Duodenal and rectal mucosal microbiota related to small intestinal bacterial overgrowth in diarrhea-predominant irritable bowel syndrome

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31674052

DOI Digital object identifier for electronic documents.

10.1111/jgh.14910

URI Uniform resource identifier for web resources.

Authors

Yang M, Zhang L, Hong G, Li Y, Li G, Qian W, Xiong H, Bai T, Song J, Hou X

Journal

Journal of gastroenterology and hepatology

Year

2020

BACKGROUND AND AIM: Small intestinal bacterial overgrowth (SIBO) has been proposed as an etiologic factor in irritable bowel syndrome, particularly the diarrhea-predominant subtype (IBS-D). We aimed to identify potential intestinal microbial pattern in IBS-D patients with SIBO. METHODS: Diarrhea-predominant irritable bowel syndrome patients fulfilling Rome III criteria were recruited and randomly divided into an exploratory cohort (57 cases) and a validation cohort (20 cases). SIBO was identified according to standard glucose hydrogen breath test. For 16S rRNA gene sequencing, samples of duodenal mucosa, duodenal fluid, rectal mucosa, and fresh feces were collected and performed. The α and β diversity, as well as differences in microbial composition and function, in SIBO+ and SIBO- IBS-D subjects were evaluated. RESULTS: The microbial diversity and composition obviously differed between SIBO+ and SIBO- IBS-D in duodenal and rectal mucosa but not in duodenal fluid and fresh feces. For rectal mucosal microbiota, it displayed markedly reduced aerobe and Gram-negative bacteria and increased facultative anaerobe and Gram-positive bacteria, moreover, altered functions of microbial metabolism in SIBO+ IBS-D. Significantly higher rectal mucosa-related microbial dysbiosis index was observed in SIBO+ IBS-D, and a cut-off value at -0.37 had a sensitivity of 56.55% and specificity of 90.91% to identify the SIBO in IBS-D subjects. CONCLUSIONS: Mucosal microbiota, rather than luminal bacteria, has a more apparent dysbiosis in SIBO+ IBS-D patients relative to those without SIBO. Rectal mucosa-associated microbiota may act as a potential predictor of SIBO in IBS-D patients.

Experiment 1

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Subjects

Location of subjects: 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: Small intestine Anterior intestine,Intestinum tenue,Mid intestine,Small bowel,Small intestine

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: irritable bowel syndrome [X]Psychogenic IBS,Adaptive colitis,Colitides, Mucous,Colitis, Mucous,Colon spasm,Colon, Irritable,Functional bowel disease,IBD,IBS,IBS - Irritable bowel syndrome,IC - Irritable colon,Irritable bowel,Irritable bowel - IBS,irritable bowel syndrome,Irritable Bowel Syndromes,Irritable Colon,irritable colon,Irritable colon (disorder),Irritable colon - Irritable bowel syndrome,Irritable colon syndrome,Membranous colitis,Mucous Colitides,Mucous colitis,mucus colitis,Nervous colitis,Psychogenic IBS,psychogenic IBS,Spastic colitis,Spastic colon,spastic colon,Syndrome, Irritable Bowel,Syndromes, Irritable Bowel

Group 0 name Corresponds to the control (unexposed) group for case-control studies: IBS.sibo-
Group 1 name Corresponds to the case (exposed) group for case-control studies: IBS.sibo+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria with SIBO
Group 0 sample size Number of subjects in the control (unexposed) group: 33
Group 1 sample size Number of subjects in the case (exposed) group: 24
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months; also includes probiotics and proton-pump inhibitors

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

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Source: Figure S3

Description: Enriched genera in duodenal mucosa obtained from LEfSe.

Abundance in Group 1: increased abundance in IBS.sibo+

NCBI	Links
Arthrobacter ⚠
Carnobacterium
Leuconostoc ⚠
Bradyrhizobium ⚠
Nevskia ⚠
Lactococcus
Pseudomonas ⚠

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Source: Figure S3B

Description: Enriched genera in duodenal mucosa obtained from LEfSe.

Abundance in Group 1: decreased abundance in IBS.sibo+

NCBI	Links
Ochrobactrum ⚠
Paenibacillus ⚠
Propionibacterium ⚠
Brevundimonas ⚠
Rhizobium ⚠
Achromobacter
Microbacterium ⚠
Micrococcus
Agrobacterium
Sphingobium ⚠
Brevibacterium ⚠
Streptomyces purpurascens
Sphingobacterium ⚠

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Experiment 2

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Subjects

Location of subjects: 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: Duodenal mucosa Doudenal mucosa,Duodenal mucous membrane,Duodenum mucosa,Mucosa of duodenum,Mucous membrane of duodenum,Duodenal mucosa

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: small intestine enteropathy small bowel enteropathy,small intestine enteropathy

Group 0 name Corresponds to the control (unexposed) group for case-control studies: IBS.sibo-
Group 1 name Corresponds to the case (exposed) group for case-control studies: IBS.sibo+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO
Group 0 sample size Number of subjects in the control (unexposed) group: 33
Group 1 sample size Number of subjects in the case (exposed) group: 24
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months; also includes probiotics and proton-pump inhibitors

Lab analysis

Sequencing type: 16S

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, Confounders controlled for: "Gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Gender, Confounders controlled for: "BMI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.BMI

Alpha Diversity

Chao1 Abundance-based estimator of species richness: increased

Experiment 3

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Subjects

Location of subjects: 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: Mucosa of rectum Mucosa of organ of rectum,Mucous membrane of rectum,Organ mucosa of rectum,Rectal mucosa,Rectal mucous membrane,Rectum mucosa,Rectum mucosa of organ,Rectum mucous membrane,Rectum organ mucosa,Mucosa of rectum

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: small intestine enteropathy small bowel enteropathy,small intestine enteropathy

Group 0 name Corresponds to the control (unexposed) group for case-control studies: IBS.sibo-
Group 1 name Corresponds to the case (exposed) group for case-control studies: IBS.sibo+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO
Group 0 sample size Number of subjects in the control (unexposed) group: 33
Group 1 sample size Number of subjects in the case (exposed) group: 24
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months; also includes probiotics and proton-pump inhibitors

Lab analysis

Sequencing type: 16S

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: LEfSe

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, Confounders controlled for: "Gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Gender, Confounders controlled for: "BMI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.BMI

Alpha Diversity

Chao1 Abundance-based estimator of species richness: decreased

Experiment 4

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Subjects

Location of subjects: 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: Duodenum Proximal intestine,Upper intestine,Duodenum

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: small intestine enteropathy small bowel enteropathy,small intestine enteropathy

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HC.sibo-
Group 1 name Corresponds to the case (exposed) group for case-control studies: HC.sibo+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Healthy controls (no IBS) with SIBO
Group 0 sample size Number of subjects in the control (unexposed) group: 12
Group 1 sample size Number of subjects in the case (exposed) group: 7
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months; also includes probiotics and proton-pump inhibitors

Lab analysis

Sequencing type: 16S

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: Chi-Square

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, Confounders controlled for: "Gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Gender, Confounders controlled for: "BMI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.BMI

Alpha Diversity

Chao1 Abundance-based estimator of species richness: unchanged

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Source: Table S1

Description: Comparisons of microbial composition at the phylum level between SIBO+ and SIBO- IBS-D patients and healthy individuals.

Abundance in Group 1: increased abundance in HC.sibo+

NCBI	Links
Bacteroidota

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Experiment 5

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Subjects

Location of subjects: 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: small intestine enteropathy small bowel enteropathy,small intestine enteropathy

Group 0 name Corresponds to the control (unexposed) group for case-control studies: IBS.sibo-
Group 1 name Corresponds to the case (exposed) group for case-control studies: IBS.sibo+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with typical clinical symptoms and normal colonoscopy presentation fulfilling the Rome III diagnostic criteria; with SIBO
Group 0 sample size Number of subjects in the control (unexposed) group: 33
Group 1 sample size Number of subjects in the case (exposed) group: 24
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months; also includes probiotics and proton-pump inhibitors

Lab analysis

Sequencing type: 16S

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

Statistical Analysis

Statistical test: Chi-Square

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "Age" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Age, Confounders controlled for: "Gender" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.Gender, Confounders controlled for: "BMI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.BMI