Faecalibacterium prausnitzii subspecies-level dysbiosis in the human gut microbiome underlying atopic dermatitis

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13
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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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 ControlLinks
Ruminococcus
Parabacteroides
Faecalibacterium
Subdoligranulum
Lachnobacterium
Megamonas
Anaerostipes
Alistipes

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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 ControlLinks
Escherichia
Shigella
Enterobacteriaceae

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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 ControlLinks
Ruminococcus

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): WikiWorks

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 ControlLinks
Turicibacter
Coprobacillus

Revision editor(s): WikiWorks

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

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

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Peptostreptococcaceae
Robinsoniella

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/13

Curated date: 2021/01/10

Curator: Lucy Mellor

Revision editor(s): Claregrieve1, WikiWorks

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 ControlLinks
Anaerotruncus
Butyricimonas
Collinsella
Coprococcus
Eubacteriales
Holdemania
Oscillospiraceae
Paraprevotella
Porphyromonadaceae

Revision editor(s): Claregrieve1, WikiWorks