Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
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 |
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Enterococcus | ||
Klebsiella | ||
Megasphaera | ||
Rhodospirillales |
Signature 2
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 |
Experiment 2
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Systemic scleroderma diffuse Scleroderma,diffuse sclerosis,Progressive systemic sclerosis,progressive systemic sclerosis,PSS (progressive systemic sclerosis),PSS - Progressive systemic sclerosis,Scleroderma,Scleroderma (& [systemic sclerosis]),Scleroderma syndrome,Scleroderma, diffuse,Scleroderma, Systemic,Scleroderma, systemic,Sclerosis, Systemic,SS - Systemic sclerosis,SSc,SSc, diffuse sclerosis,systemic Scleroderma,systemic scleroderma,Systemic sclerosis,systemic sclerosis,Systemic sclerosis (disorder),Thibierge-Weissenbach syndrome,Systemic scleroderma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Not Applicable
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Systemic Sclerosis patients with increased GIT 2.0 score
- 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, reporting more severe Gastrointestinal Tract symptoms
- Group 0 sample size Number of subjects in the control (unexposed) group
- Not specified
- Group 1 sample size Number of subjects in the case (exposed) group
- 66
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Four weeks, no antibiotics use more than 2 times in the preceding 12 months prior to the stool collection.
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Figure 3
Description: Differential abundance of specific genera based on GIT 2.0 Total Score
Abundance in Group 1: increased abundance in Systemic Sclerosis patients with increased GIT 2.0 score
NCBI | Quality Control | Links |
---|---|---|
Enterococcus | ||
Faecalibacterium sp. UBA1819 | ||
Klebsiella | ||
Lactobacillus | ||
Sphingobium |
Revision editor(s): Boadiwaa, Chloe, Hodan Issah
Signature 2
Curated date: 2023/10/11
Curator: Boadiwaa
Revision editor(s): Boadiwaa, Chloe, Peace Sandy, Hodan Issah
Source: Figure 3
Description: Differential abundance of specific genera based on GIT 2.0 Total Score
Abundance in Group 1: decreased abundance in Systemic Sclerosis patients with increased GIT 2.0 score
Revision editor(s): Boadiwaa, Chloe, Peace Sandy, Hodan Issah
Experiment 3
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Not specified
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Systemic Sclerosis patients with more severe diarrhoea
- 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, reporting more severe diarrhea based on the diarrhea score.
Lab analysis
Statistical Analysis
Alpha Diversity
- 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
Source: Supplemental Figure 1
Description: Differential abundance of specific genera based on symptom score for the diarrhea domain.
Abundance in Group 1: increased abundance in Systemic Sclerosis patients with more severe diarrhoea
NCBI | Quality Control | Links |
---|---|---|
Enterococcus | ||
Clostridiales bacterium DTU089 | ||
Veillonella | ||
Lactobacillus | ||
Sphingobium |
Revision editor(s): Boadiwaa
Signature 2
Source: Supplemental Figure 1
Description: Differential abundance of specific genera based on symptom score for the diarrhea domain.
Abundance in Group 1: decreased abundance in Systemic Sclerosis patients with more severe diarrhoea
Revision editor(s): Boadiwaa, Idiaru angela
Experiment 4
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Systemic Sclerosis patients with worsened social functioning
- 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, reporting worsened social functioning
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- four weeks
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
Signature 1
Source: Supplemental Figure 2
Description: Differential abundance of specific genera based on symptom score for the social functioning domain.
Abundance in Group 1: increased abundance in Systemic Sclerosis patients with worsened social functioning
NCBI | Quality Control | Links |
---|---|---|
Eggerthella | ||
Enterococcus | ||
Faecalibacterium sp. UBA1819 | ||
Hungatella | ||
Lachnoclostridium | ||
Lactobacillus | ||
Lactococcus | ||
Megasphaera | ||
Sphingobium | ||
Escherichia/Shigella sp. |
Signature 2
Source: Supplemental Figure 2
Description: Differential abundance of specific genera based on symptom score for the social functioning domain.
Abundance in Group 1: decreased abundance in Systemic Sclerosis patients with worsened social functioning