Mucosal microbiome dysbiosis in gastric carcinogenesis

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Reviewed Marked as Reviewed by Atrayees on 2023-8-7
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

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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
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
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, Confounders controlled for: "helicobacter pylori" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.helicobacter pylori, sex

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Fatima, Merit, WikiWorks

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

NCBI Quality ControlLinks
Alloprevotella
Catonella
Dialister
Eubacteriaceae
Fusobacterium
Parvimonas
Lactobacillus
Moryella
Peptococcus
Peptostreptococcus
Prevotella
Slackia
Streptococcus
Lactobacillales

Revision editor(s): Fatima, Merit, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
Acinetobacter
Vogesella
Methyloversatilis
Syntrophobacteraceae
Candidatus Portiera

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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

NCBI Quality ControlLinks
Streptococcus
Peptostreptococcus
Gemella
Fusobacterium
Parvimonas
Lactobacillus
Eubacterium
Alloprevotella
Prevotella
Dialister
Slackia
Eubacteriaceae
Peptococcus
Catonella
Moryella

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
Vogesella
Candidatus Portiera

Revision editor(s): WikiWorks

Experiment 3


Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Atrayees

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

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Merit, WikiWorks

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

NCBI Quality ControlLinks
Alloprevotella
Catonella
Dialister
Eubacteriaceae
Eubacterium
Fusobacterium
Gemella
Lactobacillus
Moryella
Parvimonas
Peptococcus
Peptostreptococcus
Prevotella
Slackia
Streptococcus

Revision editor(s): Merit, WikiWorks

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-8-7

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks

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 ControlLinks
Comamonadaceae
Hydrogenophaga
Acinetobacter
Vogesella
Methyloversatilis
Syntrophobacteraceae
Candidatus Portiera

Revision editor(s): WikiWorks