Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer
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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
Sims TT, Biegert GWG, Ramogola-Masire D, Ngoni K, Solley T, Ning MS, El Alam MB, Mezzari M, Petrosino J, Zetola NM, Schmeler KM, Colbert LE, Klopp AH, Grover S
Journal
International journal of gynecological cancer : official journal of the International Gynecological Cancer Society
Year
2020
Keywords:
cervical cancer, cervix uteri, gynecology, uterine cervical neoplasms
INTRODUCTION: We characterized the cervical 16S rDNA microbiome of patients in Botswana with high-grade cervical dysplasia and locally advanced cervical cancer. METHODS: This prospective study included 31 patients: 21 with dysplasia and 10 with cancer. The Shannon diversity index was used to evaluate alpha (intra-sample) diversity, while the UniFrac (weighted and unweighted) and Bray-Curtis distances were employed to evaluate beta (inter-sample) diversity. The relative abundance of microbial taxa was compared among samples using linear discriminant analysis effect size. RESULTS: Alpha diversity was significantly higher in patients with cervical cancer than in patients with cervical dysplasia (P<0.05). Beta diversity also differed significantly (weighted UniFrac Bray-Curtis, P<0.01). Neither alpha diversity (P=0.8) nor beta diversity (P=0.19) varied by HIV status. The results of linear discriminant analysis effect size demonstrated that multiple taxa differed significantly between patients with cervical dysplasia vs cancer. Lachnospira bacteria (in the Clostridia class) were particularly enriched among cervical dysplasia patients, while Proteobacteria (members of the Firmicutes phyla and the Comamonadaceae family) were enriched in patients with cervical cancer. DISCUSSION: The results of our study suggest that differences exist in the diversity and composition of the cervical microbiota between patients with cervical dysplasia and patients with cervical cancer in Botswana. Additional studies are warranted to validate these findings and elucidate their clinical significance among women living in sub-Saharan Africa, as well as other regions of the world.
Experiment 1
Subjects
- Location of subjects
- Botswana
- 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
- Cervix squamous epithelium Cervical squamous epithelium,Cervix squamous epithelium,cervix squamous epithelium
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Cervical cancer cancer of uterine cervix,cervical neoplasm,cervix cancer,cervix uteri cancer,malignant cervical neoplasm,malignant cervical tumor,malignant cervix neoplasm,malignant cervix tumor,malignant cervix uteri neoplasm,malignant cervix uteri tumor,malignant neoplasm of cervix,malignant neoplasm of cervix uteri,malignant neoplasm of the cervix,malignant neoplasm of the cervix uteri,malignant neoplasm of the uterine cervix,malignant neoplasm of uterine cervix,malignant tumor of cervix,malignant tumor of cervix uteri,malignant tumor of the cervix,malignant tumor of the cervix uteri,malignant tumor of the uterine cervix,malignant tumor of uterine cervix,malignant uterine cervix neoplasm,malignant uterine cervix tumor,tumor of the cervix uteri,uterine cervical neoplasm,uterine cervix cancer,Cervical cancer,cervical cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cervical Dysplasia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cervical Cancer patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with moderate or poorly differentiated squamous cell cancer of the cervix.
- 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
- 10
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
- 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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
Signature 1
Source: Figure 2G
Description: Differentially abundant taxa between cervical cancer patients and cervical dysplasia patients using LefSe analysis.
Abundance in Group 1: increased abundance in Cervical Cancer patients
Revision editor(s): MyleeeA
Signature 2
Source: Figure 2G
Description: Differentially abundant taxa between cervical cancer patients and cervical dysplasia patients using LefSe analysis.
Abundance in Group 1: decreased abundance in Cervical Cancer patients
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Bacillota | ||
| Lachnospira |
Revision editor(s): MyleeeA
Experiment 2
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- HIV Negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HIV Positive
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- HIV positive cervical dysplasia and cervical cancer patient’s
- 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
- 24
Lab analysis
Statistical Analysis
- 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
Signature 1
Source: Figure 1E
Description: Differentially abundant taxa between cervical cancer patients and cervical dysplasia HIV positive and negative patients using LefSe analysis.
Abundance in Group 1: increased abundance in HIV Positive
| NCBI | Quality Control | Links |
|---|---|---|
| Erysipelotrichia | ||
| Erysipelotrichales | ||
| Erysipelotrichaceae | ||
| Ruminiclostridium | ||
| Bacilli | ||
| Lactobacillales |
Revision editor(s): MyleeeA
Signature 2
Source: Figure 1E
Description: Differentially abundant taxa between cervical cancer patients and cervical dysplasia HIV positive and negative patients using LefSe analysis.
Abundance in Group 1: decreased abundance in HIV Positive
| NCBI | Quality Control | Links |
|---|---|---|
| Filifactor |
Revision editor(s): MyleeeA
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