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 (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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Human Intestinal Tract Chip
Statistical Analysis
- 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 | Links |
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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 | Links |
---|---|
Bacteroides fragilis | |
Bacteroides ovatus | |
Phocaeicola plebeius | |
Bacteroides stercoris | |
Bacteroides uniformis | |
Phocaeicola vulgatus | |
Alloprevotella tannerae | |
Bacteroidota |
Revision editor(s): WikiWorks
Experiment 2
Subjects
- Location of subjects
- Finland
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Human Intestinal Tract Chip
Statistical Analysis
- 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: 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 | Links |
---|---|
Clostridiaceae | |
Clostridium | |
Clostridia | |
Clostridiales bacterium |
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 | Links |
---|---|
Actinomycetota | |
Bacilli |
Revision editor(s): WikiWorks
Experiment 3
Subjects
- Location of subjects
- Finland
- 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
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- 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
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Human Intestinal Tract Chip
Statistical Analysis
- Statistical test
- ANOVA
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- 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 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
Revision editor(s): WikiWorks
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 | Links |
---|---|
Bifidobacterium | |
Lactiplantibacillus plantarum |
Revision editor(s): WikiWorks