Exploring the female genital tract mycobiome in young South African women using metaproteomics

Study information

EditHistoryDelete

Flag for review

Your review change was submittedAdd a new Experiment

• Quality control
  • Retracted paper
  • Contamination issues suspected
  • Batch effect issues suspected
  • Uncontrolled confounding suspected
  • Results are suspect (various reasons)
  • Apply tags

    Tags applied

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

40108637

DOI Digital object identifier for electronic documents.

10.1186/s40168-025-02066-1

URI

https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1

Authors

Gangiah TK, Alisoltani A, Potgieter M, Bell L, Ross E, Iranzadeh A, McDonald Z, Allali I, Dabee S, Barnabas S, Blackburn JM, Tabb DL, Bekker LG, Jaspan HB, Passmore JS, Mulder N, Masson L

Journal

Microbiome

Year

2025

Keywords:

Bacterial vaginosis, Female genital tract, Fungi, Metaproteomics, Mycobiome

BACKGROUND: Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women. RESULTS: We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition. CONCLUSIONS: The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract.

Experiment 1

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/25

Curator: Montana-D

Revision editor(s): Montana-D, Anne-mariesharp

Subjects

Location of subjects

South Africa

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

Wall of vagina Vaginal wall,Wall of vagina,wall of vagina

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

Bacterial vaginosis BACT VAGINITIDES,BACT VAGINITIS,BACT VAGINOSES,BACT VAGINOSIS,Bacterial Vaginitides,Bacterial Vaginitis,Bacterial Vaginoses,bacterial vaginosis,BV,Nonspecific Vaginitis,VAGINITIDES BACT,Vaginitides, Bacterial,VAGINITIS BACT,Vaginitis, Bacterial,Vaginitis, Nonspecific,VAGINOSES BACT,Vaginoses, Bacterial,VAGINOSIS BACT,Vaginosis, Bacterial,Bacterial vaginosis

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

BV- Negative (BV: Bacterial Vaginosis) at Visit 1

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

BV- Positive (BV: Bacterial Vaginosis) at Visit 1

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

women who were classified as having bacterial vaginosis (BV) based on the nugent score

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

47

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

57

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

2 weeks

Lab analysis

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

Mass spectrometry

Statistical Analysis

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

log transformation

Statistical test

Linear Regression

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

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/27

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table 1

Description: Differentially abundant fungal taxa between BV-negative and BV-positive at Visit 1.

Abundance in Group 1: increased abundance in BV- Positive (BV: Bacterial Vaginosis) at Visit 1

NCBI	Quality Control	Links
Conidiobolus coronatus
Malassezia sympodialis

Revision editor(s): Montana-D

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/27

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table 1

Description: Differentially abundant fungal taxa between BV-negative and BV-positive at Visit 1.

Abundance in Group 1: decreased abundance in BV- Positive (BV: Bacterial Vaginosis) at Visit 1

NCBI	Quality Control	Links
Alternaria alternata
Aspergillus alliaceus
Candida albicans
Candida orthopsilosis
Clavispora lusitaniae
Lichtheimia corymbifera
Linderina pennispora
Lobosporangium transversale
Lodderomyces elongisporus
Pisolithus tinctorius
Schizosaccharomyces cryophilus
Talaromyces marneffei
Trichosporon asahii
Wallemia ichthyophaga
[Candida] thasaenensis

Revision editor(s): Montana-D

Experiment 2

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/27

Curator: Montana-D

Revision editor(s): Montana-D, Anne-mariesharp

Differences from previous experiment shown

Subjects

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

BV- Intermediate (BV: Bacterial Vaginosis) at Visit 1

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

women who were classified as having an intermediate bacterial vaginosis state based on the Nugent score

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

7

Lab analysis

Statistical Analysis

Signature 3

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/27

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table 1

Description: Differentially abundant fungal taxa between BV-intermediate and BV-negative at Visit 1.

Abundance in Group 1: decreased abundance in BV- Intermediate (BV: Bacterial Vaginosis) at Visit 1

NCBI	Quality Control	Links
Clavispora lusitaniae
Lichtheimia corymbifera
Lobosporangium transversale
Lodderomyces elongisporus
Moesziomyces aphidis
Mycosarcoma maydis
Penicillium vulpinum
Pisolithus tinctorius
Pyrenochaeta sp.
Rhizoclosmatium globosum
Teratoramularia persicariae
Torulaspora delbrueckii
[Candida] thasaenensis

Revision editor(s): Montana-D

Experiment 3

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/27

Curator: Montana-D

Revision editor(s): Montana-D

Differences from previous experiment shown

Subjects

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

BV- Intermediate (BV: Bacterial Vaginosis) at Visit 1

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

BV- Positive (BV: Bacterial Vaginosis) at visit 1

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

women who were classified as having bacterial vaginosis based on the Nugent score.

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

7

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

57

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/27

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table 1

Description: Differentially abundant fungal taxa between BV-positive and BV-intermediate at Visit 1.

Abundance in Group 1: increased abundance in BV- Positive (BV: Bacterial Vaginosis) at visit 1

NCBI	Quality Control	Links
Clavispora lusitaniae

Revision editor(s): Montana-D

Experiment 4

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/28

Curator: Montana-D

Revision editor(s): Montana-D, KateRasheed, Anne-mariesharp

Differences from previous experiment shown

Subjects

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

BV- Negative (BV: Bacterial Vaginosis) at Visit 2

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

BV- Positive (BV: Bacterial Vaginosis) at Visit 2

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

38

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

37

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/28

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table S2 (Supplementary file 2)

Description: Differentially abundant fungal taxa between BV-positive and BV-negative at Visit 2.

Abundance in Group 1: increased abundance in BV- Positive (BV: Bacterial Vaginosis) at Visit 2

NCBI	Quality Control	Links
Conidiobolus coronatus
Malassezia sympodialis

Revision editor(s): Montana-D

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/28

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table S2 (supplementary file 2)

Description: Differentially abundant fungal taxa between BV-positive and BV-negative at Visit 2.

Abundance in Group 1: decreased abundance in BV- Positive (BV: Bacterial Vaginosis) at Visit 2

NCBI	Quality Control	Links
Candida albicans
Wallemia ichthyophaga
[Candida] thasaenensis

Revision editor(s): Montana-D

Experiment 5

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/28

Curator: Montana-D

Revision editor(s): Montana-D, Anne-mariesharp

Differences from previous experiment shown

Subjects

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

women classified as having bacterial vaginosis based on the Nugent score

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment

vaginal pH, Confounders controlled for: "pro-inflammatory cytokines" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.pro-inflammatory cytokines

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/28

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table S1 (supplementary file 3)

Description: Differentially abundant fungal taxa between BV-intermediate and BV-positive at Visit 2.

Abundance in Group 1: increased abundance in BV- Positive (BV: Bacterial Vaginosis) at Visit 2

NCBI	Quality Control	Links
Malassezia sympodialis
Conidiobolus coronatus

Revision editor(s): Montana-D

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/04/02

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table S1 (supplementary file 3)

Description: Differentially abundant fungal taxa between women with BV-negative and BV-Positive based on a Nugent score at Visit 2

Abundance in Group 1: decreased abundance in BV- Positive (BV: Bacterial Vaginosis) at Visit 2

NCBI	Quality Control	Links
Candida albicans
[Candida] thasaenensis

Revision editor(s): Montana-D

Experiment 8

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/30

Curator: Montana-D

Revision editor(s): Montana-D, Anne-mariesharp

Differences from previous experiment shown

Subjects

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

BV- Negative (BV: Baterial Vaginosis) at Visit 1

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

BV- Positive (BV: Baterial Vaginosis) at Visit 1

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

women classified as having bacterial vaginosis (BV) based on the nugent score

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

47

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

57

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/30

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table S1 (supplementary file 3)

Description: Differentially abundant fungal taxa between BV-negative and BV- positive at visit 1

Abundance in Group 1: increased abundance in BV- Positive (BV: Baterial Vaginosis) at Visit 1

NCBI	Quality Control	Links
Malassezia sympodialis

Revision editor(s): Montana-D

Signature 2

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/04/01

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table S1 (supplementary file 3)

Description: Differentially abundant fungal taxa between women with BV-negative and BV-Positive at visit 1

Abundance in Group 1: decreased abundance in BV- Positive (BV: Baterial Vaginosis) at Visit 1

NCBI	Quality Control	Links
[Candida] thasaenensis
Lodderomyces elongisporus
Talaromyces marneffei
Candida albicans
Wallemia ichthyophaga
Pisolithus tinctorius
Alternaria alternata
Candida orthopsilosis
Kluyveromyces marxianus
Rhizopogon vinicolor

Revision editor(s): Montana-D

Experiment 9

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/30

Curator: Montana-D

Revision editor(s): Montana-D, Anne-mariesharp

Differences from previous experiment shown

Subjects

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

BV- Intermediate (BV: Bacterial Vaginosis) at Visit 1

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

BV- Negative (BV: Baterial Vaginosis) at Visit 1

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

women classified as having an intermediate bacterial vaginosis state based on the Nugent score

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

7

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/30

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table S1 (supplementary file 3)

Description: Differentially abundant fungal taxa between BV-negative and BV-Intermediate based on the Nugent score at Visit 1

Abundance in Group 1: increased abundance in BV- Negative (BV: Baterial Vaginosis) at Visit 1

NCBI	Quality Control	Links
Penicillium vulpinum
Torulaspora delbrueckii

Revision editor(s): Montana-D

Experiment 10

EditHistoryDelete

Flag for review

Your review change was submittedDuplicate this ExperimentAdd a new Signature

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/30

Curator: Montana-D

Revision editor(s): Montana-D, Anne-mariesharp

Differences from previous experiment shown

Subjects

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

BV- Positive (BV: Bacterial Vaginosis) at visit 1

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

women classified as having bacterial vaginosis based on the Nugent score.

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

7

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

37

Lab analysis

Statistical Analysis

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2025-4-2

Curated date: 2025/03/30

Curator: Montana-D

Revision editor(s): Montana-D

Source: Table S1 (supplementary file 3)

Description: Differentially abundant fungal taxa between BV-positive and BV-intermediate at Visit 1.

Abundance in Group 1: increased abundance in BV- Positive (BV: Bacterial Vaginosis) at visit 1

NCBI	Quality Control	Links
Clavispora lusitaniae

Revision editor(s): Montana-D