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

From BugSigDB
Needs review
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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
Not specified
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

Needs review

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 Quality ControlLinks
Atopobium
Campylobacter
Ezakiella
Faecalibacterium
Escherichia/Shigella sp.
Campylobacteraceae
Coriobacteriaceae

Revision editor(s): Samara.Khan

Experiment 2


Needs review

Curated date: 2021/08/11

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Patients without endometriosis
Group 0 sample size Number of subjects in the control (unexposed) group
67

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

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 Quality ControlLinks
Atopobium
Campylobacter
Ezakiella
Faecalibacterium
Escherichia/Shigella sp.
Campylobacteraceae
Coriobacteriaceae

Revision editor(s): Samara.Khan