The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

30619779

DOI Digital object identifier for electronic documents.

10.3389/fcimb.2018.00433

URI Uniform resource identifier for web resources.

Authors

Hu YL, Pang W, Huang Y, Zhang Y, Zhang CJ

Journal

Frontiers in cellular and infection microbiology

Year

2018

Objective: Dysbiosis of gastric microbiota such as Helicobacter pylori plays a significant role in pathogenesis and progression of gastric cancer. Our aim was to evaluate the composition and functional effects of gastric microbiota in superficial gastritis (SG) and advanced gastric adenocarcinoma (GC). Methods: We carried out shotgun metagenomic sequencing on gastric wash samples from 6 patients with GC and 5 patients with SG. The taxonomic composition was profiled using MetaPhlAn2 and functional gene pathway was profiled using HUMAnN2. Differences in microbial composition and pathways between the two patient groups were assessed via LEfSe. Results: The gastric microbiota in GC patients was characterized by reduced species richness, enrichment of 13 bacterial taxa and depletion of 31 taxa (q < 0.05). The most representative taxa which were abundant in GC corresponded to the commensals or opportunistic pathogens that usually colonize the oral cavity, including genera Neisseria, Alloprevotella, and Aggregatibacter, species Streptococcus_mitis_oralis_pneumoniae and strain Porphyromonas_endodontalis.t_GCF_000174815. Each of the three GC-associated genera could separate GC from SG completely. In particular, Sphingobium yanoikuyae, a bacterium capable of degrading carcinogenic compounds, was depleted in GC. Functionally, pathways associated with the biosynthesis of lipopolysaccharide (LPS) and L-arginine were enriched in GC, whereas pathways involved in the fermentation of short chain fatty acids (SCFAs) and branched amino acid metabolism were more abundant in SG. Conclusions: Our results present new alterations in the gastric microbiome in patients with GC from a whole-genome perspective, suggesting that microbiome composition and function can be used for prognosis and diagnosis of GC.

Experiment 1

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Curated date: 2021/01/10

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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 adenocarcinoma adenocarcinoma - stomach,adenocarcinoma of stomach,adenocarcinoma of the stomach,gastric (stomach) adenocarcinoma,gastric adenocarcinoma,STAD,stomach adenocarcinoma

Group 0 name Corresponds to the control (unexposed) group for case-control studies: superficial gastritis (SG)
Group 1 name Corresponds to the case (exposed) group for case-control studies: gastric adenocarcinoma (GC)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: SG patients with mild to moderate epigastric discomfort. The disgnosis of malignancy was based on patological analysis of tissue biopsies
Group 0 sample size Number of subjects in the control (unexposed) group: 5
Group 1 sample size Number of subjects in the case (exposed) group: 6
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: WMS

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

Matched on Factors on which subjects have been matched on in a case-control study: age, sex, body mass index

Alpha Diversity

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

Signature 1

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Curated date: 2020-08-16

Curator: Rimsha Azhar

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Source: Figure 2B

Description: LDA score for differentially abundant taxonomix geatures between GC and SG groups

Abundance in Group 1: increased abundance in gastric adenocarcinoma (GC)

NCBI	Links
Neisseria sicca
Aggregatibacter
Streptococcus mitis
Streptococcus oralis
Streptococcus pneumoniae
Pasteurellaceae
Gammaproteobacteria
Neisseria
Alloprevotella

Revision editor(s): WikiWorks743

Signature 2

Edit History Delete

Mark reviewed

Your review change was submitted

Needs review

Curated date: 2020-08-16

Curator: Rimsha Azhar

Revision editor(s): WikiWorks743

Source: Figure 2B

Description: LDA score for differentially abundant taxonomix geatures between GC and SG groups

Abundance in Group 1: decreased abundance in gastric adenocarcinoma (GC)

NCBI	Links
Alphaproteobacteria
Sphingomonadaceae
Sphingobium ⚠
Sphingobium yanoikuyae ⚠
Blastomonas ⚠
Streptococcus anginosus
Streptococcus cristatus
Streptococcus sanguinis
Rothia mucilaginosa
Bifidobacteriaceae
Actinomyces
Escherichia
Streptococcus australis
Actinomyces graevenitzii
Sphingobium xenophagum ⚠
Lachnospiraceae
Prevotella denticola
Streptococcus parasanguinis

Revision editor(s): WikiWorks743