Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with 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 (11 with as active disease defined by CDAI > 150, 4 with inactive disease)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Table 2
Description: Differential microbial abundance between Crohn's patients and healthy controls
Abundance in Group 1: increased abundance in Patients with Crohn's disease
NCBI | Links |
---|---|
Abiotrophia | |
Escherichia | |
Pseudomonadota | |
Pseudoramibacter ⚠ | |
unidentified rumen bacterium RFN20 |
Revision editor(s): Claregrieve1, Suwaiba
Signature 2
Source: Table 2
Description: Differential microbial abundance between Crohn's patients and healthy controls
Abundance in Group 1: decreased abundance in Patients with Crohn's disease
NCBI | Links |
---|---|
Butyricicoccus | |
Mitsuokella | |
Haemophilus | |
Victivallis |
Revision editor(s): Claregrieve1
Experiment 2
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with ulcerative colitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with ulcerative colitis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 14
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- decreased
Signature 1
Source: Table 2
Description: Differential microbial abundance between ulcerative colitis patients and healthy controls
Abundance in Group 1: increased abundance in Patients with ulcerative colitis
NCBI | Links |
---|---|
Granulicatella | |
Peptostreptococcus | |
Schwartzia | |
Capnocytophaga | |
Pseudomonadota | |
Escherichia | |
Janthinobacterium ⚠ | |
Campylobacter | |
Actinomyces | |
Eggerthella | |
Corynebacterium | |
Spirochaetota |
Revision editor(s): Claregrieve1
Signature 2
Source: Table 2
Description: Differential microbial abundance between ulcerative colitis patients and healthy controls
Abundance in Group 1: decreased abundance in Patients with ulcerative colitis
NCBI | Links |
---|---|
Holdemania ⚠ | |
02d0602d06 | |
Lachnobacterium | |
Megamonas | |
Mitsuokella | |
Alistipes | |
Butyricimonas | |
Prevotella | |
Desulfovibrio | |
Oxalobacter ⚠ | |
Pyramidobacter | |
Synergistes | |
Lentisphaerota | |
Victivallis |
Revision editor(s): Claregrieve1
Experiment 3
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Patients with ulcerative colitis
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with 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
- 14
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- 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
Signature 1
Source: Table 2
Description: Differential abundance between patients with ulcerative colitis vs Crohn's disease
Abundance in Group 1: increased abundance in Patients with Crohn's disease
NCBI | Links |
---|---|
Desulfovibrio | |
Pseudoramibacter ⚠ | |
Slackia | |
02d0602d06 | |
Abiotrophia defectiva |
Revision editor(s): Claregrieve1, Suwaiba
Signature 2
Source: Table 2
Description: Differential abundance between patients with ulcerative colitis vs Crohn's disease
Abundance in Group 1: decreased abundance in Patients with Crohn's disease
NCBI | Links |
---|---|
Butyricicoccus | |
Moryella | |
Staphylococcus | |
Capnocytophaga | |
Haemophilus | |
Janthinobacterium ⚠ | |
Cardiobacterium | |
Lautropia | |
Propioniferax innocua | |
Shewanella ⚠ | |
Corynebacterium |
Revision editor(s): Claregrieve1