Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn's disease: a prospective trial
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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
Zou B, Liu S, Dong C, Shen H, Lv Y, He J, Li X, Ruan M, Huang Z, Shu S
Journal
Journal of translational medicine
Year
2025
Keywords:
Children, Core functional genera, Crohn’s disease, Efficacy and safety, Oral fecal microbiota capsules
BACKGROUND: Clinical data on oral fecal microbiota transplantation (FMT), a promising therapy for Crohn's disease (CD), are limited. Herein, we determined the short-term safety and feasibility of FMT for pediatric patients with active CD. METHODS: In this open-label, parallel-group, single-center prospective trial, patients with active CD were treated with oral FMT capsules combined with partial enteral nutrition (PEN) (80%). The control group comprised pediatric patients with active CD treated with PEN (80%) and immunosuppressants. Thirty-three patients (11.6 ± 1.82 years)-17 in the capsule and 16 in the control groups-were analyzed. Data regarding the adverse events, clinical reactions, intestinal microbiome composition, and biomarker parameters were collected and compared post-treatment. RESULTS: At week 10, the clinical and endoscopic remission rates did not differ between the two groups. By week 10, the mean fecal calprotectin level, C-reactive protein level, erythrocyte sedimentation rate, simple endoscopic score for CD, and pediatric CD activity index decreased significantly in the capsule group (all P < 0.05). The main adverse event was mild-to-moderate constipation. Core functional genera, Agathobacter, Akkermansia, Roseburia, Blautia, Subdoligranulum, and Faecalibacterium, were lacking pre-treatment. Post-treatment, the implantation rates of these core functional genera increased significantly, which positively correlated with the anti-inflammatory factor, interleukin (IL)-10, and negatively correlated with the pro-inflammatory factor, IL-6. The combination of these six functional genera distinguished healthy children from those with CD (area under the curve = 0.96). CONCLUSIONS: Oral FMT capsules combined with PEN (80%) could be an effective therapy for children with active CD. The six core functional genera identified here may be candidate biomarkers for identifying children with CD. TRIAL REGISTRATION: ClinicalTrials.gov, retrospectively registered, ID# NCT05321758, NCT05321745, date of registration: 2022-04-04.
Experiment 1
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
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with Crohn's disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 42
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
- Spearman Correlation
- 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
- 3.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: Within-text result of "Improvement in microbial dysbiosis following oral FMT administration"
Description: relative abundance in patients with Crohns disease vs healthy donor control
Abundance in Group 1: increased abundance in crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota |
Revision editor(s): EniolaAde
Signature 2
Source: Within-text result of "Improvement in microbial dysbiosis following oral FMT administration"
Description: relative abundance in patients with crohns disease and healthy donor control
Abundance in Group 1: decreased abundance in crohn's disease
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidia |
Revision editor(s): EniolaAde
Experiment 2
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- crohn's disease (FMT0W)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with Crohn's disease before fecal microbiota transplantation treatment (FMT0W)
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: supplementary figure 3
Description: LEfSe of the different genera in healthy donor control and patients with crohns disease before FMT
Abundance in Group 1: decreased abundance in crohn's disease (FMT0W)
Revision editor(s): EniolaAde
Signature 2
Source: supplementary figure 3
Description: LEfSe of the different genera in healthy donor control and patients with crohns disease before FMT
Abundance in Group 1: increased abundance in crohn's disease (FMT0W)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Bifidobacteriales | ||
| Bifidobacterium | ||
| Coriobacteriaceae | ||
| Enterococcaceae | ||
| Enterococcus | ||
| Morganellaceae |
Revision editor(s): EniolaAde
Experiment 3
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy donor group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT0W group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with Crohn's disease before FMT treatment
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Source: sup fig 4
Description: relative abundance of bacteria between healthy donor group and pre-FMT
Abundance in Group 1: decreased abundance in FMT0W group
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Akkermansia | ||
| Anaerostipes | ||
| Blautia | ||
| Faecalibacterium | ||
| Roseburia | ||
| Streptococcus | ||
| Subdoligranulum |
Revision editor(s): EniolaAde
Signature 2
Source: sup fig 4
Description: relative proportion of bacteria between healthy donor group and pre-FMT
Abundance in Group 1: increased abundance in FMT0W group
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides | ||
| Enterobacter | ||
| Enterococcus | ||
| Escherichia/Shigella sp. |
Revision editor(s): EniolaAde
Experiment 4
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FMT0W
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT5W
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients given fecal microbiota transplantation treatment after five weeks
- 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
- 8
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 6A
Description: relative abundance genera between FMT0W and FMT5W
Abundance in Group 1: increased abundance in FMT5W
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Subdoligranulum | ||
| Blautia |
Revision editor(s): EniolaAde
Experiment 5
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT10W
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients given FMT treatment after ten weeks
- 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
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Signature 1
Source: Figure 6A
Description: relative abundance between FMT0W and FMT10W
Abundance in Group 1: increased abundance in FMT10W
| NCBI | Quality Control | Links |
|---|---|---|
| Agathobacter | ||
| Akkermansia | ||
| Blautia | ||
| Faecalibacterium | ||
| Roseburia | ||
| Subdoligranulum |
Revision editor(s): EniolaAde
Experiment 6
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy donor group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT0W
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with crohns disease before FMT treatment
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- increased
Experiment 7
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Response to transplant Response to transplant,response to transplant
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- FMT0W
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- FMT10W
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients given FMT treatment after 10 weeks
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
Lab analysis
Statistical Analysis
- Statistical test
- Kruskall-Wallis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
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