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 2
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 children (HC) of the discovery cohort
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children with diarrhea (CD) of the discovery cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.
- 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)
- 1 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. 2D
Description: LEfSe (Linear Discriminant Analysis Effect Size) cladogram illustrating different bacterial taxa's phylogenetic relationships that are differentially abundant between the CD and HC groups.
Abundance in Group 1: increased abundance in Children with diarrhea (CD) of the discovery cohort
Revision editor(s): Jesulolufemi, Ameenatoloko
Signature 2
Source: Fig. 2D
Description: LEfSe (Linear Discriminant Analysis Effect Size) cladogram illustrating the phylogenetic relationships of bacterial taxa that are differentially abundant between the CD and HC groups.
Abundance in Group 1: decreased abundance in Children with diarrhea (CD) of the discovery cohort
Revision editor(s): Jesulolufemi, Ameenatoloko
Experiment 4
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 (CC) of the discovery cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with constipation are at risk of various health issues, including mental, behavioral, social, and physical challenges.
- Group 1 sample size Number of subjects in the case (exposed) group
- 138
Lab analysis
Statistical Analysis
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. 2C
Description: LEfSe (Linear Discriminant Analysis Effect Size) cladogram illustrating different bacterial taxa's phylogenetic relationships that are differentially abundant between the CC and HC groups.
Abundance in Group 1: increased abundance in Children with constipation (CC) of the discovery cohort
Revision editor(s): Jesulolufemi, Ameenatoloko
Signature 2
Source: Fig. 2C
Description: LEfSe (Linear Discriminant Analysis Effect Size) cladogram illustrating different bacterial taxa's phylogenetic relationships that are differentially abundant between the CC and HC groups.
Abundance in Group 1: decreased abundance in Children with constipation (CC) of the discovery cohort
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium butyricum | ||
| Clostridium neonatale | ||
| Citrobacter | ||
| Clostridiaceae | ||
| Enterobacteriaceae | ||
| Enterobacterales | ||
| Gammaproteobacteria | ||
| Pseudomonadota |
Revision editor(s): Jesulolufemi, Ameenatoloko
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls (HC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children with constipation (CC)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 398
- Group 1 sample size Number of subjects in the case (exposed) group
- 129
Lab analysis
Statistical Analysis
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, Table S7
Description: A cladogram made by LEfSe demonstrates different bacterial taxa between the CC and HC groups.
Abundance in Group 1: increased abundance in Children with constipation (CC)
Revision editor(s): Ameenatoloko
Signature 2
Source: Fig. S3, Table S7
Description: A cladogram made by LEfSe demonstrates different bacterial taxa between the CC and HC groups.
Abundance in Group 1: decreased abundance in Children with constipation (CC)
Revision editor(s): Ameenatoloko, KateRasheed
Experiment 6
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diarrhea Diarrhea,Diarrhoea,Watery stool,diarrhea
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children with diarrhea (CD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.
- Group 1 sample size Number of subjects in the case (exposed) group
- 60
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
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Source: Fig. S4, Table S8
Description: A cladogram made by LEfSe demonstrates different bacterial taxa between the CD and HC groups.
Abundance in Group 1: increased abundance in Children with diarrhea (CD)
Revision editor(s): Ameenatoloko
Signature 2
Source: Fig. S4, Table S8
Description: A cladogram made by LEfSe demonstrates different bacterial taxa between the CD and HC groups.
Abundance in Group 1: decreased abundance in Children with diarrhea (CD)
Revision editor(s): Ameenatoloko
Experiment 7
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 (CC)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with constipation are at risk of various health issues, including mental, behavioral, social, and physical challenges.
- 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
- 138
Lab analysis
Statistical Analysis
- Statistical test
- MaAsLin2
- 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
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, Confounders controlled for: "gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.gender
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 S3
Description: The significantly altered genera determined by MaAsLin2 after adjusting for age and gender between the CC and HC groups.
Abundance in Group 1: increased abundance in Children with Constipation (CC)
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Anaerostipes | ||
| Oscillospira | ||
| Coprococcus | ||
| Parabacteroides |
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S3
Description: The significantly altered genera determined by MaAsLin2 after adjusting for age and gender between the CC and HC groups.
Abundance in Group 1: decreased abundance in Children with Constipation (CC)
| NCBI | Quality Control | Links |
|---|---|---|
| Rothia |
Revision editor(s): Ameenatoloko
Experiment 8
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diarrhea Diarrhea,Diarrhoea,Watery stool,diarrhea
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children with Diarrhea (CD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Children with diarrhea experience a range of health impacts, such as difficulty in feeding, reduced immunity, malnutrition, and foodborne illness, with potential complications like viral myocarditis.
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
Lab analysis
Statistical Analysis
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
Signature 1
Source: Table S3
Description: The significantly altered genera determined by MaAsLin2 after adjusting for age and gender between the CD and HC groups.
Abundance in Group 1: increased abundance in Children with Diarrhea (CD)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium | ||
| Gemella |
Revision editor(s): Ameenatoloko
Signature 2
Source: Table S3
Description: The significantly altered genera determined by MaAsLin2 after adjusting for age and gender between the CD and HC groups.
Abundance in Group 1: decreased abundance in Children with Diarrhea (CD)
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Eggerthella | ||
| Collinsella | ||
| Coprobacillus | ||
| Bacteroides | ||
| Blautia | ||
| Ruminococcus |
Revision editor(s): Ameenatoloko
