Faecal microbiota and cytokine profiles of rural Cambodian infants linked to diet and diarrhoeal episodes
-
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
- Cambodia
- 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
- Breastfeeding duration Breastfeeding duration,breastfeeding duration
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants who are not breast-fed
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants who are breast-fed
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants that are being breastfed at the time of the research/sample collection
- Group 0 sample size Number of subjects in the control (unexposed) group
- 9
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V2
- 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).
- centered log-ratio
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- 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
- time
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 2D, 3D, Supplementary Data 3, Supplementary Data 6
Description: Bacterial genera differentially abundant between breastfed infants and infants who were not breastfed at all timepoints.
Abundance in Group 1: increased abundance in Infants who are breast-fed
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Bifidobacterium longum | ||
| Streptococcus pneumoniae | ||
| Streptococcus | ||
| Enterococcus |
Revision editor(s): Aishat, KateRasheed
Signature 2
Source: Figure 2E, 3E, Supplementary Data 3, Supplementary Data 6
Description: Bacterial species differentially abundant between breastfed infants and infants who were not breastfed at all timepoints.
Abundance in Group 1: decreased abundance in Infants who are breast-fed
Revision editor(s): Aishat, KateRasheed
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diarrhea, Infantile Diarrhea, Infantile,diarrhea, Infantile
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants without diarrhea - Timepoint 1
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants with diarrhea - Timepoint 1
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants who experienced diarrhea within the 7 days prior to sample collection.
- 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
- 6
Lab analysis
Statistical Analysis
Signature 1
Source: Figure 3G
Description: Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 1.
Abundance in Group 1: increased abundance in Infants with diarrhea - Timepoint 1
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium perfringens |
Revision editor(s): Aishat, KateRasheed
Signature 2
Source: Figure 2F-H, 3F
Description: Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 1.
Abundance in Group 1: decreased abundance in Infants with diarrhea - Timepoint 1
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Shigella | ||
| Klebsiella | ||
| Shigella flexneri |
Revision editor(s): Aishat, KateRasheed
Signature 4
Experiment 3
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Sample treatment protocol Sample treatment protocol,sample treatment protocol
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Frozen Samples
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Deoxyribonucleic Acid Shield (DNA Shield)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Deoxyribonucleic Acid Shield (DNA Shield) is a reagent that preserves the genetic integrity of samples during collection, transport, and storage.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 70
- Group 1 sample size Number of subjects in the case (exposed) group
- 94
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- 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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
Signature 1
Source: Fig. 1D, 1F, 1G
Description: Differences in genus abundance between paired frozen samples and DNAShield stored samples.
Abundance in Group 1: increased abundance in Deoxyribonucleic Acid Shield (DNA Shield)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Parabacteroides | ||
| Lachnoclostridium |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 1E, H-K
Description: Differences in genus abundance between paired frozen samples and DNAShield stored samples.
Abundance in Group 1: decreased abundance in Deoxyribonucleic Acid Shield (DNA Shield)
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia | ||
| Bifidobacterium | ||
| Streptococcus | ||
| Enterococcus | ||
| Actinomyces |
Revision editor(s): KateRasheed
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diarrhea, Infantile Diarrhea, Infantile,diarrhea, Infantile
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants without diarrhea - Timepoint 2
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants with diarrhea - Timepoint 2
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Infants who experienced diarrhea within the 7 days prior to sample collection.
- 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
- 6
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- MaAsLin2
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.25
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- time
Signature 1
Source: Fig. 2F
Description: Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 2.
Abundance in Group 1: decreased abundance in Infants with diarrhea - Timepoint 2
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 2G-H, 3F-G
Description: Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 2.
Abundance in Group 1: increased abundance in Infants with diarrhea - Timepoint 2
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridium perfringens | ||
| Klebsiella | ||
| Shigella | ||
| Shigella flexneri |
Revision editor(s): KateRasheed
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants without diarrhea - Timepoint 3
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Infants with diarrhea - Timepoint 3
Lab analysis
Statistical Analysis
Signature 1
Source: Fig. 2G-H, 3G
Description: Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 3
Abundance in Group 1: increased abundance in Infants with diarrhea - Timepoint 3
| NCBI | Quality Control | Links |
|---|---|---|
| Shigella | ||
| Klebsiella | ||
| Clostridium perfringens |
Revision editor(s): KateRasheed
Signature 2
Source: Fig. 2F, 3F
Description: Bacterial genera differentially abundant between infants with diarrheal illness and infants without diarrheal illness at time point 3.
Abundance in Group 1: decreased abundance in Infants with diarrhea - Timepoint 3
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Shigella flexneri |
Revision editor(s): KateRasheed
