Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome
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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
Authors
Wang Z, Liang L, Liu L, Wang Z, Wang Y, Yu Z, Wu B, Chen Y
Journal
Microbiology spectrum
Year
2023
Keywords:
Peutz-Jeghers syndrome, biomarkers, functional analysis, gut microbiota, intussusception
Peutz-Jeghers syndrome (PJS) is a rare hereditary disorder characterized by intestinal polyposis, and intestinal intussusception is one of the most urgent complications. While it is known that imbalance of the gut microbiota is highly associated with intestinal disorders, the role of the gut microbiome in the pathogenesis of PJS has not been reported. In this study, we performed 16S rRNA sequencing on stools from 168 patients and 68 healthy family members who lived together to determine the gut microbiome composition of PJS patients. Metagenomics sequencing was further performed on the representative samples (61 PJS patients and 27 healthy family members) to analyze the functional changes. We found that the fecal microbiome of patients with PJS showed a greater variation in β-diversity. An enhancement of Escherichia coli and a reduction of Faecalibacterium prausnitzii was identified in PJS patients. Further reduction of Faecalibacterium prausnitzii was the characteristic microbial change observed in patients with intussusception. Functional analysis revealed that the abundance of propanoate metabolism was enriched in PJS patients and further enriched in those with intussusception. Escherichia coli was the major contributor to the enrichment of this metabolism pathway, which was associated with the abnormal expression of methylglyoxal synthase (encoded by mgsA) and phosphate acetyltransferase (encoded by pta). Our findings showed a distinct gut microbiome signature in PJS patients and identified the connection between the gut microbiome and intussusception. Alterations in the gut microbiome might be involved in the pathogenesis of PJS and may serve as biomarkers for gastrointestinal surveillance. IMPORTANCE Recent research has established a link between the gut microbiome and polyps and neoplasia, and antibiotic use influences the microbiome and the development of colorectal polyps. Familial adenomatous polyposis (FAP), which is characterized by the early development of benign precursor lesions (polyps), is associated with enterotoxigenic Bacteroides fragilis and Escherichia coli biofilms. However, the relationship between the gut microbiome and the pathophysiology of PJS has not yet been established. In this study, we found that PJS patients had a distinct microbiome composition, with a greater variation in β-diversity, an increase in Escherichia coli, and a decrease in Faecalibacterium prausnitzii. A further reduction of Faecalibacterium prausnitzii was observed in patients with intussusception. Moreover, PJS involved increased propanoate metabolism as well as abnormal mgsA and pta expression. These findings may contribute to a better understanding of the etiology of PJS and improve disease control strategies.
Experiment 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
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
- Peutz-Jeghers Polyp Peutz Jeghers polyp,Peutz-Jeghers polyp,Peutz-Jeghers Polyp,peutz-Jeghers Polyp
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control (family members)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Peutz-Jeghers syndrome (PJS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who has Peutz-Jeghers syndrome (PJS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 68
- Group 1 sample size Number of subjects in the case (exposed) group
- 168
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- within 3 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
- LEfSe
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3.0
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: FIG 1 (F)
Description: LEfSe analysis identified the differentially abundant taxa between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 3.0)
Abundance in Group 1: increased abundance in Peutz-Jeghers syndrome (PJS)
Revision editor(s): Rahila, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: FIG 1 (F)
Description: LEfSe analysis identified the differentially abundant taxa between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 3.0)
Abundance in Group 1: decreased abundance in Peutz-Jeghers syndrome (PJS)
Revision editor(s): Scholastica
Experiment 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Without Intussusception (NI-PJS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- With Intussusception (I-PJS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who had undergone at least one intussusception (I-PJS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 57
- Group 1 sample size Number of subjects in the case (exposed) group
- 106
Lab analysis
Statistical Analysis
Alpha Diversity
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: FIG 2 (D)
Description: LEfSe analysis identified the differences in abundance between I-PJS and NI-PJS patients (LDA > 3.0).
Abundance in Group 1: decreased abundance in With Intussusception (I-PJS)
Revision editor(s): Rahila
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: FIG 2 (D)
Description: LEfSe analysis identified the differences in abundance between I-PJS and NI-PJS patients (LDA > 3.0).
Abundance in Group 1: increased abundance in With Intussusception (I-PJS)
Revision editor(s): Rahila
Experiment 3
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control (family members)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Peutz-Jeghers syndrome (PJS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who has Peutz-Jeghers syndrome (PJS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 61
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
Statistical Analysis
- Statistical test
- LEfSe
- Mann-Whitney (Wilcoxon)
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: FIG 3 (D)
Description: LEfSe analysis identified the differential species between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 2.0)
Abundance in Group 1: increased abundance in Peutz-Jeghers syndrome (PJS)
Revision editor(s): Rahila, Scholastica
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: FIG 3 (D)
Description: LEfSe analysis identified the differential species between Peutz-Jeghers syndrome (PJS) patients and healthy controls (LDA > 2.0)
Abundance in Group 1: decreased abundance in Peutz-Jeghers syndrome (PJS)
Revision editor(s): Scholastica
Experiment 4
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Without Intussusception (NI-PJS)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- With Intussusception (I-PJS)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who had undergone at least one intussusception (I-PJS)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 35
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: FIG 4 (D)
Description: LEfSe analysis showed the differential species between I-PJS and NI-PJS patients (LDA > 2.0).
Abundance in Group 1: increased abundance in With Intussusception (I-PJS)
| NCBI | Quality Control | Links |
|---|---|---|
| Aeromonas veronii | ||
| Collinsella sp. AF08-23 | ||
| Dialister invisus CAG:218 | ||
| Fusobacterium necrogenes | ||
| Fusobacterium sp. | ||
| unclassified Aeromonas | ||
| bacterium 1xD8-27 |
Revision editor(s): Rahila
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-6-25
Source: FIG 4 (D)
Description: LEfSe analysis showed the differential species between I-PJS and NI-PJS patients (LDA > 2.0).
Abundance in Group 1: decreased abundance in With Intussusception (I-PJS)
Revision editor(s): Rahila
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