Increased diversity of a cervical microbiome associates with cervical cancer

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/26

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Subjects

Location of subjects: Poland

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: Uterine cervix

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Cervical squamous cell carcinoma cervical squamous cell cancer,cervical squamous cell carcinoma,cervix squamous cell carcinoma,cervix uteri squamous cell carcinoma,CESC,squamous cell carcinoma of cervix,squamous cell carcinoma of cervix uteri,squamous cell carcinoma of the cervix,squamous cell carcinoma of the cervix uteri,squamous cell carcinoma of the uterine cervix,squamous cell carcinoma of uterine cervix,squamous cervical cancer,uterine cervix squamous cell carcinoma,Cervical squamous cell carcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Premenopausal healthy controls (HPV Negative women)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Premenopausal Pre-treatment group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).

Group 0 sample size Number of subjects in the control (unexposed) group: 15

Group 1 sample size Number of subjects in the case (exposed) group: 6

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 2 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V2-V9

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Ion Torrent

Statistical Analysis

Statistical test: ANCOM

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

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Table 2

Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.

Abundance in Group 1: increased abundance in

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Anaerococcus
Atopobium
Bulleidia
Campylobacter
Dialister
Fastidiosipila
Fenollaria
Fusobacterium
Gemella
Mobiluncus
Moryella
Parvimonas
Peptococcus
Peptoniphilus
Peptostreptococcus
Porphyromonas
Prevotella
Solobacterium
Stomatobaculum

Revision editor(s): Joan Chuks, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/27

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Table 2

Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.

Abundance in Group 1: decreased abundance in

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Acinetobacter
Aminobacter
Cutibacterium
Escherichia/Shigella sp.
Lactobacillus
Pseudomonas
Rheinheimera
Staphylococcus

Revision editor(s): Joan Chuks, WikiWorks

Experiment 2

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Curated date: 2024/04/28

Curator: Joan Chuks

Revision editor(s): WikiWorks, Joan Chuks, Aleru Divine, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Postmenopausal healthy controls (HPV Negative women)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Postmenopausal Pre-treatment group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected a day before starting external beam radiation therapy (EBRT).

Group 1 sample size Number of subjects in the case (exposed) group: 10

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/28

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Table 2

Description: Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.

Abundance in Group 1: increased abundance in Postmenopausal Pre-treatment group

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Arcanobacterium
Fusobacterium
Moryella
Peptococcus
Peptoniphilus
Porphyromonas
Stomatobaculum

Revision editor(s): Joan Chuks, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/28

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Table 2

Description: Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, before starting external beam radiation therapy (EBRT), as determined by ANCOM-BC Analysis.

Abundance in Group 1: decreased abundance in Postmenopausal Pre-treatment group

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Gardnerella
Gemella
Lentilitoribacter
Mesorhizobium

Revision editor(s): Joan Chuks, WikiWorks

Experiment 3

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Curated date: 2024/04/28

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Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Response to radiation Response to radiation,response to radiation

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Premenopausal healthy controls (HPV Negative women)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Premenopausal Post-treatment group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Women, aged 25–54 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.

Group 1 sample size Number of subjects in the case (exposed) group: 6

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/28

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Supplementary Table S2

Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.

Abundance in Group 1: increased abundance in

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Anaerococcus
Campylobacter
Clostridiales bacterium S5-A14a
Corynebacterium
Dialister
Finegoldia
Peptoniphilus
Peptostreptococcus
Prevotella
Streptococcus

Revision editor(s): Joan Chuks, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/28

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Supplementary Table S2

Description: Differential bacterial abundance in the cervical microbiome between premenopausal healthy controls (HPV Negative women) and premenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.

Abundance in Group 1: decreased abundance in

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Aminobacter
Bifidobacterium
Brucella
Granulicatella
Hoeflea
Ottowia
Parabacteroides
Pluralibacter

Revision editor(s): Joan Chuks, WikiWorks

Experiment 4

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/29

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Revision editor(s):

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Postmenopausal healthy controls (HPV Negative women)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Postmenopausal Post-treatment group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Women, aged 54–62 years, with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given.

Group 1 sample size Number of subjects in the case (exposed) group: 10

Lab analysis

Statistical Analysis

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/29

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Supplementary Table S2

Description: Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.

Abundance in Group 1: increased abundance in

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Caulobacter
Diaphorobacter
Porphyromonas
Renibacterium
Sphingomonas
Methylobacterium-MethylorubrumMethylobacterium-Methylorubrum

Revision editor(s): Joan Chuks, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/29

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Supplementary Table S2

Description: Differential bacterial abundance in the cervical microbiome between postmenopausal healthy controls (HPV Negative women) and postmenopausal women with squamous cell carcinoma of the cervix, immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis.

Abundance in Group 1: decreased abundance in

NCBI	Quality Control	Links
Gardnerella
Lentilitoribacter
Mesorhizobium

Revision editor(s): Joan Chuks, WikiWorks

Experiment 5

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Reviewed Marked as Reviewed by Svetlana up on 2025-1-13

Curated date: 2024/04/29

Curator:

Revision editor(s):

Differences from previous experiment shown

Subjects

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: Post-treatment and 3-month post-treatment group

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Women with squamous cell carcinoma of the cervix who were indicated for primary Radiation therapy(RT), and their samples collected immediately after the last fraction of brachytherapy (ICBT) was given and 3 months after the last fraction of brachytherapy (ICBT) was given (n=9).

Group 1 sample size Number of subjects in the case (exposed) group: 15

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: centered log-ratio

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 Svetlana up on 2025-1-13

Curated date: 2024/04/29

Curator: Joan Chuks

Revision editor(s): Joan Chuks, WikiWorks

Source: Table 3

Description: Differential bacterial abundance in the cervical microbiome of women with squamous cell carcinoma of the cervix, before starting the external beam radiation therapy (EBRT) compared to immediately after the last fraction of brachytherapy (ICBT) was given, as determined by ANCOM-BC Analysis

Abundance in Group 1: increased abundance in

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Acinetobacter
Blautia
Caulobacter
Cloacibacterium
Corynebacterium
Cupriavidus
Cutibacterium
Diaphorobacter
Finegoldia
Lactococcus
Massilia
Muribaculum
Neisseria
Pedobacter
Pseudomonas
Ralstonia
Renibacterium
Rheinheimera
Roseateles
Sphingomonas
Staphylococcus
Streptococcus
Methylobacterium- MethylorubrumMethylobacterium- Methylorubrum

Revision editor(s): Joan Chuks, WikiWorks

Signature 2