Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
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
- Diet measurement Diet measurement,diet measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Adult Systemic Sclerosis patients on a low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Adult Systemic Sclerosis patients on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Adult patients with Systemic Sclerosis of any duration, as diagnosed according to the 2013 American College of Rheumatology/European League Against Rheumatism Classification Criteria for Systemic Sclerosis, on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 19
- Group 1 sample size Number of subjects in the case (exposed) group
- 16
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- three weeks
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V4-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)
- 0.1
- 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
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-2-7
Source: Figure 4
Description: Differential abundance of specific genera between low versus non-low FODMAP groups.
Abundance in Group 1: increased abundance in Adult Systemic Sclerosis patients on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.
| NCBI | Quality Control | Links |
|---|---|---|
| Enterococcus | ||
| Klebsiella | ||
| Megasphaera | ||
| Rhodospirillales |
Signature 2
Reviewed Marked as Reviewed by Folakunmi on 2024-2-7
Source: Figure 4
Description: Differential abundance of specific genera between low versus non-low FODMAP groups.
Abundance in Group 1: decreased abundance in Adult Systemic Sclerosis patients on a non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet.
| NCBI | Quality Control | Links |
|---|---|---|
| Coprococcus sp. | ||
| Erysipelotrichaceae | ||
| Faecalibacterium sp. UBA1819 | ||
| Hungatella | ||
| Oribacterium | ||
| Peptoclostridium | ||
| Terrisporobacter | ||
| Tyzzerella sp. | ||
| uncultured Lachnospiraceae bacterium |
