Alterations in the intestinal microbiota of patients with severe and active Graves' orbitopathy: a cross-sectional study

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 9 July 2021
study design
cross-sectional observational, not case-control
Citation
PMID
URI
Authors
Shi TT, Xin Z, Hua L, Zhao RX, Yang YL, Wang H, Zhang S, Liu W, Xie RR
Journal
Journal of endocrinological investigation
Year
2019
BACKGROUND: The intestinal microbiota was linked to autoimmune diseases. Graves' orbitopathy (GO) is an autoimmune disease that is usually associated with Graves' disease. However, information on the microbiome of GO patients is yet lacking. OBJECTIVES: To investigate whether GO patients differ from healthy controls in the fecal microbiota. DESIGN: A cross-sectional study. SETTING: 33 patients with severe and active GO and 32 healthy controls of Han nationality were enrolled between March 2017 and March 2018. METHODS: The Gut microbial communities of the fecal samples of GO patients and healthy controls were analyzed and compared by 16S rRNA gene sequencing. RESULTS: Community diversity (Simpson and Shannon) was significantly reduced in fecal samples from patients with GO as compared to controls (p < 0.05). The similarity observed while assessing the community diversity (PCoA) proposed that the microbiota of patients with GO differ significantly from those of controls (p < 0.05). At the phyla levels, the proportion of Bacteroidetes increased significantly in patients with GO (p < 0.05), while at the genus and species levels, significant differences were observed in the bacterial profiles between the two groups (p < 0.05). LIMITATIONS: Single-centered study design and limited fecal samples. CONCLUSIONS: The present study indicated distinctive features of the gut microbiota in GO patients. The study provided evidence for further exploration in the field of intestinal microbiota with respect to the diagnosis and treatment of GO patients by modifying the microbiota profile.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 16 July 2021

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Fatima, Rimsha

Subjects

Location of subjects Country from which study subjects were recruited
China
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Graves ophthalmopathy Congestive Ophthalmopathy,Dysthyroid Ophthalmopathy,dysthyroid/thyroid-associated orbitopathy (TAO),Edematous Ophthalmopathy,Graves' ophthalmopathy,Graves' orbitopathy,Myopathic Ophthalmopathy,thyroid eye disease (TED),Thyroid-Associated Ophthalmopathies,Thyroid-Associated Ophthalmopathy,Graves ophthalmopathy
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
graves orbitopathy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
The diagnosis of GO was established according to the EUGOGO Guidelines. The active GO was defined by a clinical activity score (CAS)≥3/7, and the severe GO was defined by NOSPECS score≥IV. CT or MRI was used to exclude any orbital space-occupying disease such as tumor or extraocular myositis.
Group 0 sample size Number of subjects in the control (unexposed) group
32
Group 1 sample size Number of subjects in the case (exposed) group
33
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
4 weeks

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
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
Ion Torrent

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
Metastats
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)?
No
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima on 16 July 2021

Curated date: 2020-05-28

Curator: Rimsha Azhar

Revision editor(s): LGeistlinger, WikiWorks743, Fatima, Rimsha

Source: Figure 4a, 4b, 4c

Description: Comparison of the bacterial abundance at the phylum, genus and species levels in patients with graves' orbitopathy and healthy controls

Abundance in Group 1: increased abundance in graves orbitopathy

NCBI Links
Bacteroidetes
Prevotella copri
unclassified Prevotellaceae

Revision editor(s): LGeistlinger, WikiWorks743, Fatima, Rimsha

Signature 2

Reviewed Marked as Reviewed by Fatima on 9 July 2021

Curated date: 2020-05-28

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Fatima, Rimsha

Source: Figure 4a, 4b, 4c

Description: Comparison of the bacterial abundance at the phylum, genus and species levels in patients with graves' orbitopathy and healthy controls

Abundance in Group 1: decreased abundance in graves orbitopathy

NCBI Links
Alistipes shahii
Anaerobutyricum hallii
Anaerostipes
Blautia
Butyricimonas
Collinsella
Eubacterium ventriosum
Firmicutes
Fusicatenibacter
Marseillibacter massiliensis
Phocaeicola massiliensis
Ruminococcus

Revision editor(s): WikiWorks743, Fatima, Rimsha

Experiment 2


Reviewed Marked as Reviewed by Fatima on 9 July 2021

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Fatima

Subjects

Location of subjects Country from which study subjects were recruited
China
Host species Species from which microbiome was sampled (if applicable)
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
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Graves ophthalmopathy Congestive Ophthalmopathy,Dysthyroid Ophthalmopathy,dysthyroid/thyroid-associated orbitopathy (TAO),Edematous Ophthalmopathy,Graves' ophthalmopathy,Graves' orbitopathy,Myopathic Ophthalmopathy,thyroid eye disease (TED),Thyroid-Associated Ophthalmopathies,Thyroid-Associated Ophthalmopathy,Graves ophthalmopathy
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
graves orbitopathy
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
severe and active graves' orbitopathy
Group 0 sample size Number of subjects in the control (unexposed) group
32
Group 1 sample size Number of subjects in the case (exposed) group
33
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
4 weeks

Lab analysis

Sequencing type Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Ion Torrent

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
LEfSe
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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
3
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Fatima on 9 July 2021

Curated date: 2020-05-28

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Fatima

Source: Figure 5b

Description: Difference between the intestinal microbiome of patients with graves' orbitopathy and healthy controls by LEfSE

Abundance in Group 1: increased abundance in graves orbitopathy

NCBI Links
Bacteroidales
Bacteroidetes
Bacteroidia
Prevotella copri
Prevotellaceae

Revision editor(s): WikiWorks743, Fatima

Signature 2

Reviewed Marked as Reviewed by Fatima on 28 July 2021

Curated date: 2020-05-28

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Fatima

Source: Figure 5b

Description: Difference between the intestinal microbiome of patients with graves' orbitopathy and healthy controls by LEfSE

Abundance in Group 1: decreased abundance in graves orbitopathy

NCBI Links
Clostridia
Eubacteriales
Firmicutes
Lachnospiraceae

Revision editor(s): WikiWorks743, Fatima