Intestinal Microbiota Is Altered in Patients with Gastric Cancer from Shanxi Province, China

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Qi YF, Sun JN, Ren LF, Cao XL, Dong JH, Tao K, Guan XM, Cui YN, Su W
Journal
Digestive diseases and sciences
Year
2019
Keywords:
Cellular immunity, Gastric cancer, Intestinal microbiota, Shanxi Province
BACKGROUND: Many diseases have been associated with intestinal microbial dysbiosis. Host-microbial interactions regulate immune function, which influences the development of gastric cancer. AIMS: The aims were to investigate the characteristics of intestinal microbiota composition in gastric cancer patients and correlations between the intestinal microbiota and cellular immunity. METHODS: Fecal samples were collected from 116 gastric cancer patients and 88 healthy controls from Shanxi Province, China. The intestinal microbiota was investigated by 16S rRNA gene sequencing. Peripheral blood samples were also collected from the 66 gastric cancer patients and 46 healthy controls. The populations of peripheral T lymphocyte subpopulations and NK cells were analyzed by flow cytometry. RESULTS: The intestinal microbiota in gastric cancer patients was characterized by increased species richness, decreased butyrate-producing bacteria, and the enrichment of other symbiotic bacteria, especially Lactobacillus, Escherichia, and Klebsiella. Lactobacillus and Lachnospira were key species in the network of gastric cancer-associated bacterial genera. The combination of the genera Lachnospira, Lactobacillus, Streptococcus, Veillonella, and Tyzzerella_3 showed good performance in distinguishing gastric cancer patients from healthy controls. There was no significant difference in enterotype distribution between healthy controls and gastric cancer patients. The percentage of CD3+ T cells was positively correlated with the abundance of Lactobacillus and Streptococcus, and CD3+ T cells, CD4+ T cells, and NK cells were associated with Lachnospiraceae taxa. CONCLUSIONS: Our study revealed a dysbiotic intestinal microbiota in gastric cancer patients. The abundance of some intestinal bacterial genera was correlated with the population of peripheral immune cells.

Experiment 1


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

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
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
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
healthy controls
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
gastric carcinoma confirmed by pathological examination
Group 0 sample size Number of subjects in the control (unexposed) group
88
Group 1 sample size Number of subjects in the case (exposed) group
116
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
V3-V4
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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
3.5

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Figure 4

Description: Most differentially abundant taxa between healthy controls and gastric cancer patients

Abundance in Group 1: increased abundance in Gastric cancer

NCBI Quality ControlLinks
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Pseudomonadota
Prevotellaceae
Prevotella
Escherichia
Shigella
Bacilli
Lactobacillales
Klebsiella
Lactobacillaceae
Lactobacillus
Porphyromonadaceae
Streptococcaceae
Streptococcus
Rikenellaceae
Alistipes
Actinomycetes
Actinomycetota
Veillonella
Bifidobacteriales
Bifidobacteriaceae
Bifidobacterium
Christensenella
Christensenellaceae
Parabacteroides

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Figure 4

Description: Most differentially abundant taxa between healthy controls and gastric cancer patients

Abundance in Group 1: decreased abundance in Gastric cancer

NCBI Quality ControlLinks
Eubacteriales
Clostridia
Bacillota
Lachnospiraceae
Faecalibacterium
Agathobacter rectalis CAG:36
Oscillospiraceae
Roseburia
Lachnospira
Lachnoclostridium

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 sample size Number of subjects in the control (unexposed) group
48
Group 1 sample size Number of subjects in the case (exposed) group
48

Lab analysis

Statistical Analysis

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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Supplementary figure 3

Description: Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched

Abundance in Group 1: increased abundance in Gastric cancer

NCBI Quality ControlLinks
Faecalibaculum
Enterobacterales
Enterobacteriaceae
Gammaproteobacteria
Prevotellaceae
Prevotella
Escherichia
Shigella
Bacilli
Lactobacillales
Klebsiella
Streptococcaceae
Streptococcus
Actinomycetes
Actinomycetota
Lactobacillus
Lactobacillaceae
Rikenellaceae
Alistipes
Bifidobacteriales
Bifidobacteriaceae
Bifidobacterium
Veillonella
Christensenellaceae

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09

Curated date: 2021/01/10

Curator: Fatima Zohra

Revision editor(s): WikiWorks

Source: Supplementary figure 3

Description: Most differentially abundant taxa between healthy controls and gastric cancer patients who are age and sex matched

Abundance in Group 1: decreased abundance in Gastric cancer

NCBI Quality ControlLinks
Burkholderiales
Betaproteobacteria
Clostridia
Eubacteriales
Lachnospiraceae
Agathobacter rectalis CAG:36
Roseburia
Lachnospira
Lachnoclostridium

Revision editor(s): WikiWorks