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

Study information

Needs review

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

33313185

DOI Digital object identifier for electronic documents.

10.21037/atm-20-1309

URI Uniform resource identifier for web resources.

Authors

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

Journal

Annals of translational medicine

Year

2020

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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Needs review

Curated date: 2021/08/11

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled (if applicable): 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: endometriosis 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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Endometriosis patients
Group 1 name Corresponds to the case (exposed) group for case-control studies: Endometriosis/ adenomyosis 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: 25
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

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

Revision editor(s): Samara.Khan

Source: Figure 6

Description: The following taxa were increased in patients with endometriosis and adenomyosis compared to those with just endometriosis

Abundance in Group 1: increased abundance in Endometriosis/ adenomyosis patients

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

Revision editor(s): Samara.Khan

Experiment 2

Edit History Delete

Mark reviewed

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/08/11

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled (if applicable): 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

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: endometriosis 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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Patients without endometriosis
Group 1 name Corresponds to the case (exposed) group for case-control studies: Endometriosis/ adenomyosis 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: 67
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

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

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

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2021/08/11

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 6

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

Abundance in Group 1: increased abundance in Endometriosis/ adenomyosis patients

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

Revision editor(s): Samara.Khan