Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors
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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
Sarhadi V, Mathew B, Kokkola A, Karla T, Tikkanen M, Rautelin H, Lahti L, Puolakkainen P, Knuutila S
Journal
Gut pathogens
Year
2021
Keywords:
Diffuse gastric adenocarcinoma, GIST, Gut microbiota, Intestinal gastric adenocarcinoma
BACKGROUND: Gastric adenocarcinoma is associated with H. pylori infection and inflammation that can result in the dysbiosis of gastric microbiota. The association of intestinal microbiota with gastric adenocarcinoma subtypes or with gastric gastrointestinal stromal tumors (GIST) is however not well known. Therefore, we performed 16S rRNA gene sequencing on DNA isolated from stool samples of Finnish patients and controls to study differences in microbiota among different histological subtypes of gastric adenocarcinoma, gastric GIST and healthy controls. RESULTS: We found that gut microbiota alpha diversity was lowest in diffuse adenocarcinoma patients, followed by intestinal type and GIST patients, although the differences were not significant compared to controls. Beta-diversity analysis however showed significant differences in microbiota composition for all subtypes compared to controls. Significantly higher abundance of Enterobacteriaceae was observed in both adenocarcinoma subtypes, whereas lower abundance of Bifidobacteriaceae was seen only in diffuse adenocarcinoma and of Oscillibacter in intestinal adenocarcinoma. Both GIST and adenocarcinoma patients had higher abundance of Enterobacteriaceae and lower abundance of Lactobacillaceae and Oscillibacter while lower abundance of Lachnoclostridium, Bifidobacterium, Parabacteroides and Barnesiella was seen only in the adenocarcinoma patients. CONCLUSIONS: Our analysis shows association of higher Enterobacteriaceae abundance with all types of gastric tumors. Therefore it could be potentially useful as a marker of gastric malignancies. Lower gut microbiota diversity might be indicative of poorly differentiated, invasive, advanced or aggressive tumors and could possibly be a prognostic marker for gastric tumors.
Experiment 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Subjects
- Location of subjects
- Finland
- 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 adenocarcinoma adenocarcinoma - stomach,adenocarcinoma of stomach,adenocarcinoma of the stomach,gastric (stomach) adenocarcinoma,gastric adenocarcinoma,STAD,stomach adenocarcinoma,Gastric adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gastric Adenocarcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with gastric adenocarcinoma.
- 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
- 29
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 Months.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Ion Torrent
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- 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
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 2
Description: Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types
Abundance in Group 1: increased abundance in Gastric Adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Barnesiella | ||
| Bifidobacteriaceae | ||
| Bifidobacterium | ||
| Eubacteriaceae | ||
| Parabacteroides | ||
| Lactobacillaceae | ||
| Oscillospiraceae | ||
| Lachnoclostridium | ||
| Oscillibacter |
Revision editor(s): Shulamite
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 2
Description: Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types
Abundance in Group 1: decreased abundance in Gastric Adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): Shulamite
Experiment 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal Gastrointestinal Stromal Tumor colorectal (colon or rectal) gastrointestinal stromal tumor (gist),colorectal gastrointestinal stromal tumor,colorectal gastrointestinal stromal tumor (gist),colorectal gist,Colorectal Gastrointestinal Stromal Tumor,colorectal Gastrointestinal Stromal Tumor
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Gastrointestinal stromal tumors (GIST)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients diagnosed with gastrointestinal stromal tumors.
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 2 and Fig 4
Description: Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types.
Abundance in Group 1: increased abundance in Gastrointestinal stromal tumors (GIST)
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): Shulamite
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 2 and Fig 4
Description: Taxonomic groups with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer types in pair-wise comparison between gastric cancer subgroups and controls.
Abundance in Group 1: decreased abundance in Gastrointestinal stromal tumors (GIST)
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter | ||
| Lactobacillaceae |
Revision editor(s): Shulamite
Experiment 5
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastric adenocarcinoma adenocarcinoma - stomach,adenocarcinoma of stomach,adenocarcinoma of the stomach,gastric (stomach) adenocarcinoma,gastric adenocarcinoma,STAD,stomach adenocarcinoma,Gastric adenocarcinoma
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Diffuse adenocarcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subset of gastric adenocarcinoma patients with diffuse-type tumors.
- Group 1 sample size Number of subjects in the case (exposed) group
- 12
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 Months
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 3
Description: Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroup
Abundance in Group 1: increased abundance in Diffuse adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): Shulamite
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 3
Description: Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups
Abundance in Group 1: decreased abundance in Diffuse adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae |
Revision editor(s): Shulamite
Experiment 7
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Intestinal adenocarcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subset of gastric adenocarcinoma patients with intestinal-type tumors.
- 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
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 3
Description: Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups.
Abundance in Group 1: increased abundance in Intestinal adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Enterobacteriaceae |
Revision editor(s): Shulamite
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 3
Description: Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups
Abundance in Group 1: decreased abundance in Intestinal adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Oscillibacter |
Revision editor(s): Shulamite
Experiment 8
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mixed adenocarcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subset of gastric adenocarcinoma patients with mixed histological features
- Group 1 sample size Number of subjects in the case (exposed) group
- 2
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 3
Description: Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups
Abundance in Group 1: increased abundance in Mixed adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemania |
Revision editor(s): Shulamite
Experiment 9
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Colorectal Gastrointestinal Stromal Tumor colorectal (colon or rectal) gastrointestinal stromal tumor (gist),colorectal gastrointestinal stromal tumor,colorectal gastrointestinal stromal tumor (gist),colorectal gist,Colorectal Gastrointestinal Stromal Tumor,colorectal Gastrointestinal Stromal Tumor
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Gastrointestinal stromal tumors (GIST)
- Group 0 sample size Number of subjects in the control (unexposed) group
- 23
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 3
Description: Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups.
Abundance in Group 1: increased abundance in Mixed adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemania |
Revision editor(s): Shulamite
Experiment 10
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Gastric adenocarcinoma adenocarcinoma - stomach,adenocarcinoma of stomach,adenocarcinoma of the stomach,gastric (stomach) adenocarcinoma,gastric adenocarcinoma,STAD,stomach adenocarcinoma,Gastric adenocarcinoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Intestinal adenocarcinoma
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Subset of gastric adenocarcinoma patients with mixed histological features.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 15
Lab analysis
Statistical Analysis
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-5-1
Source: Table 3
Description: Taxa with significant differences (p ≤ 0.05) in pair-wise comparison of gastric cancer subgroups
Abundance in Group 1: increased abundance in Mixed adenocarcinoma
| NCBI | Quality Control | Links |
|---|---|---|
| Holdemania |
Revision editor(s): Shulamite
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