Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Zhu X, Hong G, Li Y, Yang P, Cheng M, Zhang L, Li Y, Ji L, Li G, Chen C, Zhong C, Jin Y, Yang M, Xiong H, Qian W, Ding Z, Ning K, Hou X
Journal
Microbiology spectrum
Year
2021
Keywords:
IBS-D, microbial biomarkers, multiple intestinal sites, site-specific microbial patterns
Fecal microbial community could not fully represent the intestinal microbial community. However, most studies analyzing diarrhea-dominant irritable bowel syndrome (IBS-D) were mainly based on fecal samples. We aimed to characterize the IBS-D microbial community patterns using samples at multiple intestinal sites. This study recruited 74 IBS-D patients and 20 healthy controls (HC). 22.34%, 8.51%, 14.89%, and 54.26% of them contributed to one, two, three, and four sites: duodenal mucosa (DM), duodenal lumen (DL), rectal mucosa (RM), and rectal lumen (RL) of intestinal samples, respectively. Then 16S rRNA gene analysis was performed on these 283 samples. The result showed that IBS-D microbial communities have specific patterns at each intestinal site differing from that of HC. Across hosts and sites, Bacillus, Burkholderia, and Faecalibacterium were the representative genera in duodenum of IBS-D, duodenum of HC, and rectum of HC, respectively. Samples from mucosa and lumen in rectum were highly distinguishable, regardless of IBS-D and HC. Additionally, IBS-D patients have lower microbial co-abundance network connectivity. Moreover, RM site-specific biomarker: Bacteroides used alone or together with Prevotella and Oscillospira in RM showed outstanding performance in IBS-D diagnosis. Furthermore, Bacteroides and Prevotella in RM were strongly related to the severity of abdominal pain, abdominal discomfort, and bloating in IBS-D patients. In summary, this study also confirmed fecal microbial community could not fully characterize intestinal microbial communities. Among these site-specific microbial communities, RM microbial community would be more applicable in the diagnosis of IBS-D. IMPORTANCE Microbial community varied from one site to another along the gastrointestinal tract, but current studies about intestinal microbial community in IBS-D were mainly based on fecal samples. Based on 283 intestinal samples collected from DM, DL, RM, and RL of HC and IBS-D, we found different intestinal sites had their site-specific microbial patterns in IBS-D. Notably, RM site-specific microbes Bacteroides, Prevotella, and Oscillospira could be used to discriminate IBS-D from HC accurately. Our findings could help clinicians realize the great potential of the intestinal microbial community in RM for better diagnosis of IBS-D patients.
Experiment 1
Needs review
Subjects
- Location of subjects
- China
- 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
- Duodenal mucosa Doudenal mucosa,Duodenal mucous membrane,Duodenum mucosa,Mucosa of duodenum,Mucous membrane of duodenum,Duodenal mucosa,duodenal mucosa
- 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,Irritable bowel syndrome
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (Duodenal mucosa samples)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-D patients (Duodenal mucosa samples)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with diarrhea-dominant irritable bowel syndrome (IBS-D)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 37
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Within one month before the start of this study
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
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- 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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.5
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Figure 5A
Description: Site-specific biomarkers detected by LEfSe.
Abundance in Group 1: increased abundance in IBS-D patients (Duodenal mucosa samples)
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 5A
Description: Site-specific biomarkers detected by LEfSe.
Abundance in Group 1: decreased abundance in IBS-D patients (Duodenal mucosa samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Achromobacter |
Revision editor(s): Aleru Divine
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Lumen of duodenum Doudenal lumen,Duodenal lumen,Lumen of duodenum,lumen of duodenum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (Duodenal lumen samples)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-D patients (Duodenal lumen samples)
- 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
- 43
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Figure 5A
Description: Site-specific biomarkers detected by LEfSe.
Abundance in Group 1: increased abundance in IBS-D patients (Duodenal lumen samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Bulleidia | ||
| Leptotrichia | ||
| Veillonella | ||
| Rothia |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 5A
Description: Site-specific biomarkers detected by LEfSe.
Abundance in Group 1: decreased abundance in IBS-D patients (Duodenal lumen samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Porphyromonas | ||
| Sphingomonas | ||
| Sphingobium | ||
| Flavobacterium |
Revision editor(s): Aleru Divine
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- 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,mucosa of rectum
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (Rectal mucosa samples)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-D patients (Rectal mucosa samples)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 20
- Group 1 sample size Number of subjects in the case (exposed) group
- 53
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Figure 5A
Description: Site-specific biomarkers detected by LEfSe.
Abundance in Group 1: increased abundance in IBS-D patients (Rectal mucosa samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Enhydrobacter | ||
| Thermus |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 5A
Description: Site-specific biomarkers detected by LEfSe.
Abundance in Group 1: decreased abundance in IBS-D patients (Rectal mucosa samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella | ||
| Paracoccus | ||
| Oscillospira |
Revision editor(s): Aleru Divine
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Rectal lumen Lumen of rectum,Rectal lumen,rectal lumen
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls (Rectal lumen samples)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- IBS-D patients (Rectal lumen samples)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Figure 5A
Description: Site-specific biomarkers detected by LEfSe.
Abundance in Group 1: increased abundance in IBS-D patients (Rectal lumen samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Figure 5A
Description: Site-specific biomarkers detected by LEfSe.
Abundance in Group 1: decreased abundance in IBS-D patients (Rectal lumen samples)
| NCBI | Quality Control | Links |
|---|---|---|
| Faecalibacterium | ||
| Deinococcus |
Revision editor(s): Aleru Divine
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