Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis
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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
Authors
Song H, Yoo Y, Hwang J, Na YC, Kim HS
Journal
The Journal of allergy and clinical immunology
Year
2016
Keywords:
Atopic dermatitis, Faecalibacterium prausnitzii, dysbiosis, gut microbiota, microbiome
BACKGROUND: Atopic dermatitis (AD) is a serious global epidemic associated with a modern lifestyle. OBJECTIVE: Although aberrant interactions between gut microbes and the intestinal immune system have been implicated in this skin disease, the nature of the microbiome dysfunction underlying the disease remains unclear. METHODS: The gut microbiome from 132 subjects, including 90 patients with AD, was analyzed by using 16S rRNA gene and metagenome sequence analyses. Reference genomes from the Human Microbiome Project and the KEGG Orthology database were used for metagenome analyses. Short-chain fatty acids in fecal samples were compared by using gas chromatographic-mass spectrometric analyses. RESULTS: We show that enrichment of a subspecies of the major gut species Faecalibacterium prausnitzii is strongly associated with AD. In addition, the AD microbiome was enriched in genes encoding the use of various nutrients that could be released from damaged gut epithelium, reflecting a bloom of auxotrophic bacteria. Fecal samples from patients with AD showed decreased levels of butyrate and propionate, which have anti-inflammatory effects. This is likely a consequence of an intraspecies compositional change in F prausnitzii that reduces the number of high butyrate and propionate producers, including those related to the strain A2-165, a lack of which has been implicated in patients with Crohn disease. CONCLUSIONS: The data suggest that feedback interactions between dysbiosis in F prausnitzii and dysregulation of gut epithelial inflammation might underlie the chronic progression of AD by resulting in impairment of the gut epithelial barrier, which ultimately leads to aberrant TH2-type immune responses to allergens in the skin.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Subjects
- Location of subjects
- South Korea
- 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
- Atopic eczema allergic,allergic dermatitis,allergic form of dermatitis,Atopic Dermatitides,Atopic Dermatitis,Atopic dermatitis,atopic dermatitis and related conditions,Atopic dermatitis and related conditions (disorder),atopic eczema,Atopic Neurodermatitides,Atopic Neurodermatitis,Atopic neurodermatitis,Besnier's prurigo,Dermatitides, Atopic,Dermatitis, Atopic,Disseminated Neurodermatitides,Disseminated Neurodermatitis,eczema,Eczema, Atopic,Eczema, Infantile,eczematous dermatitis,Infantile Eczema,Neurodermatitides, Atopic,Neurodermatitides, Disseminated,Neurodermatitis, Atopic,Neurodermatitis, Disseminated,OTHER ATOPIC DERMATITIS,Other atopic dermatitis and related conditions,Atopic 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
- patient with atopic dermatitis
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- infants (<1 year old) diagnosed with atopic dermatitis based on the SCORAD scoring system
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
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
- Roche454
Statistical Analysis
- Statistical test
- Random Forest Analysis
- 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
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 1, Supplemental Figure E1
Description: Bacterial genera that are distinctive between the AD and the non-AD children age <1 year old
Abundance in Group 1: increased abundance in patient with atopic dermatitis
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus | ||
| Parabacteroides | ||
| Faecalibacterium | ||
| Subdoligranulum | ||
| Lachnobacterium | ||
| Megamonas | ||
| Anaerostipes | ||
| Alistipes |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 1, Supplemental Figure E1
Description: Bacterial genera that are distinctive between the AD and the non-AD children age <1 year old
Abundance in Group 1: decreased abundance in patient with atopic dermatitis
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia | ||
| Shigella | ||
| Enterobacteriaceae |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patient age 1-6 years diagnosed with atopic dermatitis based on the SCORAD scoring system
- 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
- 58
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 1, Supplemental Figure E1
Description: Bacterial genera that are distinctive between the AD and the non-AD children age 1-6 years old
Abundance in Group 1: increased abundance in patient with atopic dermatitis
| NCBI | Quality Control | Links |
|---|---|---|
| Ruminococcus |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 1, Supplemental Figure E1
Description: Bacterial genera that are distinctive between the AD and the non-AD children age 1-6 years old
Abundance in Group 1: decreased abundance in patient with atopic dermatitis
| NCBI | Quality Control | Links |
|---|---|---|
| Turicibacter | ||
| Coprobacillus |
Revision editor(s): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Differences from previous experiment shown
Subjects
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patient age >6 years diagnosed with atopic dermatitis based on the SCORAD scoring system
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 1, Supplemental Figure E1
Description: Bacterial genera that are distinctive between the AD and the non-AD patients age >6 years old
Abundance in Group 1: increased abundance in patient with atopic dermatitis
| NCBI | Quality Control | Links |
|---|---|---|
| Peptostreptococcaceae | ||
| Robinsoniella |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
Source: Figure 1, Supplemental Figure E1
Description: Bacterial genera that are distinctive between the AD and the non-AD patients age >6 years old
Abundance in Group 1: decreased abundance in patient with atopic dermatitis
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerotruncus | ||
| Butyricimonas | ||
| Collinsella | ||
| Coprococcus | ||
| Eubacteriales | ||
| Holdemania | ||
| Oscillospiraceae | ||
| Paraprevotella | ||
| Porphyromonadaceae |
Revision editor(s): Claregrieve1, WikiWorks
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