Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome

From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-2-9
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Nguyen AD, Andréasson K, McMahan ZH, Bukiri H, Howlett N, Lagishetty V, Lee SM, Jacobs JP, Volkmann ER
Journal
Seminars in arthritis and rheumatism
Year
2023
Keywords:
FODMAP diet, Gastrointestinal microbiome, Systemic sclerosis, nutrition
BACKGROUND: Alterations in gastrointestinal (GI) microbial composition have been reported in patients with systemic sclerosis (SSc). However, it is unclear to what degree these alterations and/or dietary changes contribute to the SSc-GI phenotype. OBJECTIVES: Our study aimed to 1) evaluate the relationship between GI microbial composition and SSc-GI symptoms, and 2) compare GI symptoms and GI microbial composition between SSc patients adhering to a low versus non-low fermentable oligosaccharides, disaccharides, monosaccharides, and polyols (FODMAP) diet. METHODS: Adult SSc patients were consecutively recruited to provide stool specimens for bacterial 16S rRNA gene sequencing. Patients completed the UCLA Scleroderma Clinical Trial Consortium Gastrointestinal Tract Instrument (GIT 2.0) and the Diet History Questionnaire (DHQ) II and were classified as adhering to a low or non-low FODMAP diet. GI microbial differences were assessed using three metrics of alpha diversity (species richness, evenness, and phylogenetic diversity), as well as beta diversity (overall microbial composition). Differential abundance analysis was performed to identify specific genera associated with SSc-GI phenotype and low versus non-low FODMAP diet. RESULTS: Of the 66 total SSc patients included, the majority were women (n = 56) with a mean disease duration of 9.6 years. Thirty-five participants completed the DHQ II. Increased severity of GI symptoms (total GIT 2.0 score) was associated with decreased species diversity and differences in GI microbial composition. Specifically, pathobiont genera (e.g., Klebsiella and Enterococcus) were significantly more abundant in patients with increased GI symptom severity. When comparing low (N = 19) versus non-low (N = 16) FODMAP groups, there were no significant differences in GI symptom severity or in alpha and beta diversity. Compared with the low FODMAP group, the non-low FODMAP group had greater abundance of the pathobiont Enterococcus. CONCLUSION: SSc patients reporting more severe GI symptoms exhibited GI microbial dysbiosis characterized by less species diversity and alterations in microbial composition. A low FODMAP diet was not associated with significant alterations in GI microbial composition or reduced SSc-GI symptoms; however, randomized controlled trials are needed to evaluate the impact of specific diets on GI symptoms in SSc.

Experiment 1


Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/09

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Chloe, Tolulopeo, Folakunmi

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

Curated date: 2023/10/09

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Chloe, Tolulopeo

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 ControlLinks
Enterococcus
Klebsiella
Megasphaera
Rhodospirillales

Revision editor(s): Boadiwaa, Chloe, Tolulopeo

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-7

Curated date: 2023/10/09

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Chloe

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 ControlLinks
Coprococcus sp.
Erysipelotrichaceae
Faecalibacterium sp. UBA1819
Hungatella
Oribacterium
Peptoclostridium
Terrisporobacter
Tyzzerella sp.
uncultured Lachnospiraceae bacterium

Revision editor(s): Boadiwaa, Chloe

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/11

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Chloe, Tolulopeo, Folakunmi

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/11

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Chloe, Hodan Issah

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 ControlLinks
Enterococcus
Faecalibacterium sp. UBA1819
Klebsiella
Lactobacillus
Sphingobium

Revision editor(s): Boadiwaa, Chloe, Hodan Issah

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

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

NCBI Quality ControlLinks
Bacteroidales
Catenibacterium
Clostridia
Clostridiales bacterium
Clostridiales bacterium DTU089
Clostridium sp. CAG:352
Coprococcus
Coprococcus sp.
Cuneatibacter
Dubosiella
Methanobrevibacter
Mollicutes
Prevotella
Romboutsia
Subdoligranulum
Subdoligranulum sp.
Turicibacter
Tyzzerella
rhinovirus A89
uncultured Defluviitaleaceae bacterium
uncultured Erysipelotrichaceae bacterium
uncultured Haematococcaceae
Christensenellaceae R-7 groupChristensenellaceae R-7 group
Lachnospiraceae NK4B4 groupLachnospiraceae NK4B4 group
Lachnospiraceae ND3007 groupLachnospiraceae ND3007 group
uncultured Oscillospiraceae bacterium

Revision editor(s): Boadiwaa, Chloe, Peace Sandy, Hodan Issah

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/12

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Folakunmi

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/30

Curator: Boadiwaa

Revision editor(s): Boadiwaa

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 ControlLinks
Enterococcus
Clostridiales bacterium DTU089
Veillonella
Lactobacillus
Sphingobium

Revision editor(s): Boadiwaa

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/30

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Idiaru angela

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

NCBI Quality ControlLinks
Adlercreutzia
Anaerotruncus
Bifidobacterium
Christensenella sp.
Christensenellaceae
Clostridiales bacterium
Coprococcus
Coriobacteriales
Holdemania
Intestinibacter
Methanobrevibacter
Oscillospiraceae bacterium
Prevotella
Romboutsia
Ruminiclostridium
Ruminococcus
Candidatus Soleaferrea
Subdoligranulum
Turicibacter
Tyzzerella
uncultured Defluviitaleaceae bacterium
uncultured Lachnospiraceae bacterium
uncultured Oscillospiraceae bacterium
Family XIII AD3011 groupFamily XIII AD3011 group
GCA-900066225GCA-900066225
Family XIIIFamily XIII
Christensenellaceae R-7 groupChristensenellaceae R-7 group
Ruminococcaceae NK4A214 groupRuminococcaceae NK4A214 group
Lachnospiraceae NK4B4 groupLachnospiraceae NK4B4 group
Clostridium

Revision editor(s): Boadiwaa, Idiaru angela

Experiment 4


Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/30

Curator: Boadiwaa

Revision editor(s): Boadiwaa

Differences from previous experiment shown

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

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/30

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Folakunmi

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 ControlLinks
Eggerthella
Enterococcus
Faecalibacterium sp. UBA1819
Hungatella
Lachnoclostridium
Lactobacillus
Lactococcus
Megasphaera
Sphingobium
Escherichia/Shigella sp.

Revision editor(s): Boadiwaa, Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-9

Curated date: 2023/10/30

Curator: Boadiwaa

Revision editor(s): Boadiwaa, Welile

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

NCBI Quality ControlLinks
Coprococcus
Firmicutes bacterium CAG:56
Methanobrevibacter
Romboutsia
Ruminococcus
Subdoligranulum
Turicibacter
uncultured Erysipelotrichaceae bacterium
uncultured Oscillospiraceae bacterium
Lachnospiraceae ND3007 groupLachnospiraceae ND3007 group
Mollicutes RF39Mollicutes RF39
Christensenellaceae bacterium Phil7

Revision editor(s): Boadiwaa, Welile