Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Tsementzi D, Pena-Gonzalez A, Bai J, Hu YJ, Patel P, Shelton J, Dolan M, Arluck J, Khanna N, Conrad L, Scott I, Eng TY, Konstantinidis KT, Bruner DW
Journal
Cancer medicine
Year
2020
Keywords:
16S rRNA gene, gynecologic cancer, postmenopausal women, radiation therapy, vaginal microbiota
BACKGROUND: While the importance of commensal microbes in vaginal health is well appreciated, little is known about the effects of gynecological cancer (GynCa) and radiation therapy (RT) on the vaginal microbiome (VM) of postmenopausal women. METHODS: We studied women with GynCa, pre- (N = 65) and post-RT (N = 25) and a group of healthy controls (N = 67) by sequencing the V4 region of the 16S rRNA gene from vaginal swabs and compared the diversity and composition of VMs between the three groups accounting for potential confounding factors in multivariate analysis of variance. RESULTS: Comparisons of cancer vs healthy groups revealed that Lactobacillus and Bifidobacterium have significantly higher relative abundance in the healthy group, while the cancer group was enriched in 16 phylogroups associated with bacterial vaginosis (BV) and inflammation, including Sneathia, Prevotella, Peptoniphilus, Fusobacterium, Anaerococcus, Dialister, Moryella, and Peptostreptococcus. In our sample, RT affected the α-diversity and correlated with higher abundance of typically rare VM species, including several members of the Lacnospiraceae family, a taxon previously linked to vaginal dysbiosis. In addition to cancer and treatment modalities, age and vaginal pH were identified as significant parameters that structure the VM. CONCLUSIONS: This is among the first reports identifying VM changes among postmenopausal women with cancer. RT alone seems to affect several phylogroups (12 bacterial genera), while gynecological cancer and its treatment modalities are associated with even greater significant shifts in the vaginal microbiota including the enrichment of opportunistic bacterial pathogens, which warrants further attention.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Subjects
- Location of subjects
- United States of America
- 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
- Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina,vagina
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Genital neoplasm, female cancer of female reproductive organ,female reproductive cancer,female reproductive organ cancer,gynecologic cancer,malignant female reproductive organ neoplasm,malignant female reproductive system neoplasm,malignant female reproductive system tumor,malignant gynecologic neoplasm,malignant gynecologic tumor,malignant neoplasm of female genital organ,malignant neoplasm of female reproductive organ,malignant neoplasm of female reproductive system,malignant neoplasm of the female reproductive system,malignant tumor of female reproductive system,malignant tumor of the female reproductive system,Genital neoplasm, female,genital neoplasm, female
- 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
- Cancer Pre-Rt (Pre-Radiation Therapy)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal women (naturally or due to hysterectomy) with endometrial or cervical cancer Prior to treatment with radiotherapy with or without surgery and/or chemotherapy
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- 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
- Welch's T-Test
- 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
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Source: Figure 1A and B
Description: Differentially abundant bacterial genera between the Healthy and Cancer Pre-RT group
Abundance in Group 1: increased abundance in Cancer Pre-Rt (Pre-Radiation Therapy)
Revision editor(s): Claregrieve1, WikiWorks, MyleeeA
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/29
Source: Figure 1A and B
Description: Differentially abundant bacterial genera between the Healthy and Cancer Pre-RT group
Abundance in Group 1: decreased abundance in Cancer Pre-Rt (Pre-Radiation Therapy)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Lactobacillus | ||
| Alistipes |
Revision editor(s): Claregrieve1, WikiWorks, MyleeeA
Experiment 2
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Women with gynecological cancer
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal women (naturally or due to hysterectomy) with endometrial or cervical cancer treated with radiotherapy with or without surgery and/or chemotherapy
- Group 1 sample size Number of subjects in the case (exposed) group
- 65
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- 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
- 3
Signature 1
Source: Figure 3a
Description: Differentially abundant bacterial operational taxonomic units between healthy and cancer groups.
Abundance in Group 1: increased abundance in Women with gynecological cancer
Revision editor(s): Tosin
Signature 2
Source: Figure 3a
Description: Differentially abundant bacterial operational taxonomic units between healthy and cancer groups.
Abundance in Group 1: decreased abundance in Women with gynecological cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Lactobacillus | ||
| Shuttleworthella |
Revision editor(s): Tosin
Experiment 3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Pre-RT GynCa groups (Gynecologic cancer patients Pre-radiation therapy).
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Post-RT GynCa groups (Gynecologic cancer patients post-radiation therapy).
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal women with Gynecologic cancer post-radiation therapy.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 65
- Group 1 sample size Number of subjects in the case (exposed) group
- 25
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- increased
Signature 1
Source: Figure 3b
Description: Differentially abundant bacterial operational taxonomic units between pre- and post-RT (radiation therapy) vaginal microbiomes.
Abundance in Group 1: increased abundance in Post-RT GynCa groups (Gynecologic cancer patients post-radiation therapy).
Revision editor(s): Tosin
Signature 2
Source: Figure 3b
Description: Differentially abundant bacterial operational taxonomic units between pre- and post-RT vaginal microbiomes.
Abundance in Group 1: decreased abundance in Post-RT GynCa groups (Gynecologic cancer patients post-radiation therapy).
| NCBI | Quality Control | Links |
|---|---|---|
| Sutterella | ||
| Oscillospiraceae |
Revision editor(s): Tosin
Experiment 4
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Genital neoplasm, female cancer of female reproductive organ,female reproductive cancer,female reproductive organ cancer,gynecologic cancer,malignant female reproductive organ neoplasm,malignant female reproductive system neoplasm,malignant female reproductive system tumor,malignant gynecologic neoplasm,malignant gynecologic tumor,malignant neoplasm of female genital organ,malignant neoplasm of female reproductive organ,malignant neoplasm of female reproductive system,malignant neoplasm of the female reproductive system,malignant tumor of female reproductive system,malignant tumor of the female reproductive system,Genital neoplasm, female,genital neoplasm, female
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy cohort (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cancer Cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Postmenopausal women with gynecological cancer (GynCa)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 69
- Group 1 sample size Number of subjects in the case (exposed) group
- 65
Lab analysis
Statistical Analysis
- Statistical test
- Welch's T-Test
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Source: Supplementary Figure 2B
Description: Phylum level abundance between Cancer cohort and Healthy cohort at p≤0.05 using Welch two sample t-test.
Abundance in Group 1: increased abundance in Cancer Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota | ||
| Fusobacteriota | ||
| Mycoplasmatota | ||
| Campylobacterota |
Revision editor(s): MyleeeA
Signature 2
Source: Supplementary Figure 2B
Description: Phylum level abundance between Cancer cohort and Healthy cohort at p≤0.05 using Welch two sample t-test.
Abundance in Group 1: decreased abundance in Cancer Cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Pseudomonadota | ||
| Actinomycetota |
Revision editor(s): MyleeeA
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