Association Between Gut Microbiota and Helicobacter pylori-Related Gastric Lesions in a High-Risk Population of Gastric Cancer
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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.
URI
Authors
Gao JJ, Zhang Y, Gerhard M, Mejias-Luque R, Zhang L, Vieth M, Ma JL, Bajbouj M, Suchanek S, Liu WD, Ulm K, Quante M, Li ZX, Zhou T, Schmid R, Classen M, Li WQ, You WC, Pan KF
Journal
Frontiers in cellular and infection microbiology
Year
2018
Keywords:
16S ribosomal RNA gene sequencing, Helicobacter pylori, gastric lesions, gut microbiota, microbial diversity
Eradication of Helicobacter pylori has been found to be effective for gastric cancer prevention, but uncertainties remain about the possible adverse consequences such as the potential microbial dysbiosis. In our study, we investigated the association between gut microbiota and H. pylori-related gastric lesions in 47 subjects by deep sequencing of microbial 16S ribosomal RNA (rRNA) gene in fecal samples. The dominant phyla in fecal samples were Bacteroidetes, Firmicutes, and Proteobacteria with average relative abundances of 54.77, 31.37 and 12.91%, respectively. Microbial diversity analysis showed that observed species and Shannon index were increased in subjects with past or current H. pylori infection compared with negative subjects. As for the differential bacteria, the average relative abundance of Bacteroidetes was found to significantly decrease from H. pylori negative (66.16%) to past infection group (33.01%, p = 0.007), as well as from normal (76.49%) to gastritis (56.04%) and metaplasia subjects (46.83%, p = 0.027). For Firmicutes and Proteobacteria, the average relative abundances showed elevated trends in the past H. pylori infection group (47.11, 20.53%) compared to negative group (23.44, 9.05%, p = 0.068 and 0.246, respectively), and similar increased trends were also found from normal (18.23, 5.05%) to gastritis (35.31, 7.23%, p = 0.016 and 0.294, respectively) or metaplasia subjects (32.33, 20.07%, both p < 0.05). These findings suggest that the alterations of fecal microbiota, especially the dominant phyla of Bacteroidetes, Firmicutes and Proteobacteria, may be involved in the process of H. pylori-related gastric lesion progression and provide hints for future evaluation of microbial changes after H. pylori eradication.
Experiment 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
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
- 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
- Gastric cancer Ca body - stomach,ca greater curvature of stomach,Ca lesser curvature - stomach,cancer of stomach,gastric cancer,gastric cancer, intestinal,gastric neoplasm,malignant gastric neoplasm,malignant gastric tumor,malignant neoplasm of body of stomach,malignant neoplasm of lesser curve of stomach,malignant neoplasm of stomach,malignant neoplasm of the stomach,malignant stomach neoplasm,malignant tumor of body of stomach,malignant tumor of greater curve of stomach,malignant tumor of lesser curve of stomach,malignant tumor of stomach,malignant tumor of the stomach,stomach cancer,Gastric cancer
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non-current H.pylori infection
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- current H.pylori infection
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- patients with H.pylori infection (bacteria were histologically detected in any one of the biopsies or it was positively indicated by C-UBT)
- 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
- 24
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
- Statistical test
- Welch's T-Test
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure S2D
Description: differential microbial abundance between current or non-current H.Pylori infection subjects
Abundance in Group 1: increased abundance in current H.pylori infection
| NCBI | Quality Control | Links |
|---|---|---|
| Gemella | ||
| unclassified Erysipelotrichaceae |
Revision editor(s): Fatima, Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure S2D
Description: differential microbial abundance between current or non-current H.Pylori infection subjects
Abundance in Group 1: decreased abundance in current H.pylori infection
| NCBI | Quality Control | Links |
|---|---|---|
| Acidovorax | ||
| Acidovorax facilis | ||
| Nocardiaceae | ||
| Rhodococcus | ||
| Rhodococcus erythropolis |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- past H.pylori infection
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- current H.pylori infection patients
- Group 0 sample size Number of subjects in the control (unexposed) group
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure 2D
Description: differential microbial abundance between current and past H.Pylori infection subjects
Abundance in Group 1: increased abundance in current H.pylori infection patients
| NCBI | Quality Control | Links |
|---|---|---|
| Alcaligenaceae | ||
| Bacteroidales | ||
| Bacteroides uniformis | ||
| Bacteroidota | ||
| Bacteroidia | ||
| Betaproteobacteria | ||
| Burkholderiales | ||
| Prevotella | ||
| Segatella copri | ||
| Prevotellaceae | ||
| Sutterella |
Revision editor(s): Fatima, Claregrieve1, WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- H.pylori negative
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- past H.pylori infection
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects with evidence of past H.pylori infection but no current infection
- 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
- 8
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure 2D
Description: differential microbial abundance between past H.Pylori infection subjects and individuals who are H.Pylori negative
Abundance in Group 1: decreased abundance in past H.pylori infection
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroides eggerthii | ||
| Bacteroides fragilis | ||
| Bacteroides uniformis | ||
| Bacteroidota | ||
| Bacteroidia | ||
| Parabacteroides | ||
| Phocaeicola coprocola | ||
| Porphyromonadaceae |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- normal
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- gastritis cases
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects with gastric lesions (gastritis)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure 4
Description: differential microbial abundance between gastritis and non-gastritis (normal) subjects
Abundance in Group 1: increased abundance in gastritis cases
Revision editor(s): Claregrieve1, Rukky, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure 4
Description: differential microbial abundance between gastritis and non-gastritis (normal) subjects
Abundance in Group 1: decreased abundance in gastritis cases
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidota | ||
| Bacteroidia |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 5
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- subjects with metaplasia
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- subjects with metaplasia
- Group 1 sample size Number of subjects in the case (exposed) group
- 22
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure 4
Description: differential microbial abundance between subjects with metaplasia and normal subjects
Abundance in Group 1: increased abundance in subjects with metaplasia
Revision editor(s): Claregrieve1, WikiWorks, Merit
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure 4
Description: differential microbial abundance between subjects with metaplasia and normal subjects
Abundance in Group 1: decreased abundance in subjects with metaplasia
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidales | ||
| Bacteroidota | ||
| Bacteroidia |
Revision editor(s): Claregrieve1, WikiWorks
Experiment 6
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- subjects with gastritis
- Group 0 sample size Number of subjects in the control (unexposed) group
- 18
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure 4
Description: differential microbial abundance between gastritis and metaplastia subjects
Abundance in Group 1: increased abundance in subjects with metaplasia
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacterales | ||
| Enterobacteriaceae | ||
| Gammaproteobacteria | ||
| Pseudomonadota |
Revision editor(s): Claregrieve1, WikiWorks
Signature 2
Reviewed Marked as Reviewed by Claregrieve1 on 2022/07/20
Source: Figure 4
Description: differential microbial abundance between gastritis and metaplastia subjects
Abundance in Group 1: decreased abundance in subjects with metaplasia
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridia | ||
| Clostridiaceae | ||
| Clostridiales bacterium |
Revision editor(s): Claregrieve1, WikiWorks, Merit
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