Microbiota composition and distribution along the female reproductive tract of women with endometriosis

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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Wei W, Zhang X, Tang H, Zeng L, Wu R
Journal
Annals of clinical microbiology and antimicrobials
Year
2020
Keywords:
16S rRNA gene amplicon sequencing, Endometriosis, Microbial community composition, Microbial distribution
Endometriosis (EMS) is a multifactorial disease that affects 10%-15% women of reproductive age and is associated with chronic pelvic pain and infertility. The pathogenesis of EMS has not been consistently explained until now. In this study, we involved 36 endometriosis patients and 14 control subjects who performed laparoscopic surgery due to gynecological benign tumor. The samples from lower third of vagina (CL), posterior vaginal fornix (CU), cervical mucus (CV), endometrium (ET) and peritoneal fluid (PF), were collected and sequenced by 16S rRNA amplicon. The continuous change of the microbiota distribution was identified along the reproductive tract. The flora in lower reproductive tract (CL, CU) were dominated by Lactobacillus. Significant difference of the community diversity began showing in the CV of EMS patients and gradually increased upward the reproductive tract. It indicates the microbiota in cervical samples is expected to be an indicator for the risk of EMS. This study also highlights the decreasing of Lactobacillus in vaginal flora and the increasing of signature Operational Taxonomic Units (OTUs) in transaction zone (CV) and upper reproductive tract (ET, PF) of EMS patients, which reflect the alteration of microbial community associated with EMS, participation of specific colonized bacteria in the EMS pathogenesis and relationship between microbiota and development of disease.

Experiment 1


Needs review

Curated date: 2021/08/09

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
Lower part of vagina Caudal vagina,Lower third of vagina,Lower vagina,Perineal part of vagina,Sinus vagina,Vagina lower part,Vaginal bulb,Lower part of vagina
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
Controls undergoing laparoscopic surgery for benign tumors
Group 1 name Corresponds to the case (exposed) group for case-control studies
Endometriosis patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
This experiment only curates unknown species up to the genus level so it needs to be deleted.
Group 0 sample size Number of subjects in the control (unexposed) group
14
Group 1 sample size Number of subjects in the case (exposed) group
36
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
This experiment only curates unknown species up to the genus level so it needs to be deleted.

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4-V5
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

Statistical Analysis

Statistical test
Mann-Whitney (Wilcoxon)
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


Signature 1

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: Created in error - this figure only curates unidentified species up to the genus level. This experiment needs to be deleted.

Abundance in Group 1: increased abundance in Endometriosis patients

NCBI Quality ControlLinks

Revision editor(s): Samara.Khan

Experiment 2


Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Posterior fornix of vagina Pars posterior fornicis vaginae,Posterior fornix,Posterior part of fornix of vagina,Posterior fornix of vagina
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients were diagnosed with endometriosis via laparoscopic surgery and stages were categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Patients were excluded if they had taken antibiotics within 6 months before the study

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: Lactobacillus iners was decreased in the posterior fornix of the vagina of endometriosis patients compared to controls.

Abundance in Group 1: decreased abundance in Endometriosis patients

NCBI Quality ControlLinks
Lactobacillus iners

Revision editor(s): Samara.Khan

Signature 2

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: Created in error - this signature only curates unidentified species up to the genus level. This signature needs to be deleted.

Abundance in Group 1: increased abundance in Endometriosis patients

NCBI Quality ControlLinks

Revision editor(s): Samara.Khan

Experiment 3


Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks

Differences from previous experiment shown

Subjects

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


Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: The following taxa were increased in the cervical mucus of endometriosis patients compared to control patients.

Abundance in Group 1: increased abundance in Endometriosis patients

NCBI Quality ControlLinks
Caulobacteraceae
Comamonadaceae
Erysipelotrichaceae
Lactobacillus iners
Leptotrichiaceae
Pseudomonadaceae
Pseudomonas viridiflava

Revision editor(s): Samara.Khan

Signature 2

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: The following taxa were decreased in the cervical mucus of endometriosis patients compared to controls. Some species were unidentified and were excluded from curation

Abundance in Group 1: decreased abundance in Endometriosis patients

NCBI Quality ControlLinks
Micrococcaceae
Pseudomonas viridiflava

Revision editor(s): Samara.Khan

Experiment 4


Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Endometrium Tunica mucosa (endometrium),Tunica mucosa uteri,Uterine endometrium,Uterine mucosa,Uterine mucous membrane,Endometrium


Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: The following taxa were increased in the endometrium of endometriosis patients compared to controls.

Abundance in Group 1: increased abundance in Endometriosis patients

NCBI Quality ControlLinks
Coriobacteriaceae
Enterococcus casseliflavus
Exiguobacterium
Hyphomicrobiales
Leptotrichiaceae
Macrococcus caseolyticus
Segatella copri
Pseudomonas viridiflava
Paracoccaceae
[Ruminococcus] gnavus
Clostridium

Revision editor(s): Samara.Khan

Signature 2

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: The following taxa were decreased in the endometrium of endometriosis patients compared to controls.

Abundance in Group 1: decreased abundance in Endometriosis patients

NCBI Quality ControlLinks
Erysipelotrichaceae
Tissierellaceae
Stenotrophomonas acidaminiphila

Revision editor(s): Samara.Khan

Experiment 5


Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Peritoneal fluid Peritoneal fluid


Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: The following taxa were increased in the peritoneal fluid of endometriosis patients compared to controls.

Abundance in Group 1: increased abundance in Endometriosis patients

NCBI Quality ControlLinks
Acinetobacter guillouiae
Clostridium
Enterobacteriaceae
Micrococcaceae
Pseudomonadaceae
Pseudomonas viridiflava
Sphingobacterium multivorum

Revision editor(s): Samara.Khan

Signature 2

Needs review

Curated date: 2021/08/09

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 2 and Results section

Description: The following taxa were decreased in the peritoneal fluid of endometriosis patients compared to controls.

Abundance in Group 1: decreased abundance in Endometriosis patients

NCBI Quality ControlLinks
Pseudomonas fragi

Revision editor(s): Samara.Khan