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

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-29

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

Authors

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

Journal

Frontiers in cellular and infection microbiology

Year

2018

Keywords:

gastric adenocarcinoma, human, inflammation, microbiome, shotgun metagenomics

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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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-29

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Peace Sandy

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 adenocarcinoma adenocarcinoma - stomach,adenocarcinoma of stomach,adenocarcinoma of the stomach,gastric (stomach) adenocarcinoma,gastric adenocarcinoma,STAD,stomach adenocarcinoma,Gastric 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): Use of antibiotics within 6 months

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

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: 2

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

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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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-29

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, Peace Sandy

Source: Figure 2A and Figure 2B

Description: Taxonomic changes in GC microbiome. (A) Cladogram of the gastric microbial taxa associated with GC and SG. GC-enriched taxa are colored in red and SG-enriched taxa are in green. (B) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant taxonomic features between GC and SG groups. Significance obtained by LDA effect size (LEfSe) at p < 0.05 (Kruksal–Wallis test) and LDAscore>2.

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

NCBI	Quality Control	Links
Aggregatibacter
Alloprevotella
Gammaproteobacteria
Neisseria
Neisseria sicca
Pasteurellaceae
Streptococcus mitis
Streptococcus oralis
Streptococcus pneumoniae
Porphyromonas
Porphyromonadaceae
Porphyromonas endodontalis
Aggregatibacter segnis
Neisseriaceae

Revision editor(s): WikiWorks, Peace Sandy

Signature 2

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Reviewed Marked as Reviewed by Peace Sandy on 2024-2-29

Curated date: 2021/01/10

Curator: Rimsha Azhar

Revision editor(s): WikiWorks, Peace Sandy, MyleeeA

Source: Figure 2A and Figure 2B

Description: Taxonomic changes in GC microbiome. (A) Cladogram of the gastric microbial taxa associated with GC and SG. GC-enriched taxa are colored in red and SG-enriched taxa are in green. (B) Histogram of the linear discriminant analysis (LDA) scores for differentially abundant taxonomic features between GC and SG groups. Significance obtained by LDA effect size (LEfSe) at p < 0.05 (Kruksal–Wallis test) and LDAscore>2.

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

NCBI	Quality Control	Links
Actinomyces
Actinomyces graevenitzii
Alphaproteobacteria
Atopobium
Bifidobacteriaceae
Blastomonas
Coriobacteriaceae
Escherichia
Escherichia sp.
Eubacteriales
Lachnospiraceae
Lancefieldella parvula
Oribacterium sinus
Prevotella denticola
Prevotella denticola F0289
Rothia mucilaginosa
Sphingobium
Sphingobium yanoikuyae
Sphingomonadaceae
Streptococcus anginosus
Streptococcus australis
Streptococcus cristatus
Streptococcus parasanguinis
Streptococcus sanguinis
[Eubacterium] infirmum
Sphingobium xenophagum

Revision editor(s): WikiWorks, Peace Sandy, MyleeeA