Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study

Study information

Reviewed Marked as Reviewed by Folakunmi on 2023-12-8

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

33313185

DOI Digital object identifier for electronic documents.

10.21037/atm-20-1309

URI

Authors

Chen S, Gu Z, Zhang W, Jia S, Wu Y, Zheng P, Dai Y, Leng J

Journal

Annals of translational medicine

Year

2020

Keywords:

16s-rRNA sequencing, Endometriosis, bioinformatic analysis, microbiome

Background: Endometriosis is a benign, chronic, gynecological disease which affect the women in reproductive age. The dysfunction of immune system is associated with endometriosis and the diversity of microbiota in genital tract. According to previous studies, microbiota significantly contributes to multi-systemic function, but the evidence of relationship between microbiota and endometriosis remains insufficient. Methods: There are 68 participants were included in this study and 134 samples obtained from the cervical canal, posterior fornix and uterine cavity were analyzed by 16s-rRNA sequencing. The raw data was filtered, analyzed, and visualized, and bio-information methods were used to identify the characteristics of microbiota. Results: Two different locations near the cervix, cervical canal, and posterior fornix, exhibited no differences in alpha diversity. The microbiota profile of adenomyosis with endometriosis patients is different from control group through PCoA. Among the different disease groups, five microbiotas were distinctive in the genus level, and Atopobium presented with the greatest significance in adenomyoisis-endometriosis patients. The LeFSe analysis failed to identify the special biomarkers, while several characteristic functions were identified through PICRUSt. Conclusions: Lactobacillus is the predominant genus in the female lower genital tract, and Atopobium is higher in patients with endometriosis combined with adenomyosis. Several different functions of microbiota were explored, some of them are found to be associated with endometriosis or adenomyosis, other functions are needed to be further verified. These findings may provide a new concept of microbiota/immune system/endometriosis system.

Experiment 1

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-8

Curated date: 2021/08/11

Curator: Samara.Khan

Revision editor(s): WikiWorks, Samara.Khan, Peace Sandy, Folakunmi

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: Cervical cavity Canal of the cervix,Cavity of cervix,Cervical canal,Cervical canal of uterus,Endocervical,Endocervical canal,Endocervix,Lumen of cervix of uterus,Cervical cavity,cervical cavity

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Endometriosis , Adenomyosis endometriosis,Endometriosis (clinical),endometriosis (disease),Endometriosis (disorder),Endometriosis (morphologic abnormality),ENDOMETRIOSIS NEC,Endometriosis NOS,Endometriosis NOS (disorder),Endometriosis of other specified sites,Endometriosis, site unspecified,Endometriosis,uterine corpus adenomyosis,Adenomyosis,adenomyosis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Endometriosis patients (EM) and Patients without endometriosis(Control-CT)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Endometriosis/ adenomyosis patients (AMEM)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: All participants were diagnosed with adenomyosis accompanied with endometriosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery

Group 0 sample size Number of subjects in the control (unexposed) group: 92

Group 1 sample size Number of subjects in the case (exposed) group: 14

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): No antibiotic use within 30 days

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-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

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Richness Number of species: unchanged

Signature 1

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Curated date: 2021/08/11

Curator: Samara.Khan

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Source: within results text(under "Microbiota composition of different diseases" ,paragraph 5, lines 4-7), figure 6

Description: The following taxa were increased in patients with endometriosis and adenomyosis compared to those with just endometriosis, as well as those without endometriosis (control).

Abundance in Group 1: increased abundance in Endometriosis/ adenomyosis patients (AMEM)

NCBI	Quality Control	Links
Atopobium
Campylobacter
Campylobacteraceae
Coriobacteriaceae
Escherichia/Shigella sp.
Ezakiella
Faecalibacterium

Revision editor(s): Samara.Khan, Folakunmi

Experiment 2

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Curated date: 2021/08/11

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Patients without endometriosis (CT), patients with only endometriosis(EM)) and patients with only adenomysis(AM)

Group 0 sample size Number of subjects in the control (unexposed) group: 120

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

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

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-8

Curated date: 2021/08/11

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Source: within results text(under "Microbiota composition of different diseases" ,paragraph 5, lines 4-7), figure 6

Description: The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those without endometriosis, patients with only endometriosis and patients with only adenomysis.

Abundance in Group 1: increased abundance in Endometriosis/ adenomyosis patients (AMEM)

NCBI	Quality Control	Links
Campylobacteraceae
Coriobacteriaceae

Revision editor(s): Samara.Khan, Folakunmi

Experiment 3

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-8

Curated date: 2023/11/14

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: All participants were diagnosed with endometriosis and/or adenomyosis (a condition where endometrial tissue grows into the uterine wall) through laparoscopic surgery

Group 0 sample size Number of subjects in the control (unexposed) group: 28

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: Not specified

Statistical test: Not specified

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

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

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Folakunmi on 2023-12-8

Curated date: 2023/11/15

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: within results text (under "Microbiota composition of different diseases" ,paragraph 5, lines 4-7), figure 6

Description: The following taxa had increased abundance in patients with endometriosis and adenomyosis compared to those with only adenomyosis.

Abundance in Group 1: increased abundance in Endometriosis/ adenomyosis patients (AMEM)

NCBI	Quality Control	Links
Atopobium
Campylobacter
Ezakiella
Faecalibacterium

Revision editor(s): Folakunmi