Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations
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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
Chang HW, Yan D, Singh R, Bui A, Lee K, Truong A, Milush JM, Somsouk M, Liao W
Journal
JID innovations : skin science from molecules to population health
Year
2022
Keywords:
IBD, inflammatory bowel disease, RNA-seq, RNA sequencing
Psoriasis is a chronic, inflammatory skin disease that affects 2‒3% of the global population. Besides skin manifestations, patients with psoriasis have increased susceptibility to a number of comorbidities, including psoriatic arthritis, cardiovascular disease, and inflammatory bowel disease. To understand the systemic component of psoriasis pathogenesis, we performed a pilot study to examine the fecal metagenome, host colonic transcriptome, and host peripheral blood immune profiles of patients with psoriasis and healthy controls. Our study showed increased functional diversity in the gut microbiome of patients with psoriasis. In addition, we identified microbial species that preferentially associate with patients with psoriasis and which have been previously found to associate with other autoimmune diseases. Intriguingly, our data revealed three psoriasis subgroups that have distinct microbial and host features. Integrating these features revealed host‒microbe associations that are specific to psoriasis or particular psoriasis subgroups. Our findings provide insight into the factors that may affect the development of comorbidities in patients with psoriasis and may hold diagnostic potential for early identification of patients with psoriasis at risk for these comorbidities.
Experiment 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Subjects
- Location of subjects
- United States of America
- 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
- Psoriasis Other and unspecified pityriasis,OTHER PSORIASIS,Other psoriasis and similar disorders,Other psoriasis and similar disorders (disorder),Other psoriasis and similar disorders excluding psoriatic arthropathy,Palmoplantaris Pustulosis,PITYRIASIS NEC & NOS,PSORIAS RELATED DIS NEC,Psoriases,psoriasis,Psoriasis and similar disorders,Psoriasis and similar disorders (disorder),Psoriasis and similar disorders (navigational concept),Psoriasis and similar disorders NOS,Psoriasis and similar disorders NOS (disorder),Pustular Psoriasis of Palms and Soles,PUSTULAR PSORIASIS OF PALMS SOLES,Pustulosis of Palms and Soles,PUSTULOSIS OF PALMS SOLES,Pustulosis Palmaris et Plantaris,Psoriasis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Psoriasis patients (PSO)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Psoriasis had a diagnosis of psoriasis from a physician for at least 6 months before study enrollment and had a normal-appearing lower gastrointestinal endoscopic examination.
- 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
- 33
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 1 month
Lab analysis
- Sequencing type
- WMS
- 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
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
- 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)?
- Yes
- Matched on Factors on which subjects have been matched on in a case-control study
- age, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Confounders controlled for: "experimental batch" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.experimental batch
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Source: Figure 2B and Supplementary Table 1
Description: Differentially abundant microbial species between Psoriasis patients and Healthy controls.
Abundance in Group 1: increased abundance in Psoriasis patients (PSO)
Revision editor(s): MyleeeA, Anne-mariesharp
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Source: Figure 2B and Supplementary Table 1
Description: Differentially abundant microbial species between Psoriasis patients and Healthy controls.
Abundance in Group 1: decreased abundance in Psoriasis patients (PSO)
Revision editor(s): MyleeeA, Anne-mariesharp
Experiment 3
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Psoriasis patients (PSO 1/C1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Psoriasis patients (PSO 2/C2)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Psoriasis patients in subgroup 2
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 9
Lab analysis
Statistical Analysis
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- Matched on Factors on which subjects have been matched on in a case-control study
- Not specified
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Source: Supplementary Table 5
Description: Differentially abundant microbial species between subgroups, Psoriasis (PSO 2/C2) vs Psoriasis (PSO 1/C1) in the cohort.
Abundance in Group 1: increased abundance in Psoriasis patients (PSO 2/C2)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides xylanisolvens |
Revision editor(s): MyleeeA
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Source: Supplementary Table 5
Description: Differentially abundant microbial species between subgroups, Psoriasis (PSO 2/C2) vs Psoriasis (PSO 1/C1) in the cohort.
Abundance in Group 1: decreased abundance in Psoriasis patients (PSO 2/C2)
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus sp. ART55_1 | ||
| Phascolarctobacterium succinatutens | ||
| Segatella copri | ||
| Streptococcus thermophilus | ||
| Turicibacter sanguinis | ||
| unclassified Megamonas | ||
| unclassified Turicibacter |
Revision editor(s): MyleeeA, Anne-mariesharp
Experiment 4
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Psoriasis patients (PSO 3/C3)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Source: Supplementary Table 5
Description: Differentially abundant microbial species between subgroups, Psoriasis (PSO 2/C2) vs Psoriasis (PSO 3/C3) in the cohort.
Abundance in Group 1: decreased abundance in Psoriasis patients (PSO 2/C2)
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus sp. ART55_1 | ||
| Phascolarctobacterium succinatutens | ||
| Streptococcus thermophilus | ||
| Turicibacter sanguinis | ||
| unclassified Megamonas | ||
| unclassified Turicibacter |
Revision editor(s): MyleeeA, Anne-mariesharp
Experiment 5
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Psoriasis patients (PSO 1/C1)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Psoriasis patients (PSO 3/C3)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Psoriasis patients in subgroup 3
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-7-3
Source: Supplementary Table 5
Description: Differentially abundant microbial species between subgroups, Psoriasis (PSO 3/C3) vs Psoriasis (PSO 1/C1) in the cohort.
Abundance in Group 1: decreased abundance in Psoriasis patients (PSO 3/C3)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae bacterium 1_1_57FAA | ||
| Ruminococcaceae bacterium D16 | ||
| Turicibacter sanguinis |
Revision editor(s): MyleeeA, Anne-mariesharp
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