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
Coker OO, Dai Z, Nie Y, Zhao G, Cao L, Nakatsu G, Wu WK, Wong SH, Chen Z, Sung JJY, Yu J
Journal
Gut
Year
2018
Keywords:
Gastric cancer, mucosal microbiome dysbiosis, oral bacteria
OBJECTIVES: We aimed to characterise the microbial changes associated with histological stages of gastric tumourigenesis. DESIGN: We performed 16S rRNA gene analysis of gastric mucosal samples from 81 cases including superficial gastritis (SG), atrophic gastritis (AG), intestinal metaplasia (IM) and gastric cancer (GC) from Xi'an, China, to determine mucosal microbiome dysbiosis across stages of GC. We validated the results in mucosal samples of 126 cases from Inner Mongolia, China. RESULTS: We observed significant mucosa microbial dysbiosis in IM and GC subjects, with significant enrichment of 21 and depletion of 10 bacterial taxa in GC compared with SG (q<0.05). Microbial network analysis showed increasing correlation strengths among them with disease progression (p<0.001). Five GC-enriched bacterial taxa whose species identifications correspond to Peptostreptococcus stomatis, Streptococcus anginosus, Parvimonas micra, Slackia exigua and Dialister pneumosintes had significant centralities in the GC ecological network (p<0.05) and classified GC from SG with an area under the receiver-operating curve (AUC) of 0.82. Moreover, stronger interactions among gastric microbes were observed in Helicobacter pylori-negative samples compared with H. pylori-positive samples in SG and IM. The fold changes of selected bacteria, and strengths of their interactions were successfully validated in the Inner Mongolian cohort, in which the five bacterial markers distinguished GC from SG with an AUC of 0.81. CONCLUSIONS: In addition to microbial compositional changes, we identified differences in bacterial interactions across stages of gastric carcinogenesis. The significant enrichments and network centralities suggest potentially important roles of P. stomatis, D. pneumosintes, S. exigua, P. micra and S. anginosus in GC progression.
Experiment 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
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
- Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,Stomach,stomach
- 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
- intestinal metaplasia
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- gastric cancer
- Group 0 sample size Number of subjects in the control (unexposed) group
- 37
- Group 1 sample size Number of subjects in the case (exposed) group
- 17
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
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).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex, Helicobacter pylori
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Source: Supplementary Figure 1
Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer
Abundance in Group 1: increased abundance in gastric cancer
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Source: Supplementary Figure 1
Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer
Abundance in Group 1: decreased abundance in gastric cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Vogesella | ||
| Methyloversatilis | ||
| Syntrophobacteraceae | ||
| Candidatus Portiera |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- atrophic gastric
- Group 1 sample size Number of subjects in the case (exposed) group
- 74
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Source: Supplementary Figure 1
Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer
Abundance in Group 1: increased abundance in gastric cancer
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Source: Supplementary Figure 1
Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer
Abundance in Group 1: decreased abundance in gastric cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Vogesella | ||
| Candidatus Portiera |
Revision editor(s): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- superficial gastric
- Group 1 sample size Number of subjects in the case (exposed) group
- 77
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Source: Supplementary Figure 1
Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer
Abundance in Group 1: increased abundance in gastric cancer
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-8-7
Source: Supplementary Figure 1
Description: The abundance of gastric cancer -enriched and -depleted operational taxonomic units across stages of gastric cancer
Abundance in Group 1: decreased abundance in gastric cancer
| NCBI | Quality Control | Links |
|---|---|---|
| Comamonadaceae | ||
| Hydrogenophaga | ||
| Acinetobacter | ||
| Vogesella | ||
| Methyloversatilis | ||
| Syntrophobacteraceae | ||
| Candidatus Portiera |
Revision editor(s): WikiWorks
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