Study 501

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,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,Endometriosis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Women scheduled for laparoscopic surgery for benign uterine/ ovarian conditions as well as women with Stage I or Stage II endometriosis

Group 1 name Corresponds to the case (exposed) group for case-control studies: One (1) Stage III Endometriosis patient

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: One (1) Stage III Endometriosis patient was diagnosed via laparoscopic surgery and categorized according to the revised American Society for Reproductive Medicine scoring system (r-ASRM).

Group 0 sample size Number of subjects in the control (unexposed) group: 17

Group 1 sample size Number of subjects in the case (exposed) group: 1

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

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

Statistical Analysis

Statistical test: PERMANOVA

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

Richness Number of species: increased

Signature 1

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Curated date: 2021/08/08

Curator: Samara.Khan

Revision editor(s): Samara.Khan

Source: Table 2

Description: In this experiment, 9 patients had stage I, II or III endometriosis. The nine patients in the control group were undergoing laparoscopic surgery for other gynecological reasons, for a total of 18 patients.

The researchers found no difference when comparing the microbiome composition of control patients to experimental patients. However, when they compared the one (1) stage III endometriosis patient to the rest of the 17 patient cohort, they found 56 OTUs were significantly different, with 22 OTUs only present in the cervix of the stage III patient.

The results of this signature are therefore not statistically reliable. However, the OTUs present in the stage III endometriosis patients can be used as a reference when looking at other studies who involved stage III endometriosis patients.

It should also be noted that multiple unidentified species of Barnesiella were reported to be significantly different, but researchers did not specify which species so these were excluded from curation. There were also multiple unidentified species of Ruminococcus and Clostridium.

Abundance in Group 1: increased abundance in One (1) Stage III Endometriosis patient

NCBI	Quality Control	Links
Acetivibrio
Achromobacter
Alkalitalea
Allobaculum
Anaerotruncus
Bacteroides
Butyricicoccus
Coprobacillus
Coprococcus
Flavonifractor
Lactobacillus
Parabacteroides
Propionibacterium
Sneathia
Staphylococcus
Turicibacter

Revision editor(s): Samara.Khan