Altered Gut Microbiome in Patients With Dermatomyositis

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-23

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

35615912

DOI Digital object identifier for electronic documents.

10.1002/acr2.11436

URI

https://onlinelibrary.wiley.com/doi/pdf/10.1002/acr2.11436

Authors

Bae SS, Dong TS, Wang J, Lagishetty V, Katzka W, Jacobs JP, Charles-Schoeman C

Journal

ACR open rheumatology

Year

2022

OBJECTIVE: The study objective was to compare the microbial composition of patients with dermatomyositis (DM) and healthy controls (HCs) and determine whether microbial alterations are associated with clinical manifestations of DM. METHODS: The 16S ribosomal RNA gene sequencing was performed on fecal samples from patients with DM and HCs. Microbial composition and diversity were compared between subjects with DM and HCs and in association with several DM-specific clinical variables, including myositis-specific autoantibodies (MSAs). Differentially abundant microbial taxa and genes associated with clinical characteristics were identified, and functional analysis was performed using predicted metagenomics. Dietary intake was assessed using a 24-hour dietary recall. RESULTS: The fecal microbiome of 36 patients with DM and 26 HCs were analyzed. Patients with DM trended toward lower microbial diversity compared with HCs. The higher physician global damage score was significantly correlated with the lower microbial diversity in patients with DM. Patients with interstitial lung disease (ILD)-associated MSA (antisynthetase antibody (ab), anti-melanoma differentiation-associated protein 5 ab, n = 12) had significant differences in microbial composition and lower microbial diversity compared with HCs. Differential abundance testing demonstrated a unique taxonomic signature in the ILD-MSA subgroup, and predictive metagenomics identified functional alterations in a number of metabolic pathways. A significant increase in the relative abundance of Proteobacteria was positively correlated with multiple pathways involved in lipopolysaccharide synthesis and transport in the ILD-MSA group. CONCLUSION: Patients with DM, particularly with ILD-associated MSAs, have lower microbial diversity and a distinct taxonomic composition compared with HCs. Further studies are needed to validate our findings and elucidate specific pathogenetic mechanisms that link the gut microbiome to clinical and pathological features of DM.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-23

Curated date: 2023/03/12

Curator: Merit

Revision editor(s): Merit, Fatima, Claregrieve1, Peace Sandy

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: Dermatomyositis [X]Dermatopolymyositis, unspecified,[X]Dermatopolymyositis, unspecified (disorder),adult dermatomyositis,Adult Type Dermatomyositides,Adult Type Dermatomyositis,Amyopathic dermatomyositis,Dermatomyositides,Dermatomyositides, Adult Type,dermatomyositis,Dermatomyositis (disorder),Dermatomyositis, Adult Type,Dermatomyositis, Childhood Type,Dermatopolymyositides,Dermatopolymyositis,dermatopolymyositis,Dermatopolymyositis, unspecified,Dermatopolymyositis, unspecified (disorder),DM,DM - Dermatomyositis,Polydermatomyositis,Polymyositis Dermatomyositis,Polymyositis with skin involvement,polymyositis with skin involvement,Polymyositis-Dermatomyositides,Polymyositis-Dermatomyositis,Wagner-Unverricht syndrome,Dermatomyositis

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: dermatomyositis - ILD-MSA

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with dermatomyositis - ILD-associated myositis antibodies subgroup

Group 0 sample size Number of subjects in the control (unexposed) group: 26

Group 1 sample size Number of subjects in the case (exposed) group: 12

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-23

Curated date: 2023/03/12

Curator: Merit

Revision editor(s): Merit, Claregrieve1

Source: Text

Description: Differential microbial abundance between healthy controls and ILD-MSA dermatomyositis patients

Abundance in Group 1: increased abundance in dermatomyositis - ILD-MSA

NCBI	Quality Control	Links
Bacteroidaceae

Revision editor(s): Merit, Claregrieve1

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-23

Curated date: 2023/05/23

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Peace Sandy

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: dermatomyositis - Cancer-MSA

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with dermatomyositis - cancer-associated myositis antibodies subgroup

Group 1 sample size Number of subjects in the case (exposed) group: 13

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-23

Curated date: 2023/05/23

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Text

Description: Differential microbial abundance between healthy controls and cancer-MSA dermatomyositis patients

Abundance in Group 1: decreased abundance in dermatomyositis - Cancer-MSA

NCBI	Quality Control	Links
Lachnospiraceae

Revision editor(s): Claregrieve1

Experiment 3

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by Lwaldron on 2024-2-26

Curated date: 2023/12/15

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: dermatomyositis - Cancer-MSA

Group 1 name Corresponds to the case (exposed) group for case-control studies: dermatomyositis - ILD-MSA

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with dermatomyositis - ILD associated myositis antibodies

Group 0 sample size Number of subjects in the control (unexposed) group: 13

Group 1 sample size Number of subjects in the case (exposed) group: 12

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Lwaldron on 2024-2-26

Curated date: 2023/12/15

Curator: Peace Sandy

Revision editor(s): Peace Sandy, Atrayees

Source: Text , Figure 2F-H

Description: Patients with DM with ILD�MSA also had significant depletion of the Christensenellaceae R-7 group (within the Christensenellaceae family), and multiple ASVs within the Ruminococcaceae family (Ruminococcus 1, Ruminococ�caceae UCG-002, and Subdoligranulum) compared with controls and the cancer-MSA group.

Abundance in Group 1: decreased abundance in dermatomyositis - ILD-MSA

NCBI	Quality Control	Links
Christensenellaceae
Oscillospiraceae

Revision editor(s): Peace Sandy, Atrayees