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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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Nylund L, Satokari R, Nikkilä J, Rajilić-Stojanović M, Kalliomäki M, Isolauri E, Salminen S, de Vos WM
Journal
BMC microbiology
Year
2013
BACKGROUND: Deviations in composition and diversity of intestinal microbiota in infancy have been associated with both the development and recurrence of atopic eczema. Thus, we decided to use a deep and global microarray-based method to characterize the diversity and temporal changes of the intestinal microbiota in infancy and to define specific bacterial signatures associated with eczema. Faecal microbiota at 6 and 18 months of age were analysed from 34 infants (15 with eczema and 19 healthy controls) selected from a prospective follow-up study based on the availability of faecal samples. The infants were originally randomized to receive either Lactobacillus rhamnosus GG or placebo. RESULTS: Children with eczema harboured a more diverse total microbiota than control subjects as assessed by the Simpson's reciprocal diversity index of the microarray profiles. Composition of the microbiota did not differ between study groups at age of 6 months, but was significantly different at age of 18 months as assessed by MCPP (p=0.01). At this age healthy children harboured 3 -fold greater amount of members of the Bacteroidetes (p=0.01). Microbiota of children suffering from eczema had increased abundance of the Clostridium clusters IV and XIVa, which are typically abundant in adults. Probiotic Lactobacillus rhamnosus GG supplementation in early infancy was observed to have minor long-term effects on the microbiota composition. CONCLUSION: A diverse and adult-type microbiota in early childhood is associated with eczema and it may contribute to the perpetuation of eczema.
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
Needs review
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 |
|---|---|
| Ruminococcus bromii | |
| [Clostridium] nexile | |
| [Ruminococcus] lactaris | |
| [Clostridium] leptum | |
| [Clostridium] cellulosi |
Signature 2
Needs review
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
Needs review
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
Needs review
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
Needs review
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
Needs review
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
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