Alterations of bacteriome, mycobiome and metabolome characteristics in PCOS patients with normal/overweight individuals

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/03

Curator: Joiejoie

Revision editor(s): Joiejoie, Nithya, Anne-mariesharp

Subjects

Location of subjects: China

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: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Polycystic ovary syndrome Cystic disease of ovaries,hyperandrogenemia,Multicystic ovaries,multicystic ovaries,Ovarian Degeneration, Sclerocystic,Ovarian Syndrome, Polycystic,Ovarian Syndromes, Polycystic,Ovaries, Sclerocystic,Ovary Syndrome, Polycystic,Ovary, Sclerocystic,PCO - Polycystic ovaries,Pco1,PCOD - Polycystic ovarian disease,PCOS,Pcos,PCOS - Polycystic ovarian syndrome,PCOS1,Polycystic ovarian disease,polycystic ovarian disease,Polycystic ovarian syndrome,Polycystic ovaries,polycystic ovaries,Polycystic ovaries (disorder),polycystic ovary,polycystic ovary syndrome,polycystic ovary syndrome 1,Sclerocystic Ovarian Degeneration,Sclerocystic Ovaries,Sclerocystic Ovary,Sclerocystic Ovary Syndrome,Stein Leventhal Syndrome,Stein-Leventhal synd.,Stein-Leventhal Syndrome,Stein-Leventhal syndrome,Syndrome, Polycystic Ovary,Syndrome, Stein-Leventhal,Polycystic ovary syndrome

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: PCOS (Polycystic ovary syndrome) Patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group comprises women diagnosed with Polycystic Ovary Syndrome (PCOS)

Group 0 sample size Number of subjects in the control (unexposed) group: 41

Group 1 sample size Number of subjects in the case (exposed) group: 47

Lab analysis

Sequencing type: 16S

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).: relative abundances

Statistical test: LEfSe

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)?: No

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/05

Curator: Nithya

Revision editor(s): Nithya, Joiejoie

Source: Fig. 2D

Description: Characteristic bacterial taxa based on LDA effect size (LEfSe) analysis between PCOS patients and healthy individuals.

Abundance in Group 1: increased abundance in PCOS (Polycystic ovary syndrome) Patients

NCBI	Quality Control	Links
Escherichia/Shigella sp.
Hungatella
Lachnospira
Erysipelotrichaceae UCG-003Erysipelotrichaceae UCG-003

Revision editor(s): Nithya, Joiejoie

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/05

Curator: Nithya

Revision editor(s): Nithya, Joiejoie, Anne-mariesharp

Source: Fig. 2D

Description: Characteristic bacterial taxa based on LDA effect size (LEfSe) analysis between PCOS patients and healthy individuals.

Abundance in Group 1: decreased abundance in PCOS (Polycystic ovary syndrome) Patients

NCBI	Quality Control	Links
Alloprevotella
Barnesiella
Collinsella
Coprobacillus
Desulfovibrio
Eubacterium ventriosum
Lachnospira eligens
Slackia
Lachnospiraceae_UCG-001Lachnospiraceae_UCG-001
Ruminococcaceae_UCG-010Ruminococcaceae_UCG-010
Ruminococcaceae UCG-014Ruminococcaceae UCG-014
Ruminococcus
Coprococcus
Ruminiclostridium

Revision editor(s): Nithya, Joiejoie, Anne-mariesharp

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie, Nithya, Anne-mariesharp

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy-HB (High Body mass index) Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group refers to Polycystic ovary syndrome (PCOS) patients with a high body mass index (BMI ≥ 24)

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 25

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/06

Curator: Nithya

Revision editor(s): Nithya, Joiejoie, Anne-mariesharp

Source: Additional file 2: Figure S2b

Description: Reveal of characteristic bacterial taxa based on LDA Effect Size (LEfSe) analysis between Healthy-HB and PCOS-HB

Abundance in Group 1: increased abundance in PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients

NCBI	Quality Control	Links
Blautia
Dorea
Lachnoclostridium
Lachnospira
Mediterraneibacter gnavus
Erysipelotrichaceae_UCG-003Erysipelotrichaceae_UCG-003
[Clostridium] innocuum

Revision editor(s): Nithya, Joiejoie, Anne-mariesharp

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/06

Curator: Nithya

Revision editor(s): Nithya, Joiejoie, Anne-mariesharp

Source: Additional file 2: Figure S2b

Description: Reveal of characteristic bacterial taxa based on LDA Effect Size (LEfSe) analysis between Healthy-HB and PCOS-HB

Abundance in Group 1: decreased abundance in PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients

NCBI	Quality Control	Links
Oxalobacter
Slackia
Peptococcus
Adlercreutzia
Eubacterium xylanophilum
Family_XIII_UCG-001Family_XIII_UCG-001
Ruminiclostridium
Desulfovibrio
Lachnospiraceae_UCG-001Lachnospiraceae_UCG-001
Odoribacter
Eubacterium ventriosum
Barnesiella
Paraprevotella
Ruminococcaceae_UCG-010Ruminococcaceae_UCG-010
Ruminococcaceae bacterium UCG-005
Ruminococcaceae_UCG-014Ruminococcaceae_UCG-014
Christensenellaceae_R-7_groupChristensenellaceae_R-7_group
Coprococcus
Collinsella
Parabacteroides
Ruminococcus
Dialister
Alistipes
Agathobacter

Revision editor(s): Nithya, Joiejoie, Anne-mariesharp

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/04

Curator: Joiejoie

Revision editor(s): Joiejoie, Nithya, Anne-mariesharp

Differences from previous experiment shown

Subjects

Lab analysis

Sequencing type: ITS / ITS2

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/07

Curator: Joiejoie

Revision editor(s): Joiejoie, Nithya, Anne-mariesharp

Source: Additional file 2: Figure S5

Description: Reveal of characteristic fungal taxa based on LDA Effect Size (LEfSe) analysis. Comparison between Healthy-HB and PCOS-HB.

Abundance in Group 1: increased abundance in PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients

NCBI	Quality Control	Links
Bolbitius
Candida
Cladosporium
Coniochaeta
Kazachstania
Malassezia
Meyerozyma
Neurospora
Thyridium
Trichoderma
Xeromyces

Revision editor(s): Joiejoie, Nithya, Anne-mariesharp

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/07

Curator: Joiejoie

Revision editor(s): Joiejoie, Nithya, Anne-mariesharp

Source: Additional file 2: Figure S5

Description: Reveal of characteristic fungal taxa based on LDA Effect Size (LEfSe) analysis. Comparison between Healthy-HB and PCOS-HB.

Abundance in Group 1: decreased abundance in PCOS-HB (Polycystic ovary syndrome - High Body mass index) Patients

NCBI	Quality Control	Links
Acaulium
Acrocalymma
Acrophialophora
Archaeorhizomyces sp.
Cadophora
Calonectria
Cephalotrichum
Cercophora
Chaetomium
Chrysosporium
Cladophialophora
Clavulinopsis
Colletotrichum
Cordyceps
Cuphophyllus
Dactylonectria
Dichotomopilus
Didymella
Endophoma
Epicoccum
Exophiala
Fusarium
Gymnoascus
Herpotrichia
Hypomyces
Idriella
Ilyonectria
Knufia
Lachnum
Lectera
Leohumicola
Metarhizium
Microascus
Minimedusa
Mortierella
Ophiosphaerella
Pezizella
Plenodomus
Pseudogymnoascus
Purpureocillium
Pyrenochaetopsis
Rachicladosporium
Remersonia
Sagenomella
Schizothecium
Scolecobasidium
Scytalidium
Serendipita
Solicoccozyma
Staphylotrichum
Syncephalis
Tetracladium
Thelonectria
Trichocladium

Revision editor(s): Joiejoie, Nithya, Anne-mariesharp

Experiment 7

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/07

Curator: Nithya

Revision editor(s): Nithya, Joiejoie, Anne-mariesharp

Differences from previous experiment shown

Subjects

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: PCOS (Polycystic ovary syndrome) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group comprises polycystic ovary syndrome (PCOS) patients

Group 0 sample size Number of subjects in the control (unexposed) group: 41

Group 1 sample size Number of subjects in the case (exposed) group: 47

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/07

Curator: Nithya

Revision editor(s): Nithya, Joiejoie

Source: Fig. 3F

Description: Characteristic fungal taxa based on LDA effect size (LEfSe) analysis between PCOS patients and healthy individuals

Abundance in Group 1: increased abundance in PCOS (Polycystic ovary syndrome) patients

NCBI	Quality Control	Links
Aspergillus
Cephaliophora
Coniochaeta
Hanseniaspora
Kazachstania
Malassezia
Microascus
Paraphoma
Schizophyllum

Revision editor(s): Nithya, Joiejoie

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/07

Curator: Nithya

Revision editor(s): Nithya, Joiejoie

Source: Fig. 3F

Description: Characteristic fungal taxa based on LDA effect size (LEfSe) analysis between PCOS patients and healthy individuals.

Abundance in Group 1: decreased abundance in PCOS (Polycystic ovary syndrome) patients

NCBI	Quality Control	Links
Acrocalymma
Acrophialophora
Cadophora
Calonectria
Cephalotrichum
Cercophora
Chaetomidium
Chaetomium
Chrysosporium
Cladophialophora
Clavulinopsis
Clonostachys
Cordyceps
Cuphophyllus
Dactylonectria
Dichotomopilus
Didymella
Entoloma
Epicoccum
Exophiala
Fusarium
Gymnoascus
Herpotrichia
Idriella
Ilyonectria
Knufia
Lectera
Leohumicola
Metarhizium
Minimedusa
Mortierella
Nectria
Oidiodendron
Ophiosphaerella
Pseudogymnoascus
Purpureocillium
Remersonia
Sagenomella
Sarocladium
Schizothecium
Serendipita
Setophoma
Solicoccozyma
Staphylotrichum
Stropharia
Syncephalis
Tausonia
Tetracladium

Revision editor(s): Nithya, Joiejoie

Experiment 8

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/07

Curator: Joiejoie

Revision editor(s): Joiejoie, Nithya, Anne-mariesharp

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy-LB (Normal Body mass index) subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: PCOS-LB (Polycystic ovary syndrome - Normal Body mass index) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: This group comprises Polycystic ovary syndrome (PCOS) patients with a body mass index (BMI < 24)

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 22

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: decreased

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-6-11

Curated date: 2025/05/09

Curator: Nithya

Revision editor(s): Nithya, Anne-mariesharp

Source: Additional file 2: Figure S4

Description: Reveal of characteristic fungal taxa based on LDA Effect Size (LEfSe) analysis. Comparison between Healthy-LB and PCOS-LB.

Abundance in Group 1: increased abundance in PCOS-LB (Polycystic ovary syndrome - Normal Body mass index) patients

NCBI	Quality Control	Links
Thyridium

Revision editor(s): Nithya, Anne-mariesharp

Signature 2