Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic 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
- Finland
- 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
- Eczema Eczema,eczema
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- child with eczema
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- child with eczema
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Human Intestinal Tract Chip
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- ANOVA
- 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
Alpha Diversity
- 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: Table 2
Description: Differences in microbiota of healthy and eczematous children at 18 months of age
Abundance in Group 1: increased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus bromii | ||
| [Clostridium] nexile | ||
| [Ruminococcus] lactaris | ||
| [Clostridium] leptum | ||
| [Clostridium] cellulosi |
Signature 2
Source: Table 2
Description: Differences in microbiota of healthy and eczematous children at 18 months of age
Abundance in Group 1: decreased abundance in child with eczema
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides fragilis | ||
| Bacteroides ovatus | ||
| Phocaeicola plebeius | ||
| Bacteroides stercoris | ||
| Bacteroides uniformis | ||
| Phocaeicola vulgatus | ||
| Alloprevotella tannerae | ||
| Bacteroidota |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Age Age,age
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- infant at 6 months
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- infant at 18 months
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infant 18 months of age
- Group 0 sample size Number of subjects in the control (unexposed) group
- 34
- Group 1 sample size Number of subjects in the case (exposed) group
- 34
Lab analysis
Statistical Analysis
Alpha Diversity
- 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
Curated date: 2021/01/10
Curator: Lucy Mellor
Revision editor(s): WikiWorks, Merit, Folakunmi, Aleru Divine
Source: Figure 1
Description: Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age
Abundance in Group 1: increased abundance in infant at 18 months
| NCBI | Quality Control | Links |
|---|---|---|
| Blautia coccoides |
Revision editor(s): WikiWorks, Merit, Folakunmi, Aleru Divine
Signature 2
Source: Figure 1
Description: Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age
Abundance in Group 1: decreased abundance in infant at 18 months
| NCBI | Quality Control | Links |
|---|---|---|
| Actinomycetota | ||
| Bacilli |
Revision editor(s): WikiWorks
Experiment 3
Subjects
Lab analysis
Statistical Analysis
Alpha Diversity
- 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: Table 1
Description: Genus-like phylogenetic groups changing statistically significantly from 6 to 18 months of age as assessed by HITChip analysis
Abundance in Group 1: increased abundance in infant at 18 months
Signature 2
Source: Table 1
Description: Genus-like phylogenetic groups changing statistically significantly from 6 to 18 months of age as assessed by HITChip analysis
Abundance in Group 1: decreased abundance in infant at 18 months
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacterium | ||
| Lactiplantibacillus plantarum |
Revision editor(s): WikiWorks
Experiment 4
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Lactobacillus rhamnosus GG Lactobacillus rhamnosus ATCC 53103,Lactobacillus rhamnosus str. GG,Lactobacillus rhamnosus strain GG,Lactobacillus rhamnosus GG,lactobacillus rhamnosus GG
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- placebo group at 18 months
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- children supplemented with LGG at 18 months
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- children who have been supplemented with L. rhamnosus GG at the age of 18 months i.e. a year after the cessation of the probiotic supplementation
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
- Group 1 sample size Number of subjects in the case (exposed) group
- 19
Lab analysis
Statistical Analysis
Signature 1
Source: Additional file 9
Description: The microbiota differences between the intervention groups (LGG or placebo) at the age of 18 months as assessed by HITChip analysis.
Abundance in Group 1: increased abundance in children supplemented with LGG at 18 months
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerostipes caccae | ||
| Eubacterium ventriosum |
Revision editor(s): Folakunmi
Signature 2
Source: Additional file 9
Description: The microbiota differences between the intervention groups (LGG or placebo) at the age of 18 months as assessed by HITChip analysis.
Abundance in Group 1: decreased abundance in children supplemented with LGG at 18 months
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides difficile |
Revision editor(s): Folakunmi
