Gut microbiome in patients with early-stage and late-stage endometriosis
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Cai Z, Zhou Z, Huang S, Ma S, Chen Y, Cao Y, Ma Y
Journal
BMC women's health
Year
2025
Keywords:
Dysmenorrhea, Endometriosis, Gut microbiota
BACKGROUND: Endometriosis is a chronic inflammatory gynecological disease. Previous studies have explored relationships between endometriosis and the microbiota, but none have focused on differences in gut microbiota between early-stage and late-stage endometriosis patients or their connections to dysmenorrhea symptoms. This study compared gut microbiota compositions between early-stage and late-stage endometriosis patients using amplicon sequencing and further analyzed their dysmenorrhea symptoms. METHODS: To minimize seasonal and dietary impacts, we recruited Guangdong residents hospitalized for surgery at Zhujiang Hospital. Participants underwent preoperative screening based on enrollment criteria and fecal samples were collected. Endometriosis was classified according to the American Society for Reproductive Medicine (ASRM) staging system based on surgincal and pathological findings. Stage I-II cases were designated as early-stage endometriosis, and Stage III-IV as late-stage endometriosis. RESULTS: A total of 112 patient fecal samples were collected, with 75 (median age, 32 years [range, 18-49 years]) meeting the enrollment criteria, including 39 early-stage (32 Stage I and 7 Stage II) and 36 late-stage (16 Stage III and 20 Stage IV) patients. The gut microbiota structure and functions in early-stage patients significantly differed from those in late-stage cases. Dysmenorrhea was associated with specific microbial traits. Late-stage patients with dysmenorrhea displayed distinctly different gut profiles compared to other endometriosis groups. Bartonella, Snodgrassella, and other taxa were enriched in late-stage cases, while Bacteroides, and Prevotella were decreased. CONCLUSION: The gut microbial community structure in early-stage endometriosis patients significantly differs from that in late-stage cases, with late-stage patients experiencing dysmenorrhea displaying particularly distinct gut profiles. Predicted functional analysis indicated suppressed steroid biosynthesis pathways in the gut of late-stage endometriosis patients. In conclusion, it is plausible that the multiple effects of steroids on the lower gastrointestinal tract may involve microbiota alterations, suggesting the need for further investigations.
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Differences from previous experiment shown
Subjects
- Location of subjects
- China
- 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
- 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,feces
- 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
- Early-stage Endometriosis (Stage I-II)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late-stage Endometriosis (Stage III-IV)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with late-stage endometriosis (Stage III and Stage IV) according to the revised American Society for Reproductive Medicine (r-ASRM) classification system, confirmed by surgical and pathological examination.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 39
- 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)
- 6 months
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).
- relative abundances
- Statistical test
- T-Test
- 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)?
- Yes
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 2D & Fig. S1A
Description: Differential microbes between the early- and late-stage endometriosis groups.
Abundance in Group 1: increased abundance in Late-stage Endometriosis (Stage III-IV)
Revision editor(s): Joiejoie, KateRasheed
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 2D & Fig. S1A
Description: Differential microbes between the early- and late-stage endometriosis groups.
Abundance in Group 1: decreased abundance in Late-stage Endometriosis (Stage III-IV)
Revision editor(s): Joiejoie, KateRasheed
Experiment 5
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Dysmenorrhea Painful menstruation,Dysmenorrhea,dysmenorrhea
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early-Stage-F (patients without dysmenorrhea)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Early-Stage-T (patients with dysmenorrhea)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of patients diagnosed with early-stage endometriosis (Stage I–II) who reported experiencing preoperative dysmenorrhea.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 4A
Description: Differential species between dysmenorrhea positive and negative subgroups within the early-stage endometriosis group
Abundance in Group 1: increased abundance in Early-Stage-T (patients with dysmenorrhea)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactococcus lactis | ||
| Rothia mucilaginosa | ||
| Ruminococcus flavefaciens | ||
| Ruoffia tabacinasalis | ||
| Streptococcus anginosus | ||
| unclassified Weissella | ||
| unclassified Coprococcus |
Revision editor(s): Joiejoie
Experiment 6
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Late-Stage-F (patients without dysmenorrhea)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late-Stage-T (patients with dysmenorrhea)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to patients diagnosed with late-stage endometriosis (Stage III–IV) who reported experiencing preoperative dysmenorrhea.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 4A
Description: Differential species between dysmenorrhea-positive and negative subgroups within the late-stage endometriosis group.
Abundance in Group 1: increased abundance in Late-Stage-T (patients with dysmenorrhea)
Revision editor(s): Joiejoie
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 4A
Description: Differential species between dysmenorrhea-positive and negative subgroups within the late-stage endometriosis group.
Abundance in Group 1: decreased abundance in Late-Stage-T (patients with dysmenorrhea)
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillales |
Revision editor(s): Joiejoie
Experiment 7
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early-stage-T
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late-stage-T
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to patients with dysmenorrhea diagnosed with late-stage endometriosis, as analyzed for gut microbiota composition.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 6D
Description: Relative abundance levels of 10 differential species consistently enriched between early-stage and late-stage groups.
Abundance in Group 1: increased abundance in Late-stage-T
| NCBI | Quality Control | Links |
|---|---|---|
| Bombella | ||
| Commensalibacter | ||
| Snodgrassella | ||
| uncultured Hyphomicrobiales bacterium |
Revision editor(s): Joiejoie, KateRasheed
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 6D
Description: Relative abundance levels of 10 differential species consistently enriched between early-stage and late-stage groups.
Abundance in Group 1: decreased abundance in Late-stage-T
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides caecimuris | ||
| Xylanibacter ruminicola | ||
| Bacteroidales RF16 groupBacteroidales RF16 group | ||
| uncultured rumen bacterium |
Revision editor(s): Joiejoie, KateRasheed
Experiment 8
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Early-stage-F
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Late-stage-F
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group refers to patients without dysmenorrhea who are diagnosed with late-stage endometriosis, as examined for gut microbiota differences.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 6D
Description: Relative abundance levels of 10 differential species consistently enriched between early-stage and late-stage groups.
Abundance in Group 1: increased abundance in Late-stage-F
| NCBI | Quality Control | Links |
|---|---|---|
| Bombella | ||
| Commensalibacter | ||
| Snodgrassella | ||
| uncultured Hyphomicrobiales bacterium |
Revision editor(s): Joiejoie, KateRasheed
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-4-29
Source: Fig. 6D
Description: Relative abundance levels of 10 differential species consistently enriched between early-stage and late-stage groups
Abundance in Group 1: decreased abundance in Late-stage-F
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides caecimuris | ||
| Xylanibacter ruminicola | ||
| Bacteroidales RF16 groupBacteroidales RF16 group | ||
| uncultured rumen bacterium |
Revision editor(s): Joiejoie, KateRasheed
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