Inferences in microbial structural signatures of acne microbiome and mycobiome

Study information

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

33565055

DOI Digital object identifier for electronic documents.

10.1007/s12275-021-0647-1

URI

Authors

Kim J, Park T, Kim HJ, An S, Sul WJ

Journal

Journal of microbiology (Seoul, Korea)

Year

2021

Keywords:

16S rRNA gene sequencing, ITS1 region sequencing, Staphylococcus, acne, microbiome, mycobiome, skin

Acne vulgaris, commonly known as acne, is the most common skin disorder and a multifactorial disease of the sebaceous gland. Although the pathophysiology of acne is still unclear, bacterial and fungal factors are known to be involved in. This study aimed to investigate whether the microbiomes and mycobiomes of acne patients are distinct from those of healthy subjects and to identify the structural signatures of microbiomes related to acne vulgaris. A total of 33 Korean female subjects were recruited (Acne group, n = 17; Healthy group, n = 16), and microbiome samples were collected swabbing the forehead and right cheek. To characterize the fungal and bacterial communities, 16S rRNA V4-V5 and ITS1 region, respectively, were sequenced and analysed using Qiime2. There were no significant differences in alpha and beta diversities of microbiomes between the Acne and Healthy groups. In comparison with the ratio of Cutibacterium to Staphylococcus, the acne patients had higher abundance of Staphylococcus compared to Cutibacterium than the healthy individuals. In network analysis with the dominant microorganism amplicon sequence variants (ASV) (Cutibacterium, Staphylococcus, Malassezia globosa, and Malassezia restricta) Cutibacterium acnes was identified to have hostile interactions with Staphylococcus and Malassezia globosa. Accordingly, this results suggest an insight into the differences in the skin microbiome and mycobiome between acne patients and healthy controls and provide possible microorganism candidates that modulate the microbiomes associated to acne vulgaris.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Chinelsy, Folakunmi

Subjects

Location of subjects

South Korea

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

Cheek , Forehead Buccae,Jowl,Cheek,cheek,Fore head,Sinciput,Forehead,forehead

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

Acne acne,acne (disease),acne varioliformis,Acne Vulgaris,acne vulgaris,acne, ADULT,frontalis acne,Acne

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

Healthy group

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

Acne group

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

Korean women aged 19-28 years with acne, a common skin condition that affects the hair follicles and sebaceous (oil) glands in the skin.

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

16

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

17

Lab analysis

Sequencing type

16S

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

V4-V5

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).

relative abundances

Statistical test

LEfSe

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

0.05

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Signature 1

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Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Folakunmi

Source: Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3A

Description: Result of linear discriminant analysis effect size (LEfSe) for bacteria in the cheek between acne and healthy groups

Abundance in Group 1: increased abundance in Acne group

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Aeromonadaceae
Bacteria
Corynebacterium
Stenotrophomonas

Revision editor(s): Deacme, Folakunmi

Signature 2

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Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Davvve, Folakunmi

Source: Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3A

Description: Result of linear discriminant analysis effect size (LEfSe)for bacteria in the cheek between acne and healthy groups

Abundance in Group 1: decreased abundance in Acne group

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Actinomyces
Candidatus Korobacter versatilis
Corynebacterium durum
Dietzia
Escherichia coli
Finegoldia
Leptotrichia
Moryella
Porphyromonas
Prevotella
Stramenopiles

Revision editor(s): Deacme, Davvve, Folakunmi

Experiment 2

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Chinelsy, Folakunmi

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Folakunmi

Source: Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3), Figure S3B

Description: Result of linear discriminant analysis effect size (LEfSe) for bacteria in the forehead between acne and healthy groups

Abundance in Group 1: decreased abundance in Acne group

NCBI	Quality Control	Links
Corynebacterium
Porphyromonas

Revision editor(s): Deacme, Folakunmi

Experiment 3

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Chinelsy, Folakunmi

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Alpha Diversity

Simpson Estimator of species richness and species evenness: more weight on species evenness

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Signature 1

EditHistoryDelete

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Folakunmi

Source: Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2),Figure S3C

Description: Result of linear discriminant analysis effect size (LEfSe) for fungi in the cheek microbiome between acne and healthy groups.

Abundance in Group 1: increased abundance in Acne group

NCBI	Quality Control	Links
Densospora
Malassezia globosa

Revision editor(s): Deacme, Folakunmi

Signature 2

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Folakunmi

Source: Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 2), Figure S3C

Description: Result of linear discriminant analysis effect size (LEfSe) for fungi in the cheek microbiome between acne and healthy groups.

Abundance in Group 1: decreased abundance in Acne group

NCBI	Quality Control	Links
Malassezia restricta
Malassezia slooffiae
Malasseziales
Saccharomyces cerevisiae

Revision editor(s): Deacme, Folakunmi

Experiment 4

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Chinelsy, Folakunmi

Differences from previous experiment shown

Subjects

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample

unchanged

Signature 1

EditHistoryDelete

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Folakunmi

Source: Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3),Figure S3D

Description: Result of linear discriminant analysis effect size (LEfSe)for fungi in the forehead mycobiome between acne and healthy groups

Abundance in Group 1: increased abundance in Acne group

NCBI	Quality Control	Links
Malassezia globosa

Revision editor(s): Deacme, Folakunmi

Signature 2

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-19

Curated date: 2023/11/10

Curator: Deacme

Revision editor(s): Deacme, Folakunmi

Source: Within results text(Taxonomic signatures of acne in bacterial and fungal ASVs, paragraph 3), Figure S3D

Description: Result of linear discriminant analysis effect size (LEfSe)for fungi in the forehead mycobiome between acne and healthy groups

Abundance in Group 1: decreased abundance in Acne group

NCBI	Quality Control	Links
Malassezia globosa
Xylodon flaviporus

Revision editor(s): Deacme, Folakunmi