Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Hernandes C, Silveira P, Rodrigues Sereia AF, Christoff AP, Mendes H, Valter de Oliveira LF, Podgaec S
Journal
Diagnostics (Basel, Switzerland)
Year
2020
Keywords:
16S rRNA, endometriosis, microbiome, next generation sequencing (NGS), pathogenesis, vaginal fluid
This work aimed to identify and compare the bacterial patterns present in endometriotic lesions, eutopic endometrium and vaginal fluid from endometriosis patients with those found in the vaginal fluid and eutopic endometrium of control patients. Vaginal fluid, eutopic endometrium and endometriotic lesions were collected. DNA was extracted and the samples were analyzed to identify microbiome by high-throughput DNA sequencing of the 16S rRNA marker gene. Amplicon sequencing from vaginal fluid, eutopic endometrium and endometriotic lesion resulted in similar profiles of microorganisms, composed most abundantly by the genus Lactobacillus, Gardnerella, Streptococcus and Prevotella. No significant differences were found in the diversity analysis of microbiome profiles between control and endometriotic patients; however deep endometriotic lesions seems to present different bacterial composition, less predominant of Lactobacillus and with more abundant Alishewanella, Enterococcus and Pseudomonas.

Experiment 1


Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

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

Subjects

Location of subjects
Brazil
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
Vagina Vagina,vagina,Distal oviductal region,Distal portion of oviduct,Vaginae
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,Endometriosis
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Control group
Group 1 name Corresponds to the case (exposed) group for case-control studies
Vaginal Fluid
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Vaginal samples were collected and processed for the evaluation of their bacterial profile:
Group 0 sample size Number of subjects in the control (unexposed) group
11
Group 1 sample size Number of subjects in the case (exposed) group
21
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
within 30 days prior to sample collection

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).
raw counts
Statistical test
DESeq2
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
Yes

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 4B

Description: There was increased abundance of gemella and streptococcus when comparing the vaginal fluid of endometriosis patients to healthy controls

Abundance in Group 1: increased abundance in Vaginal Fluid

NCBI Quality ControlLinks
Gemella
Streptococcus

Revision editor(s): Samara.Khan

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 4B

Description: There was decreased abundance of aerococcus in vaginal fluid of endometriosis patients compared to healthy controls. Atopobium, which is normally found in the lower female reproductive tract, was completely absent in vaginal fluid of endometriosis patients.

Abundance in Group 1: decreased abundance in Vaginal Fluid

NCBI Quality ControlLinks
Aerococcus
Atopobium

Revision editor(s): Samara.Khan

Experiment 2


Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

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

Differences from previous experiment shown

Subjects

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
Uterus Uterus,uterus
Group 1 name Corresponds to the case (exposed) group for case-control studies
Eutopic Endometrium Samples
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Eutopic Endometrium samples were collected and processed for the evaluation of their bacterial profile:
Group 1 sample size Number of subjects in the case (exposed) group
18

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 4B

Description: There was increased abundance of bifidobacterium when comparing the endometrial lining of endometriosis patients to healthy controls

Abundance in Group 1: increased abundance in Eutopic Endometrium Samples

NCBI Quality ControlLinks
Bifidobacterium

Revision editor(s): Samara.Khan

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 4B

Description: There was decreased abundance of atopobium, mobiluncus, campylobacter, chromohalobacter, and alcanivorax when comparing the endometrial lining of endometriosis patients to healthy controls

Abundance in Group 1: decreased abundance in Eutopic Endometrium Samples

NCBI Quality ControlLinks
Alcanivorax
Atopobium
Campylobacter
Chromohalobacter
Mobiluncus

Revision editor(s): Samara.Khan

Experiment 3


Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

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

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Controls group
Group 1 name Corresponds to the case (exposed) group for case-control studies
endometriotic lesion samples
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
endometriotic lesion samples collected and processed for the evaluation of their bacterial profile:
Group 1 sample size Number of subjects in the case (exposed) group
8

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 4B

Description: When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were increased: aerococcus, staphylococcus, sphingomonas, alishewanella, pseudomonas, and enterococcus

Abundance in Group 1: increased abundance in endometriotic lesion samples

NCBI Quality ControlLinks
Aerococcus
Staphylococcus
Sphingomonas
Alishewanella
Pseudomonas
Enterococcus

Revision editor(s): Samara.Khan

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2023-12-19

Curated date: 2021/07/01

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Figure 4B

Description: When comparing tissue from endometrial lesions to tissue from endometrium of healthy controls, the following species were decreased: prevotella, atopobium, afipia, mobiluncus, campylobacter, and facklamia

Abundance in Group 1: decreased abundance in endometriotic lesion samples

NCBI Quality ControlLinks
Prevotella
Atopobium
Afipia
Mobiluncus
Campylobacter
Facklamia

Revision editor(s): Samara.Khan