Altered Gut Microbiome in Patients With Dermatomyositis/Experiment 3
From BugSigDB
Reviewed Marked as Reviewed by Lwaldron on 2024-2-26
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
- 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
- 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
Reviewed Marked as Reviewed by Lwaldron on 2024-2-26
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
