Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

39390034

DOI Digital object identifier for electronic documents.

https://doi.org/10.1038/s41598-024-74513-2

URI

https://www.nature.com/articles/s41598-024-74513-2

Authors

Delanghe L, De Boeck I, Van Malderen J, Allonsius CN, Van Rillaer T, Bron PA, Claes I, Hagendorens M, Lebeer S, Leysen J

Journal

Scientific reports

Year

2024

Atopic dermatitis is the most common inflammatory skin condition with a severe negative impact on patients' quality of life. The etiology of AD is complex and depends on age, genetics, the immune system, environmental factors, and the skin microbiome, with a key role for pathogenic Staphylococcus aureus in the development of severe AD. However, the composition of the skin microbiome in mild AD is understudied. Here, using metagenomic shallow shotgun sequencing, we showed that mild AD lesions did not show a significant difference in the diversity of the skin microbiome compared to samples from non-AD patients and that the relative abundance of S. aureus did not differ in these mild AD lesions. However, when we assessed other taxa, Mycobacterium ostraviense, Pedobacter panaciterrae_A and four Streptomyces species were identified with higher abundances in mild AD lesions and species of 15 genera were decreased in abundance. The highest fold decreases were observed for Paracoccus marcusii, Microbacterium lacticum, Micrococcus luteus, and Moraxella sp002478835. These microbiome compositional insights are a first step towards novel microbiome-based diagnostics and therapeutics for early intervention at the stage of mild AD and provide a path forward for the functional study of species involved in this often-overlooked patient population.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

Curated date: 2024/10/12

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine

Subjects

Location of subjects

Belgium

Host species Species from which microbiome was sampled. Contact us to have more species added.

Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Skin of body Entire integument,Entire skin,Integument,Integumental organ,Pelt,Skin,Skin organ,Skin of body,skin of body

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Dermatitis inflammation of skin,inflammation of the skin,inflammation of zone of skin,inflammatory skin disease,skin inflammation,zone of skin inflammation,Dermatitis,dermatitis

Group 0 name Corresponds to the control (unexposed) group for case-control studies

healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies

mild atopic dermatitis (AD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Participants diagnosed with mild atopic dermatitis (AD). This group specifically includes individuals who exhibit mild lesions characterized by limited symptoms.

Group 0 sample size Number of subjects in the control (unexposed) group

49

Group 1 sample size Number of subjects in the case (exposed) group

28

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

N/A

Lab analysis

Sequencing type

WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

log transformation

Statistical test

MaAsLin2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

Yes

Signature 1

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Curated date: 2024/10/12

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine

Source: Figure 3a

Description: Differential abundance analysis for mild AD patients compared to healthy participants using Maaslin2

Abundance in Group 1: increased abundance in mild atopic dermatitis (AD)

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Bifidobacterium pullorum
Burkholderia
Burkholderia sp.
Haemophilus parainfluenzae
Mycobacterium ostraviense
Paeniglutamicibacter antarcticus
Paraburkholderia
Pedobacter panaciterrae
Photobacterium chitinilyticum
Pyramidobacter sp.
Sodaliphilus pleomorphus
Staphylococcus aureus
Staphylococcus epidermidis
Stenotrophomonas maltophilia
Streptococcus oralis
Streptomyces
Streptomyces fumigatiscleroticus
Streptosporangiaceae
Streptosporangium violaceochromogenes
Chroococcus hegewaldiChroococcus hegewaldi
Thiorhodococcus violaceaThiorhodococcus violacea
Bacteroidales bacterium Barb7
Streptomyces malachitofuscus
Streptomyces griseoincarnatus
Crocosphaera chwakensis
Streptomyces kurssanovii
Limosilactobacillus alvi
Spirillospora cremeaSpirillospora cremea
Aestuariibaculum marinum
Flavobacterium hauense
Caproicibacter sp.
Mariprofundus erugo
Mycobacterium sp.
Chromatium weissei
Butyricimonas sp.
IAFGDP01 spIAFGDP01 sp
Staphylococcus schweitzeri
Paraburkholderia sp.

Revision editor(s): Joiejoie, Aleru Divine

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

Curated date: 2024/10/12

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine

Source: Figure 3a

Description: Differential abundance analysis for mild AD patients compared to healthy participants using Maaslin2

Abundance in Group 1: decreased abundance in mild atopic dermatitis (AD)

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Acinetobacter
Acinetobacter lwoffii
Alphaproteobacteria
Bacteroidia
Bradyrhizobium
Brevundimonas
Epilithonimonas hominis
Hyphomicrobiales
Kaistella
Kaistella haifensis
Kocuria
Kocuria palustris
Microbacteriaceae
Micrococcaceae
Micrococcus endophyticus
Moraxella
Moraxella osloensis
Moraxella sp.
Moraxellaceae
Neisseria cinerea
Nocardioides
Paracoccaceae
Paracoccus
Pseudomonadales
Rothia
Sphingomonas
Sphingopyxis
Xanthobacteraceae
Agrobacterium pusense
Micrococcus cohnii
Kocuria salsicia
Bifidobacterium vaginaleBifidobacterium vaginale
Allorhizobium rosettiformansAllorhizobium rosettiformans
Kaistella senegalenseKaistella senegalense
Brevundimonas bullata
Acinetobacter idrijaensis
Haematobacter massiliensis
Paracoccus marcusii
Paracoccus aeridis
Acidovorax temperans
Microbacterium lacticum

Revision editor(s): Joiejoie, Aleru Divine

Experiment 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

Curated date: 2024/10/16

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

healthy controls under 12 years

Group 1 name Corresponds to the case (exposed) group for case-control studies

mild atopic dermatitis (AD) under 12 years

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Participants diagnosed with mild atopic dermatitis (AD) who are under 12 years old.

Group 0 sample size Number of subjects in the control (unexposed) group

30

Group 1 sample size Number of subjects in the case (exposed) group

11

Lab analysis

Statistical Analysis

Alpha Diversity

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa

unchanged

Richness Number of species

unchanged

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

Curated date: 2024/10/23

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine

Source: Figure 3a

Description: Differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (under 12 years old)

Abundance in Group 1: increased abundance in mild atopic dermatitis (AD) under 12 years

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Photobacterium chitinilyticum
Staphylococcus aureus
Chroococcus hegewaldiiChroococcus hegewaldii
Streptosporangiaceae
Streptosporangium violaceochromogenes
Thiorhodococcus violaceaThiorhodococcus violacea
Bacteroidales bacterium Barb7
Streptomyces kurssanovii
Stenotrophomonas maltophilia
Pedobacter panaciterrae
Sodaliphilus pleomorphus
Limosilactobacillus alvi
Spirillospora cremeaSpirillospora cremea
Pyramidobacter sp.
Aestuariibaculum marinum
Mycobacterium ostraviense
Paeniglutamicibacter antarcticus
Haemophilus parainfluenzae
Mycobacterium sp.
Streptomyces
IAFGDP01 spIAFGDP01 sp
Streptomyces fumigatiscleroticus
Streptomyces malachitofuscus
Streptomyces griseoincarnatus

Revision editor(s): Joiejoie, Aleru Divine

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

Curated date: 2024/10/23

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine

Source: Figure 3a

Description: Differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (under 12 years old)

Abundance in Group 1: decreased abundance in mild atopic dermatitis (AD) under 12 years

NCBI	Quality Control	Links
Paracoccus denitrificans
Microbacteriaceae
Hyphomicrobiales
Micrococcaceae
Micrococcus endophyticus
Kaistella haifensis

Revision editor(s): Joiejoie, Aleru Divine

Experiment 3

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

Curated date: 2024/10/16

Curator: Joiejoie

Revision editor(s): Joiejoie, Aleru Divine

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

healthy controls above 12 years

Group 1 name Corresponds to the case (exposed) group for case-control studies

mild atopic dermatitis (AD) above 12 years Old

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Participants diagnosed with mild atopic dermatitis (AD) who are above 12 years old.

Group 0 sample size Number of subjects in the control (unexposed) group

19

Group 1 sample size Number of subjects in the case (exposed) group

17

Lab analysis

Statistical Analysis

Alpha Diversity

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa

unchanged

Richness Number of species

unchanged

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

Curated date: 2024/10/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine

Source: Figure 3a

Description: Differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (above 12 years old)

Abundance in Group 1: increased abundance in mild atopic dermatitis (AD) above 12 years Old

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Chroococcus hegewaldiiChroococcus hegewaldii
Pyramidobacter sp.
Streptomyces fumigatiscleroticus
Mycobacterium ostraviense
Paeniglutamicibacter antarcticus
Burkholderia sp.
Paraburkholderia sp.

Revision editor(s): Aleru Divine

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-11-6

Curated date: 2024/10/24

Curator: Aleru Divine

Revision editor(s): Aleru Divine, Scholastica

Source: Figure 3a

Description: Differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (above 12 years old)

Abundance in Group 1: decreased abundance in mild atopic dermatitis (AD) above 12 years Old

NCBI	Quality Control	Links
Kaistella

Revision editor(s): Aleru Divine, Scholastica