Microbial imbalance in Chinese children with diarrhea or constipation
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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. 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
- Diarrhea Diarrhea,Diarrhoea,Watery stool,diarrhea
- 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
- Children with diarrhea
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with diarrhea.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 414
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- one month
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)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 3
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: Fig S4
Description: Differentially abundant taxa in diarrhea patients compared to healthy controls, identified using LEfSe analysis.
Abundance in Group 1: increased abundance in Children with diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Coriobacteriaceae | ||
| Eggerthellaceae | ||
| Coriobacteriales | ||
| Bacteroidia | ||
| Clostridiaceae_222000Clostridiaceae_222000 | ||
| Defluviitaleaceae | ||
| Lachnospiraceae | ||
| Gemellaceae |
Revision editor(s): Jesulolufemi
Signature 2
Source: Fig S4
Description: Differentially abundant taxa in diarrhea patients compared to healthy controls, identified using LEfSe analysis.
Abundance in Group 1: decreased abundance in Children with diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| StaphylococcalesStaphylococcales | ||
| Enterobacterales_A_737866Enterobacterales_A_737866 | ||
| Gammaproteobacteria |
Revision editor(s): Jesulolufemi
Experiment 2
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with diarrhea
Lab analysis
Statistical Analysis
- Statistical test
- MaAsLin2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- 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 S8
Description: Differentially abundant taxa in diarrhea patients compared to healthy controls, identified using MaAsLin2 analysis, adjusting for age and gender.
Abundance in Group 1: increased abundance in Children with diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium piliformeClostridium piliforme |
Revision editor(s): Jesulolufemi
Signature 2
Source: Table S8
Description: Differentially abundant taxa in diarrhea patients compared to healthy controls, identified using MaAsLin2 analysis, adjusting for age and gender.
Abundance in Group 1: decreased abundance in Children with diarrhea
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospira | ||
| Mediterraneibacter | ||
| Streptococcus | ||
| Blautia A_141781Blautia A_141781 | ||
| Hungatella A_128155Hungatella A_128155 | ||
| Bifidobacterium longum |
Revision editor(s): Jesulolufemi
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Constipation Constipation,Costiveness,Dyschezia,constipation
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children with constipation
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with constipation.
- Group 1 sample size Number of subjects in the case (exposed) group
- 138
Lab analysis
Statistical Analysis
- Statistical test
- LEfSe
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Fig S3
Description: Differentially abundant taxa in constipation patients compared to healthy controls, identified using LEfSe analysis.
Abundance in Group 1: increased abundance in Children with constipation
Revision editor(s): Jesulolufemi
Signature 2
Source: Fig S3
Description: Differentially abundant taxa in constipation patients compared to healthy controls, identified using LEfSe analysis
Abundance in Group 1: decreased abundance in Children with constipation
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales_A_737866Enterobacterales_A_737866 | ||
| Gammaproteobacteria |
Revision editor(s): Jesulolufemi
Experiment 4
Subjects
Lab analysis
Statistical Analysis
- Statistical test
- MaAsLin2
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
Signature 1
Source: Table S7
Description: Differentially abundant taxa in constipation patients compared to healthy controls, identified using MaAsLin2 analysis, adjusting for age and gender.
Abundance in Group 1: increased abundance in Children with constipation
Revision editor(s): Jesulolufemi
Signature 2
Source: Table S7
Description: Differentially abundant taxa in constipation patients compared to healthy controls, identified using MaAsLin2 analysis, adjusting for age and gender.
Abundance in Group 1: decreased abundance in Children with constipation
Revision editor(s): Jesulolufemi
