Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls

Study information

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30800106

DOI Digital object identifier for electronic documents.

https://doi.org/10.3389/fmicb.2019.00164

URI

Authors

Bodkhe R, Shetty SA, Dhotre DP, Verma AK, Bhatia K, Mishra A, Kaur G, Pande P, Bangarusamy DK, Santosh BP, Perumal RC, Ahuja V, Shouche YS, Makharia GK

Journal

Frontiers in microbiology

Year

2019

Keywords:

H. pylori, butyrate, celiac, duodenal microbiota, gluten, gut microbiota

Recent studies on celiac disease (CeD) have reported alterations in the gut microbiome. Whether this alteration in the microbial community is the cause or effect of the disease is not well understood, especially in adult onset of disease. The first-degree relatives (FDRs) of CeD patients may provide an opportunity to study gut microbiome in pre-disease state as FDRs are genetically susceptible to CeD. By using 16S rRNA gene sequencing, we observed that ecosystem level diversity measures were not significantly different between the disease condition (CeD), pre-disease (FDR) and control subjects. However, differences were observed at the level of amplicon sequence variant (ASV), suggesting alterations in specific ASVs between pre-disease and diseased condition. Duodenal biopsies showed higher differences in ASVs compared to fecal samples indicating larger disruption of the microbiota at the disease site. The duodenal microbiota of FDR was characterized by significant abundance of ASVs belonging to Parvimonas, Granulicatella, Gemella, Bifidobacterium, Anaerostipes, and Actinomyces genera. The duodenal microbiota of CeD was characterized by higher abundance of ASVs from genera Megasphaera and Helicobacter compared to the FDR microbiota. The CeD and FDR fecal microbiota had reduced abundance of ASVs classified as Akkermansia and Dorea when compared to control group microbiota. In addition, predicted functional metagenome showed reduced ability of gluten degradation by CeD fecal microbiota in comparison to FDRs and controls. The findings of the present study demonstrate differences in ASVs and predicts reduced ability of CeD fecal microbiota to degrade gluten compared to the FDR fecal microbiota. Further research is required to investigate the strain level and active functional profiles of FDR and CeD microbiota to better understand the role of gut microbiome in pathophysiology of CeD.

Experiment 1

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Curated date: 2024/03/11

Curator: Olaitan

Revision editor(s): Olaitan, Temi, Scholastica

Subjects

Location of subjects

India

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

Duodenum Proximal intestine,Upper intestine,Duodenum,duodenum

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Celiac disease CD - Celiac disease,CD - Coeliac disease,CELIAC DIS,celiac disease,Celiac disease (disorder),Celiac disease NOS,Celiac disease NOS (disorder),Celiac rickets,Celiac rickets (disorder),Celiac Sprue,celiac sprue,Celiac syndrome,Coeliac disease,coeliac disease,Coeliac disease [Ambiguous],Coeliac disease NOS,Coeliac rickets,Coeliac sprue,Coeliac syndrome,CS - Celiac sprue,CS - Coeliac sprue,Disease, Celiac,Enteropathies, Gluten,Enteropathies, Gluten-Sensitive,Enteropathy, Gluten,Enteropathy, Gluten-Sensitive,Gluten Enteropathies,Gluten enteropathy,Gluten Sensitive Enteropathy,Gluten-Induced Enteropathy,gluten-induced enteropathy,Gluten-induced enteropathy syndrome,Gluten-responsive sprue,Gluten-Sensitive Enteropathies,Gluten-Sensitive Enteropathy,GSE - Gluten-sensitive enteropathy,Idiopathic steatorrhea,idiopathic steatorrhea,Idiopathic steatorrhoea,Non Tropical Sprue,non tropical sprue,Non-tropical sprue,Nontropical Sprue,Sprue,Sprue, Celiac,Sprue, Nontropical,Steatorrhoea - idiopathic,Wheat-sensitive enteropathy,Celiac disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Disease Control (DC)

Group 1 name Corresponds to the case (exposed) group for case-control studies

First-degree relatives (FDRs) of celiac disease (CeD) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD)

Group 0 sample size Number of subjects in the control (unexposed) group

14

Group 1 sample size Number of subjects in the case (exposed) group

13

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

None

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)

0.01

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

Signature 1

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Curator: Temi

Revision editor(s): Temi, Scholastica

Source: Figure 3A

Description: Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) group versus First-degree relatives (FDRs)

Abundance in Group 1: increased abundance in First-degree relatives (FDRs) of celiac disease (CeD) patients

NCBI	Quality Control	Links
Streptococcus
Ruminococcus
Prevotella
Parvimonas
Methanomassiliicoccus
Megasphaera
Lactobacillus
Intestinibacter
Helicobacter
Granulicatella
Gemella
Eubacterium
Catenibacterium
Bifidobacterium
Bacteroides
Anaerostipes
Actinomyces

Revision editor(s): Temi, Scholastica

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Curated date: 2024/03/30

Curator: Temi

Revision editor(s): Temi, Scholastica

Source: Figure 3A

Description: Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) group versus First-degree relatives (FDRs)

Abundance in Group 1: decreased abundance in First-degree relatives (FDRs) of celiac disease (CeD) patients

NCBI	Quality Control	Links
Turicibacter
Streptococcus
Ruminococcus
Moraxella
Methanomassiliicoccus
Lactobacillus
Intestinibacter
Eubacterium
Blautia
Barnesiella

Revision editor(s): Temi, Scholastica

Experiment 2

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Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

First-degree relatives (FDRs) of celiac disease (CeD) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Celiac disease (CeD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients with celiac disease (CeD)

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

16

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Signature 1

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Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 3B

Description: Comparison of differential abundance of microbial ASVs in duodenal microbiota of celiac disease versus disease control (DC) group

Abundance in Group 1: increased abundance in Celiac disease (CeD)

NCBI	Quality Control	Links
Methanomassiliicoccus
Megasphaera
Lactobacillus
Helicobacter
Eubacterium
Catenibacterium
Blautia
Akkermansia

Revision editor(s): Scholastica

Signature 2

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Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 3B

Description: Comparison of differential abundance of microbial ASVs in duodenal microbiota of celiac disease versus disease control (DC) group

Abundance in Group 1: decreased abundance in Celiac disease (CeD)

NCBI	Quality Control	Links
Turicibacter
Streptococcus
Ruminococcus
Parvimonas
Methanomassiliicoccus
Intestinibacter
Granulicatella
Gemella
Eubacterium
Catenibacterium
Bifidobacterium
Anaerostipes
Actinomyces

Revision editor(s): Scholastica

Experiment 3

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Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

Disease Control (DC)

Group 0 sample size Number of subjects in the control (unexposed) group

14

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 3C

Description: Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) versus celiac disease (CeD) patients

Abundance in Group 1: increased abundance in Celiac disease (CeD)

NCBI	Quality Control	Links
Prevotella
Methanomassiliicoccus
Megasphaera
Lactobacillus
Helicobacter
Catenibacterium
Blautia

Revision editor(s): Scholastica

Signature 2

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Curated date: 2024/05/29

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Revision editor(s): Scholastica

Source: Figure 3C

Description: Comparison of differential abundance of microbial ASVs in duodenal microbiota of disease control (DC) versus celiac disease (CeD) patients

Abundance in Group 1: decreased abundance in Celiac disease (CeD)

NCBI	Quality Control	Links
Turicibacter
Ruminococcus
Moraxella
Methanomassiliicoccus
Lactobacillus
Intestinibacter
Eubacterium
Blautia
Barnesiella

Revision editor(s): Scholastica

Experiment 4

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Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

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

Group 1 name Corresponds to the case (exposed) group for case-control studies

First-degree relatives (FDRs) of celiac disease (CeD) patients

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Fecal samples of first-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD)

Group 0 sample size Number of subjects in the control (unexposed) group

23

Group 1 sample size Number of subjects in the case (exposed) group

15

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 5A

Description: Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) group versus First-degree relatives (FDRs)

Abundance in Group 1: increased abundance in First-degree relatives (FDRs) of celiac disease (CeD) patients

NCBI	Quality Control	Links
Methanomassiliicoccus

Revision editor(s): Scholastica

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 5A

Description: Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) group versus First-degree relatives (FDRs)

Abundance in Group 1: decreased abundance in First-degree relatives (FDRs) of celiac disease (CeD) patients

NCBI	Quality Control	Links
Methanomassiliicoccus
Lactobacillus
Haemophilus
Dorea
Akkermansia

Revision editor(s): Scholastica

Experiment 5

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

First-degree relatives (FDRs) of celiac disease (CeD) patients genetically susceptible to celiac disease (CeD)

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 5B

Description: Comparison of differential abundance of microbial ASVs in fecal microbiota of celiac disease versus disease control (DC) group

Abundance in Group 1: increased abundance in First-degree relatives (FDRs) of celiac disease (CeD) patients

NCBI	Quality Control	Links
Methanomassiliicoccus
Lactobacillus

Revision editor(s): Scholastica

Signature 2

EditHistoryDelete

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 5B

Description: Comparison of differential abundance of microbial ASVs in fecal microbiota of celiac disease versus disease control (DC) group

Abundance in Group 1: decreased abundance in First-degree relatives (FDRs) of celiac disease (CeD) patients

NCBI	Quality Control	Links
Pediococcus
Methanomassiliicoccus
Intestinibacter
Dorea
Blautia

Revision editor(s): Scholastica

Experiment 6

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Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies

First-degree relatives (FDRs) of celiac disease (CeD) patients

Group 1 name Corresponds to the case (exposed) group for case-control studies

Celiac disease (CeD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients with celiac disease (CeD)

Group 0 sample size Number of subjects in the control (unexposed) group

15

Group 1 sample size Number of subjects in the case (exposed) group

21

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

unchanged

Signature 1

EditHistoryDelete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 5C

Description: Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) versus celiac disease (CeD) patients

Abundance in Group 1: increased abundance in Celiac disease (CeD)

NCBI	Quality Control	Links
Methanomassiliicoccus
Lactobacillus

Revision editor(s): Scholastica

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2024-5-30

Curated date: 2024/05/29

Curator: Scholastica

Revision editor(s): Scholastica

Source: Figure 5C

Description: Comparison of differential abundance of microbial ASVs in fecal microbiota of disease control (DC) versus celiac disease (CeD) patients

Abundance in Group 1: decreased abundance in Celiac disease (CeD)

NCBI	Quality Control	Links
Prevotella
Methanomassiliicoccus
Lactobacillus
Dorea
Akkermansia

Revision editor(s): Scholastica