Alterations of gastric mucosal microbiota across different stomach microhabitats in a cohort of 276 patients with gastric cancer

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Liu X, Shao L, Liu X, Ji F, Mei Y, Cheng Y, Liu F, Yan C, Li L, Ling Z
Journal
EBioMedicine
Year
2019
BACKGROUND: As part of the tumor microenvironment, the gastric microbiota play vital roles in tumor initiation, progression and metastasis, but stomach microhabitats are not always uniform. We aimed to characterize differences of gastric microbiota in stomach microhabitats associated with gastric cancer (GC) development. METHODS: A cohort of 276 GC patients without preoperative chemotherapy was enrolled retrospectively, and 230 normal, 247 peritumoral and 229 tumoral tissues were obtained for gastric microbiota analysis targeting the 16S rRNA gene by MiSeq sequencing. The microbial diversity and composition, bacterial co-occurrence correlations and predictive functional profiles were compared across different microhabitats. FINDINGS: GC-specific stomach microhabitats, not GC stages or types, determine the composition and diversity of the gastric microbiota. Most notably, bacterial richness was decreased in peritumoral and tumoral microhabitats, and the correlation network of abundant gastric bacteria was simplified in tumoral microhabitat. Helicobacter pylori (HP), Prevotella copri and Bacteroides uniformis were significantly decreased, whereas Prevotella melaninogenica, Streptococcus anginosus and Propionibacterium acnes were increased in tumoral microhabitat. Higher HP colonisation influenced the overall structure of the gastric microbiota in normal and peritumoral microhabitats. PiCRUSt analysis revealed that genes associated with nucleotide transport and metabolism and amino acid transport and metabolism were significantly enriched in tumoral microbiota, while gastric acid secretion was significantly higher in HP positive group of the tumoral microbiota. INTERPRETATION: Our present study provided new insights into the roles of gastric microbiota in different stomach microhabitats in gastric carcinogenesis, especially the pathogenesis of HP. FUND: National Natural Science Foundation of China.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
normal tissues
Group 1 name Corresponds to the case (exposed) group for case-control studies
peritumoral tissues
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer
Group 0 sample size Number of subjects in the control (unexposed) group
230
Group 1 sample size Number of subjects in the case (exposed) group
247
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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
sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-04-20

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 2a, 2c, 2f

Description: Comparison of the relative abundance of dominant bacterial taxa at different levels

Abundance in Group 1: increased abundance in peritumoral tissues

NCBI Links
Pseudomonadota
Helicobacteraceae
Halomonadaceae
Streptococcaceae
Veillonellaceae
Shewanellaceae
Lactobacillaceae
Peptostreptococcaceae
Helicobacter
Halomonas
Streptococcus
Shewanella
Lactobacillus
Veillonella
Methylobacterium
Peptostreptococcus
Selenomonas
Aquabacter
Bacteroides fragilis
Akkermansia muciniphila

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-04-20

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 2a, 2c, 2f

Description: Comparison of the relative abundance of dominant bacterial taxa at different levels

Abundance in Group 1: decreased abundance in peritumoral tissues

NCBI Links
Bacillota
Bacteroidota
Acidobacteriota
Fusobacteriota
Chloroflexota
Oscillospiraceae
Enterobacteriaceae
Prevotellaceae
Sphingomonadaceae
Bacteroidaceae
Bacillaceae
Porphyromonadaceae
Prevotella
Sphingomonas
Faecalibacterium
Pseudomonas
Bacteroides
Bacillus
Fusobacterium
Propionibacterium
Corynebacterium
Phascolarctobacterium
Prevotella copri
Bacillus cereus

Revision editor(s): WikiWorks743

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
peritumoral tissues
Group 1 name Corresponds to the case (exposed) group for case-control studies
tumoral tissues
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer
Group 0 sample size Number of subjects in the control (unexposed) group
247
Group 1 sample size Number of subjects in the case (exposed) group
229
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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
sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-04-20

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 2a, 2c, 2f

Description: Comparison of the relative abundance of dominant bacterial taxa at different levels

Abundance in Group 1: increased abundance in tumoral tissues

NCBI Links
Acidobacteriota
Chloroflexota
Enterobacteriaceae
Prevotellaceae
Lachnospiraceae
Azotobacter group
Prevotella
Pseudomonas
Bacillus
Prevotella melaninogenica
Streptococcus anginosus
Propionibacterium
Bacillus cereus

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-04-20

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 2a, 2c, 2f

Description: Comparison of the relative abundance of dominant bacterial taxa at different levels

Abundance in Group 1: decreased abundance in tumoral tissues

NCBI Links
Pseudomonadota
Halomonadaceae
Oscillospiraceae
Sphingobacteriaceae
Shewanellaceae
Porphyromonadaceae
Halomonas
Shewanella
Sphingomonas
Faecalibacterium
Phascolarctobacterium
Helicobacter pylori

Revision editor(s): WikiWorks743

Experiment 3


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
normal tissues
Group 1 name Corresponds to the case (exposed) group for case-control studies
tumoral tissues
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer
Group 0 sample size Number of subjects in the control (unexposed) group
230
Group 1 sample size Number of subjects in the case (exposed) group
229
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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
sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased
Richness Number of species
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-04-20

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 2a, 2c, 2f

Description: Comparison of the relative abundance of dominant bacterial taxa at different levels

Abundance in Group 1: increased abundance in tumoral tissues

NCBI Links
Bacillota
Actinomycetota
Fusobacteriota
Veillonellaceae
Lachnospiraceae
Shewanellaceae
Peptostreptococcaceae
Halomonas
Streptococcus
Shewanella
Lactobacillus
Bacillus
Selenomonas
Fusobacterium
Propionibacterium
Corynebacterium
Prevotella melaninogenica
Streptococcus anginosus
Cutibacterium acnes
Akkermansia muciniphila

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-04-20

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 2a, 2c, 2f

Description: Comparison of the relative abundance of dominant bacterial taxa at different levels

Abundance in Group 1: decreased abundance in tumoral tissues

NCBI Links
Pseudomonadota
Helicobacteraceae
Azotobacter group
Bacteroidaceae
Helicobacter
Sphingomonas
Pseudomonas
Bacteroides
Helicobacter pylori
Prevotella copri
Bacteroides uniformis

Revision editor(s): WikiWorks743

Experiment 4


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
early stage normal
Group 1 name Corresponds to the case (exposed) group for case-control studies
early stage tumor
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer
Group 0 sample size Number of subjects in the control (unexposed) group
112
Group 1 sample size Number of subjects in the case (exposed) group
116
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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
sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Claregrieve1

Source: Figure 4k, 4l, 4m, 4n

Description: Early-stage gastric microbiota between normal and tumor samples

Abundance in Group 1: increased abundance in early stage tumor

NCBI Links
Cutibacterium acnes
Streptococcus anginosus

Revision editor(s): WikiWorks743, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Claregrieve1

Source: Figure 4k, 4l, 4m, 4n

Description: Early-stage gastric microbiota between normal and tumor samples

Abundance in Group 1: decreased abundance in early stage tumor

NCBI Links
Prevotella copri
Sphingomonas yabuuchiae

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 5


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
early stage normal
Group 1 name Corresponds to the case (exposed) group for case-control studies
early stage peritumor
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer
Group 0 sample size Number of subjects in the control (unexposed) group
112
Group 1 sample size Number of subjects in the case (exposed) group
118
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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
sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Claregrieve1

Source: Figure 4k, 4l, 4m, 4n

Description: Early-stage gastric microbiota in normal and peritumor samples

Abundance in Group 1: decreased abundance in early stage peritumor

NCBI Links
Sphingomonas yabuuchiae

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 6


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
late stage normal
Group 1 name Corresponds to the case (exposed) group for case-control studies
late stage tumor
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer
Group 0 sample size Number of subjects in the control (unexposed) group
118
Group 1 sample size Number of subjects in the case (exposed) group
113
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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
sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Claregrieve1

Source: Figure 4k, 4l, 4m, 4n

Description: Late-stage gastric microbiota in normal and tumor samples

Abundance in Group 1: increased abundance in late stage tumor

NCBI Links
Cutibacterium acnes
Streptococcus anginosus

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 8


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
late stage normal
Group 1 name Corresponds to the case (exposed) group for case-control studies
late stage peritumor
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer
Group 0 sample size Number of subjects in the control (unexposed) group
118
Group 1 sample size Number of subjects in the case (exposed) group
129
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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
sex, age

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Claregrieve1

Source: Figure 4k, 4l, 4m, 4n

Description: late-stage gastric microbiota in normal vs peritumor samples

Abundance in Group 1: decreased abundance in late stage peritumor

NCBI Links
Prevotella copri

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 9


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
normal HP-
Group 1 name Corresponds to the case (exposed) group for case-control studies
normal HP+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
normal samples that are H. Pylori positive
Group 0 sample size Number of subjects in the control (unexposed) group
64
Group 1 sample size Number of subjects in the case (exposed) group
166
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
LEfSe
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


Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 5l, Supp FigS9

Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat

Abundance in Group 1: increased abundance in normal HP+

NCBI Links
Burkholderiales
Massilia
Oxalobacteraceae
Bifidobacteriaceae
Bifidobacterium
Bifidobacteriales
Corynebacterium
Corynebacteriaceae
Actinomycetaceae
Actinomyces
Methylobacterium
Methylobacteriaceae
Lachnospiraceae
Sphingomonadales
Sphingomonas
Sphingomonadaceae
Alphaproteobacteria
Streptococcaceae
Streptococcus
Helicobacteraceae
Helicobacter
Campylobacterales
Campylobacterota
Pseudomonadota

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Claregrieve1

Source: Figure 5, Supp FigS9

Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in normal microhabitat

Abundance in Group 1: decreased abundance in normal HP+

NCBI Links
Acidaminococcaceae
Alteromonadales
Betaproteobacteria
Blautia
Clostridia
Dialister
Eubacteriales
Faecalibacterium
Bacillota
Gemmiger
Halomonadaceae
Halomonas
Oceanospirillales
Oscillospiraceae
Phascolarctobacterium
Prevotella
Prevotellaceae
Roseburia
Ruminococcus
Shewanella
Shewanellaceae
Lachnospiraceae incertae sedis

Revision editor(s): WikiWorks743, Claregrieve1

Experiment 10


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
peritumor HP-
Group 1 name Corresponds to the case (exposed) group for case-control studies
peritumor HP+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
peritumor samples that are H. Pylori positive
Group 0 sample size Number of subjects in the control (unexposed) group
65
Group 1 sample size Number of subjects in the case (exposed) group
182
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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


Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743, Claregrieve1

Source: Figure S10

Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat

Abundance in Group 1: increased abundance in peritumor HP+

NCBI Links
Bacillaceae
Bacillales
Bacillus
Campylobacterales
Campylobacterota
Gemella
Helicobacter
Helicobacteraceae
Pseudomonadota
Streptococcaceae
Streptococcus
Bacillales Family X. Incertae Sedis

Revision editor(s): WikiWorks743, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-15

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure S10

Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in peritumor microhabitat

Abundance in Group 1: decreased abundance in peritumor HP+

NCBI Links
Clostridia
Phascolarctobacterium
Acidaminococcaceae
Eubacteriales
Roseburia
Faecalibacterium
Alistipes
Rikenellaceae
Dialister
Oscillospiraceae
Gemmiger
Megamonas
Bacillus
Lactobacillales
Parabacteroides

Revision editor(s): WikiWorks743

Experiment 11


Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Claregrieve1

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
Stomach Anterior intestine,Gaster,Mesenteron,Stomach chamber,Ventriculus,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
Group 0 name Corresponds to the control (unexposed) group for case-control studies
tumor HP-
Group 1 name Corresponds to the case (exposed) group for case-control studies
tumor HP+
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
tumor samples that are H. Pylori positive
Group 0 sample size Number of subjects in the control (unexposed) group
77
Group 1 sample size Number of subjects in the case (exposed) group
152
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

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


Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-29

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure S11

Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat

Abundance in Group 1: increased abundance in tumor HP+

NCBI Links
Staphylococcaceae
Staphylococcus
Bacteroidaceae
Bacteroides
Caulobacterales
Caulobacteraceae
Brevundimonas
Hyphomicrobiales
Alphaproteobacteria
Blautia
Burkholderiales
Massilia
Sphingomonadales
Sphingobacteriaceae
Novosphingobium
Helicobacteraceae
Helicobacter
Campylobacterales
Campylobacterota

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/09/27

Curated date: 2020-05-29

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure S11

Description: Taxonomic difference of gastric mucosal microbiota between histopathological H. pylori (HP+ and HP-) groups of gastric cancer in tumor microhabitat

Abundance in Group 1: decreased abundance in tumor HP+

NCBI Links
Acinetobacter
Moraxellaceae
Ruminococcus
Pseudomonas
Azotobacter group
Pseudomonadales
Betaproteobacteria
Brucellaceae
Sphingomonas
Bifidobacteriales
Bifidobacterium
Bifidobacteriaceae
Pseudomonadota

Revision editor(s): WikiWorks743