Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods

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Needs review
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Eun CS, Kim BK, Han DS, Kim SY, Kim KM, Choi BY, Song KS, Kim YS, Kim JF
Journal
Helicobacter
Year
2014
Keywords:
16S ribosomal RNA, H. pylori, carcinogenesis, gastric cancer
BACKGROUND: Helicobacter pylori (H. pylori) infection plays an important role in the early stage of cancer development. However, various bacteria that promote the synthesis of reactive oxygen and nitrogen species may be involved in the later stages. We aimed to determine the microbial composition of gastric mucosa from the patients with chronic gastritis, intestinal metaplasia, and gastric cancer using 454 GS FLX Titanium. METHODS: Gastric mucosal biopsy samples were collected from 31 patients during endoscopy. After the extraction of genomic DNA, variable region V5 of the 16S rRNA gene was amplified. PCR products were sequenced using 454 high-throughput sequencer. The composition, diversity, and richness of microbial communities were compared between three groups. RESULTS: The composition of H. pylori-containing Epsilonproteobacteria class appeared to be the most prevalent, but the relative increase in the Bacilli class in the gastric cancer group was noticed, resulting in a significant difference compared with the chronic gastritis group. By analyzing the Helicobacter-dominant group at a family level, the relative abundance of Helicobacteraceae family was significantly lower in the gastric cancer group compared with chronic gastritis and intestinal metaplasia groups, while the relative abundance of Streptococcaceae family significantly increased. In a UPGMA clustering of Helicobacter-dominant group based on UniFrac distance, the chronic gastritis group and gastric cancer group were clearly separated, while the intestinal metaplasia group was distributed in between the two groups. The evenness and diversity of gastric microbiota in the gastric cancer group was increased compared with other groups. CONCLUSIONS: In Helicobacter predominant patients, the microbial compositions of gastric mucosa from gastric cancer patients are significantly different to chronic gastritis and intestinal metaplasia patients. These alterations of gastric microbial composition may play an important, as-yet-undetermined role in gastric carcinogenesis of Helicobacter predominant patients.

Experiment 1


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Subjects

Location of subjects
South Korea
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
Mucosa of stomach Magenschleimhaut,Gastric mucosa,Gastric mucous membrane,Mucosa of organ of stomach,Mucosa of organ of ventriculus,Mucosa of ventriculus,Mucous membrane of stomach,Mucous membrane of ventriculus,Organ mucosa of stomach,Organ mucosa of ventriculus,Stomach mucosa,Stomach mucosa of organ,Stomach mucous membrane,Stomach organ mucosa,Tunica mucosa (gaster),Tunica mucosa gastricae,Tunica mucosa gastris,Ventriculus mucosa,Ventriculus mucosa of organ,Ventriculus mucous membrane,Ventriculus organ mucosa,Mucosa of 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
chronic gastritis and intestinal metaplasia
Group 1 name Corresponds to the case (exposed) group for case-control studies
gastric cancer
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
diagnosis confirmed by hisotpathology
Group 0 sample size Number of subjects in the control (unexposed) group
21
Group 1 sample size Number of subjects in the case (exposed) group
10
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
V5
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

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)?
No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Needs review

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Supplemental Fig S1, S2

Description: Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer

Abundance in Group 1: increased abundance in gastric cancer

NCBI Quality ControlLinks
Bacilli
Streptococcaceae

Revision editor(s): WikiWorks

Signature 2

Needs review

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Supplemental Fig S1, S2

Description: Relative bacterial abundance of gastric mucosa at the class and family level in Helicobacter-dominant patients with chronic gastritis, intestinal metplasia and gastric cancer

Abundance in Group 1: decreased abundance in gastric cancer

NCBI Quality ControlLinks
Campylobacterota
Helicobacteraceae

Revision editor(s): WikiWorks

Experiment 2


Needs review

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
H. pylori negative
Group 1 name Corresponds to the case (exposed) group for case-control studies
H. pylori postive
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
by conventional laboratory method including rapid urease test and histopathology
Group 0 sample size Number of subjects in the control (unexposed) group
3
Group 1 sample size Number of subjects in the case (exposed) group
7

Lab analysis

Statistical Analysis

Signature 1

Needs review

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Supplemental Fig S3

Description: Comparison of the gastric microbial profiles between H. pylori positive and H. pylori negative chronic gastritis patients

Abundance in Group 1: decreased abundance in H. pylori postive

NCBI Quality ControlLinks
Nitrobacteraceae
Caulobacteraceae
Lactobacillaceae
Burkholderiaceae

Revision editor(s): WikiWorks