Taxonomic and Functional Differences in Cervical Microbiome Associated with Cervical Cancer Development

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

32546712

DOI Digital object identifier for electronic documents.

10.1038/s41598-020-66607-4

URI

Authors

Tango CN, Seo SS, Kwon M, Lee DO, Chang HK, Kim MK

Journal

Scientific reports

Year

2020

The cervical microbiome is associated with cervical cancer risk, but how microbial diversity and functional profiles change in cervical cancer remains unclear. Herein, we investigated microbial-compositional and functional differences between a control group and a high-grade cervical intraepithelial neoplasia and cervical cancer (CIN2/3-CC) group. After retrospective collection of 92 cervical swab samples, we carried out 16S rRNA amplicon sequencing on 50 and 42 samples from the control and CIN2/3-CC groups, respectively. The EzBioCloud pipeline was applied to identify the genomic features associated with the groups using 16S rRNA data. A linear discriminant analysis effect size (LEfSe) was performed to assess the enrichment in the assigned taxonomic and functional profiles. We found a lower richness in the control group relative to the CIN2/3-CC group; however, the β-diversity tended to be similar between the groups. The LEfSe analysis showed that a phylum Sacchaaribacteria_TM7, 11 genera, and 21 species were more abundant in the CIN2/3-CC group and that one uncharacterized Gardnerella species was more abundant only in the control group. Further characterization of the functional pathways using EzBioCloud showed that the 4 KEGG orthologs (Phosphotransferase system [PTS] sucrose-specific IIA, IIB, IIC components and PTS cellubiose-specific IIC component) were involved in the KEGG pathway of starch and sucrose metabolism. The two pathways of folate biosynthesis and oxidative phosphorylation were more abundant in the CIN2/3-CC group. Further confirmation of these results in larger samples can help to elucidate the potential association between the cervical microbiome and cervical cancer.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Peace Sandy

Subjects

Location of subjects: South Korea

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 Canalis cervicis uteri,Caudal segment of uterus,Cervical canal,Cervical canal of uterus,Cervix,Cervix of uterus,Cervix uteri,Neck of uterus,Uterine cervix,uterine cervix

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Cervical glandular intraepithelial neoplasia , Cervical cancer Cervical glandular intraepithelial neoplasia,cervical glandular intraepithelial neoplasia,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: Healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: CIN2/3-CC

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: patients diagnosed with CIN2/3 or cervical cancer during screening of the cervical tract

Group 0 sample size Number of subjects in the control (unexposed) group: 50

Group 1 sample size Number of subjects in the case (exposed) group: 42

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): antibiotic therapy within 3 months

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: Roche454

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: increased

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

Richness Number of species: increased

Signature 1

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Curated date: 2021/01/10

Curator: Cynthia Anderson

Revision editor(s): WikiWorks, Peace Sandy

Source: figure 2

Description: Diferences in relative abundances of microbial taxa (genus and species) between groups by LEfSe analysis

Abundance in Group 1: increased abundance in CIN2/3-CC

NCBI	Quality Control	Links
Corynebacterium striatum
Cutibacterium
Cutibacterium acnes
Enhydrobacter
Enhydrobacter aerosaccus
Fusobacterium nucleatum
Lactobacillus fornicalis
Latilactobacillus sakei
Massilia alkalitolerans
Micrococcus
Micrococcus luteus
Prevotella amnii
Staphylococcus
Streptococcus
Streptococcus pneumoniae
Weissella
Weissella koreensis
Veillonella
Peptoniphilaceae
Pseudomonas
Enterobacteriaceae
Corynebacterium
Massilia
Ureaplasma
Sphingomonas
Lachnospiraceae
Gardnerella