. The bacterial 16S rRNA region from tape strip samples of the stratum corneum of AD patients (non-lesional skin) and non-AD controls was metabarcoded. We processed metabarcoding data with two different bioinformatic pipelines (an OTU clustering method and DADA2), which were analysed with and without technical replication (sampling strategy).Results. We found that OTU clustering and DADA2 performed well for community-level studies, as demonstrated by the identification of significant differences in the skin bacterial communities associated with AD. However, the OTU clustering approach inflated bacterial richness, which was worsened by not having technical replication. Data processed with DADA2 likely handled sequencing errors more effectively and thereby did not inflate molecular richness.Conclusion. We believe that DADA2 represents an improvement over an OTU clustering approach, and that biological replication rather than technical replication is a more effective use of resources. However, neither OTU clustering nor DADA2 gave insights into Staphylococcus community dynamics, and caution should remain in not overinterpreting the taxonomic assignments at lower taxonomic ranks.

KW - Adult

KW - Aged

KW - Cluster Analysis

KW - Computational Biology

KW - DNA Barcoding, Taxonomic

KW - Dermatitis, Atopic/microbiology

KW - Female

KW - Humans

KW - Male

KW - Microbiota

KW - Middle Aged

KW - RNA, Ribosomal, 16S/genetics

KW - Skin/microbiology

KW - Staphylococcus aureus/classification

KW - Young Adult

U2 - 10.1099/jmm.0.001256

DO - 10.1099/jmm.0.001256

M3 - Journal article

C2 - 32965212

VL - 69

SP - 1293

EP - 1302

JO - Journal of Medical Microbiology

JF - Journal of Medical Microbiology

SN - 0022-2615

IS - 11

ER -

ID: 61745583