The Endobiota Study: Comparison of Vaginal, Cervical and Gut Microbiota Between Women with Stage 3/4 Endometriosis and Healthy Controls

From BugSigDB
Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Ata B, Yildiz S, Turkgeldi E, Brocal VP, Dinleyici EC, Moya A, Urman B
Journal
Scientific reports
Year
2019
Dysbiosis in the genital tract or gut microbiome can be associated with endometriosis. We sampled vaginal, cervical and gut microbiota from 14 women with histology proven stage 3/4 endometriosis and 14 healthy controls. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Despite overall similar vaginal, cervical and intestinal microbiota composition between stage 3/4 endometriosis group and controls, we observed differences at genus level. The complete absence of Atopobium in the vaginal and cervical microbiota of the stage 3/4 endometriosis group was noteworthy. In the cervical microbiota, Gardnerella, Streptococcus, Escherichia, Shigella, and Ureoplasma, all of which contain potentially pathogenic species, were increased in stage 3/4 endometriosis. More women in the stage 3/4 endometriosis group had Shigella/Escherichia dominant stool microbiome. Further studies can clarify whether the association is causal, and whether dysbiosis leads to endometriosis or endometriosis leads to dysbiosis.

Experiment 1


Needs review

Curated date: 2021/06/24

Curator: Samara.Khan

Revision editor(s): Samara.Khan, WikiWorks

Subjects

Location of subjects
Turkey
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
Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,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
Healthy controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Stage 3/4 endometriosis patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification.

Diagnosis of endometriosis was verified through histology.

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
14
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Participants were excluded if they had taken antibiotics within the past 8 weeks

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

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

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2021/06/24

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 3 and Table 1

Description: Gemella and Atopobium were completely absent in the vagina of endometriosis stage 3/4 patients when compared to healthy controls.

Abundance in Group 1: decreased abundance in Stage 3/4 endometriosis patients

NCBI Quality ControlLinks
Atopobium
Gemella

Revision editor(s): Samara.Khan

Experiment 2


Needs review

Curated date: 2021/06/24

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
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification. Diagnosis of endometriosis was verified through histology.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2021/06/24

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 3 and Table 1

Description: Atopobium and Sneathia bacteria were decreased in endometriosis stage 3/4 patients compared to healthy controls. Atopobium bacteria were completely absent in endometriosis patients.

Abundance in Group 1: decreased abundance in Stage 3/4 endometriosis patients

NCBI Quality ControlLinks
Atopobium
Sneathia

Revision editor(s): Samara.Khan

Signature 2

Needs review

Curated date: 2021/06/24

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Table 1

Description: Alloprevotella bacteria were significantly increased in endometriosis stage 3/4 patients when compared to healthy controls

Abundance in Group 1: increased abundance in Stage 3/4 endometriosis patients

NCBI Quality ControlLinks
Alloprevotella

Revision editor(s): Samara.Khan

Experiment 3


Needs review

Curated date: 2021/06/24

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
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to

American Fertility Society Revised Classification. Diagnosis of endometriosis was verified through histology.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2021/06/24

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Table 1 and Figure 3

Description: Gardnerella, Sneathia, and Barnesiella bacteria were significantly decreased in endometriosis stage 3/4 patients when compared to healthy controls

Abundance in Group 1: decreased abundance in Stage 3/4 endometriosis patients

NCBI Quality ControlLinks
Gardnerella
Sneathia
Barnesiella

Revision editor(s): Samara.Khan

Experiment 4


Needs review

Curated date: 2021/08/04

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
Vagina Distal oviductal region,Distal portion of oviduct,Vaginae,Vagina
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification.

Diagnosis of endometriosis was verified through histology.

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Participants were excluded if they had taken antibiotics within the past 8 weeks.

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2021/08/04

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Table 1

Description: Gardnerella and Escherichia/Shigella bacteria were significantly increased in endometriosis stage 3/4 patients when compared to healthy controls. This was part of a sensitivity analysis excluding all Lactobacillus species since Lactobacillus is the predominant species in the lower female reproductive tract.

Abundance in Group 1: increased abundance in Stage 3/4 endometriosis patients

NCBI Quality ControlLinks
Gardnerella
Escherichia/Shigella sp.

Revision editor(s): Samara.Khan

Experiment 5


Needs review

Curated date: 2021/08/04

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
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
All women in the endometriosis group had moderate to severe (stage 3–4) endometriosis according to American Fertility Society Revised Classification. Diagnosis of endometriosis was verified through histology.
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Participants were excluded if they had taken antibiotics within the past 8 weeks

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Needs review

Curated date: 2021/08/04

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Table 1

Description: Gardnerella, Escherichia/Shigella, Streptococcus, and Ureaplasma bacteria were significantly increased in endometriosis stage 3/4 patients when compared to healthy controls. This was part of a sensitivity analysis excluding all Lactobacillus species since Lactobacillus is the predominant species in the lower female reproductive tract.

Abundance in Group 1: increased abundance in Stage 3/4 endometriosis patients

NCBI Quality ControlLinks
Gardnerella
Streptococcus
Ureaplasma
Escherichia/Shigella sp.

Revision editor(s): Samara.Khan

Signature 2

Needs review

Curated date: 2021/08/04

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Table 1

Description: Prevotella, Dialister, and Megasphaera bacteria were significantly increased in endometriosis stage 3/4 patients when compared to healthy controls. This was part of a sensitivity analysis excluding all Lactobacillus species since Lactobacillus is the predominant species in the lower female reproductive tract.

Abundance in Group 1: decreased abundance in Stage 3/4 endometriosis patients

NCBI Quality ControlLinks
Prevotella
Dialister
Megasphaera

Revision editor(s): Samara.Khan