Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

study design

cross-sectional observational, not case-control

Citation

PMID PubMed identifier for scientific articles.

29102920

DOI Digital object identifier for electronic documents.

10.1136/gutjnl-2017-314205

URI Uniform resource identifier for web resources.

Authors

Ferreira RM, Pereira-Marques J, Pinto-Ribeiro I, Costa JL, Carneiro F, Machado JC, Figueiredo C

Journal

Gut

Year

2018

OBJECTIVE: Gastric carcinoma development is triggered by Helicobacter pylori. Chronic H. pylori infection leads to reduced acid secretion, which may allow the growth of a different gastric bacterial community. This change in the microbiome may increase aggression to the gastric mucosa and contribute to malignancy. Our aim was to evaluate the composition of the gastric microbiota in chronic gastritis and in gastric carcinoma. DESIGN: The gastric microbiota was retrospectively investigated in 54 patients with gastric carcinoma and 81 patients with chronic gastritis by 16S rRNA gene profiling, using next-generation sequencing. Differences in microbial composition of the two patient groups were assessed using linear discriminant analysis effect size. Associations between the most relevant taxa and clinical diagnosis were validated by real-time quantitative PCR. Predictive functional profiling of microbial communities was obtained with PICRUSt. RESULTS: The gastric carcinoma microbiota was characterised by reduced microbial diversity, by decreased abundance of Helicobacter and by the enrichment of other bacterial genera, mostly represented by intestinal commensals. The combination of these taxa into a microbial dysbiosis index revealed that dysbiosis has excellent capacity to discriminate between gastritis and gastric carcinoma. Analysis of the functional features of the microbiota was compatible with the presence of a nitrosating microbial community in carcinoma. The major observations were confirmed in validation cohorts from different geographic origins. CONCLUSIONS: Detailed analysis of the gastric microbiota revealed for the first time that patients with gastric carcinoma exhibit a dysbiotic microbial community with genotoxic potential, which is distinct from that of patients with chronic gastritis.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks

Subjects

Location of subjects: Portugal

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 carcinoma Ca fundus - stomach,cancer of fundus of stomach,cancer of stomach,cancer of the stomach,carcinoma of stomach,carcinoma of the stomach,fundus of stomach cancer,gastric (stomach) cancer,gastric cancer,gastric cancer, NOS,gastric carcinoma,gastric fundus cancer,malignant fundus of stomach neoplasm,malignant neoplasm of fundus of stomach,malignant tumor of fundus of stomach,stomach cancer,stomach carcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: chronic gastritis
Group 1 name Corresponds to the case (exposed) group for case-control studies: gastric carcinoma
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: gastric carcinoma
Group 0 sample size Number of subjects in the control (unexposed) group: 81
Group 1 sample size Number of subjects in the case (exposed) group: 54

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V5-V6

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Ion Torrent

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: 4

Matched on Factors on which subjects have been matched on in a case-control study: age

Alpha Diversity

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

Signature 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3, Figure S4

Description: Differential microbial abundance between chronic gastritis and gastric carcinoma patients by LefSe

Abundance in Group 1: increased abundance in gastric carcinoma

NCBI	Links
Achromobacter sp.
Actinomycetota
Burkholderiales
Chryseobacterium sp. ⚠
Citrobacter sp.
Clostridium sp.
Enterobacterales
Enterobacteriaceae
Gammaproteobacteria
Nocardiaceae
Phyllobacterium sp. ⚠
Pseudomonadota
Pseudomonas sp. ⚠
Rhodococcus sp. (in: high G+C Gram-positive bacteria) ⚠
Xanthomonadaceae
Xanthomonadales

Revision editor(s): Claregrieve1, WikiWorks

Signature 2

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Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): Claregrieve1, WikiWorks

Source: Figure 3, Figure S4

Description: Differential microbial abundance between chronic gastritis and gastric carcinoma patients by LefSe

Abundance in Group 1: decreased abundance in gastric carcinoma

NCBI	Links
Bacilli
Bacteroidia
Bacteroidota
Campylobacterales
Campylobacterota
Bacillota
Fusobacteriota
Fusobacteriia
Helicobacter sp.
Helicobacteraceae
Lactobacillales
Neisseria sp.
Neisseriales
Prevotella sp.
Prevotellaceae
Streptococcaceae
Streptococcus sp.
Gemella sp.

Revision editor(s): Claregrieve1, WikiWorks