Mucosa-Associated Microbiota in Gastric Cancer Tissues Compared With Non-cancer Tissues

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Reviewed Marked as Reviewed by Folakunmi on 2024-2-29
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Chen XH, Wang A, Chu AN, Gong YH, Yuan Y
Journal
Frontiers in microbiology
Year
2019
Keywords:
16S rDNA, cancer microenvironment, gastric cancer, microbiota, risk
The link between microbiota and gastric cancer (GC) has attracted widespread attention. However, the phylogenetic profiles of niche-specific microbiota in the tumor microenvironment is still unclear. Here, mucosa-associated microorganisms from 62 pairs of matched GC tissues and adjacent non-cancerous tissues were characterized by 16S rRNA gene sequencing. Functional profiles of the microbiota were predicted using PICRUSt, and a co-occurrence network was constructed to analyze interactions among gastric microbiota. Results demonstrated that mucosa-associated microbiota from cancerous and non-cancerous tissues established micro-ecological systems that differed in composition, structure, interaction networks, and functions. Microbial richness and diversity were increased in cancerous tissues, with the co-occurrence network exhibiting greater complexity compared with that in non-cancerous tissue. The bacterial taxa enriched in the cancer samples were predominantly represented by oral bacteria (such as Peptostreptococcus, Streptococcus, and Fusobacterium), while lactic acid-producing bacteria (such as Lactococcus lactis and Lactobacillus brevis) were more abundant in adjacent non-tumor tissues. Colonization by Helicobacter pylori, which is a GC risk factor, also impacted the structure of the microbiota. Enhanced bacterial purine metabolism, carbohydrate metabolism and denitrification functions were predicted in the cancer associated microbial communities, which was consistent with the increased energy metabolism and concentration of nitrogen-containing compounds in the tumor microenvironment. Furthermore, the microbial co-occurrence networks in cancerous and non-cancerous tissues of GC patients were described for the first time. And differential taxa and functions between the two groups were identified. Changes in the abundance of certain bacterial taxa, especially oral microbiota, may play a role in the maintenance of the local microenvironment, which is associated with the development or progression of GC.

Experiment 1


Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): LGeistlinger, WikiWorks, Folakunmi

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,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,Gastric cancer
Group 0 name Corresponds to the control (unexposed) group for case-control studies
adjacent normal tissue
Group 1 name Corresponds to the case (exposed) group for case-control studies
cancer tissue
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer patients who underwent subtotal gastrectomy
Group 0 sample size Number of subjects in the control (unexposed) group
62
Group 1 sample size Number of subjects in the case (exposed) group
62
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
V4-V5
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
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
3

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2021/01/10

Curator: Valentina Pineda

Revision editor(s): WikiWorks

Source: Figure 3

Description: Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis

Abundance in Group 1: increased abundance in cancer tissue

NCBI Quality ControlLinks
Hyphomicrobiales
Thermoleophilia
Acidobacteriota
Selenomonas
Prevotella
Segatella oris
Lachnoanaerobaculum
Streptococcus
Selenomonadales
Negativicutes
Veillonellaceae
Peptostreptococcus
Lachnospiraceae
Sphingomonas
Actinomycetota
Peptostreptococcaceae
Prevotella denticola
Acinetobacter
Moraxellaceae
Prevotellaceae
Acinetobacter baumannii
Eubacteriales
Clostridia
Bacillaceae
Bacillus
Bacteroidales
Bacteroidia
Bacilli
Bacteroidota
Bacillales
Pseudomonas aeruginosa
Bacillota

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2021/01/10

Curator: Valentina Pineda

Revision editor(s): WikiWorks

Source: Figure3

Description: Differential bacteria between non-cancerous tissues and cancerous tissues in Gastric Cancer Patients by LEfSe analysis

Abundance in Group 1: decreased abundance in cancer tissue

NCBI Quality ControlLinks
Enterobacteriaceae
Enterobacterales
Serratia
Helicobacter pylori
Helicobacteraceae
Helicobacter
Serratia marcescens
Campylobacterales
Campylobacterota
Niveispirillum
Rhodospirillaceae
Rhodospirillales
Levilactobacillus brevis
Lactococcus
Lactococcus lactis
Lysobacterales

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2024/02/29

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
H-pylori sequencing negative
Group 1 name Corresponds to the case (exposed) group for case-control studies
H-pylori sequencing positive
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
H-pylori sequencing positive non-cancerous samples while studying the correlation between non-cancerous tissue microbiota and gastric cancer risk factors
Group 0 sample size Number of subjects in the control (unexposed) group
44
Group 1 sample size Number of subjects in the case (exposed) group
18

Lab analysis

Statistical Analysis

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2024/02/29

Curator: Folakunmi

Revision editor(s): Folakunmi, KateRasheed

Source: supplementary figure 2

Description: Differential bacteria between H.pylori-sequencing positive and H.pylori-sequencing negative non-cancer samples by LEfSe analysis

Abundance in Group 1: increased abundance in H-pylori sequencing positive

NCBI Quality ControlLinks
Actinomyces graevenitzii
Actinomyces naeslundii
Aggregatibacter
Alishewanella
Alteromonadaceae
Atopostipes
Bacilli
Bacillota

Revision editor(s): Folakunmi, KateRasheed

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2024/02/29

Curator: Folakunmi

Revision editor(s): Folakunmi, KateRasheed

Source: supplementary figure 2

Description: Differential bacteria between H.pylori-sequencing positive and H.pylori-sequencing negative non-cancer samples by LEfSe analysis

Abundance in Group 1: decreased abundance in H-pylori sequencing positive

NCBI Quality ControlLinks
Gammaproteobacteria
Prevotella intermedia
Prevotellaceae
Pseudomonadaceae
Pseudomonadales
Pseudomonadota
Pseudomonas
Pseudomonas aeruginosa
Sphingomonadaceae

Revision editor(s): Folakunmi, KateRasheed

Experiment 3


Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2024/02/29

Curator: Folakunmi

Revision editor(s): Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
adjacent normal tissue
Group 1 name Corresponds to the case (exposed) group for case-control studies
cancer tissue
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
gastric cancer patients who underwent subtotal gastrectomy
Group 0 sample size Number of subjects in the control (unexposed) group
62
Group 1 sample size Number of subjects in the case (exposed) group
62

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
DESeq2
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
Not specified

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2024/02/29

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: supplementary table S5

Description: Significantly differential bacteria identified among the top 20 abundant genera of the cancer and non-cancer groups

Abundance in Group 1: increased abundance in cancer tissue

NCBI Quality ControlLinks
Acinetobacter
Bacillus
Bacteroides
Sphingomonas
Peptostreptococcus
Streptococcus
Fusobacterium
Prevotella sp.

Revision editor(s): Folakunmi

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-29

Curated date: 2024/02/29

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: supplementary table S5

Description: Significantly differential bacteria identified among the top 20 abundant genera of the cancer and non-cancer groups

Abundance in Group 1: decreased abundance in cancer tissue

NCBI Quality ControlLinks
Helicobacter
Lactobacillus

Revision editor(s): Folakunmi