Gut microbiota shifts in patients with gastric cancer in perioperative period

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Liang W, Yang Y, Wang H, Wang H, Yu X, Lu Y, Shen S, Teng L
Journal
Medicine
Year
2019
Gastric cancer (GC) is one of the common malignant tumors in China, with a high morbidity and mortality. With the development and application of high-throughput sequencing technologies and metagenomics, a great quantity of studies have shown that gastrointestinal microbiota is closely related to digestive system diseases. Although some studies have reported the effect of long-term follow-up after subtotal gastrectomy on intestinal flora changes in patients with GC. However, the features of gut microbiota and their shifts in patients with GC in perioperative period remain unclear.This study was designed to characterize fecal microbiota shifts of the patients with GC before and after the radical distal gastrectomy (RDG) during their hospital staying periods. Furthermore, fecal microbiota was also compared between the GC patients and healthy individuals.Patients who were diagnosed with advanced gastric adenocarcinoma at distal stomach were enrolled in the study. The bacterial burden within fecal samples was determined using quantitative polymerase chain reaction. To analyze the diversity and composition of gut microbiota from fecal DNA of 20 GC patients and 22 healthy controls, amplicons of the 16S rRNA gene from all subjects were pyrosequenced. To study gut microbiota shifts, the fecal microbiota from 6 GC patients before and after RDG was detected and subsequently analyzed. Short-chain fatty acids were also detected by chromatography spectrometer in these 6 GC patients.RDG had a moderate effect on bacterial richness and evenness, but had pronounced effects on the composition of postoperative gut microbiota compared with preoperative group. The relative abundances of genera Akkermansia, Esherichia/Shigella, Lactobacillus, and Dialister were significant changed in perioperative period. Remarkably, higher abundances of Escherichia/Shigella, Veillonella, and Clostridium XVIII and lower abundances of Bacteroides were observed in gut microbiota of overall GC patients compared to healthy controls.This study is the first study to characterize the altered gut microbiota within fecal samples from GC patients during perioperative period, and provide a new insights on such microbial perturbations as a potential effector of perioperative period phenotype. Further research must validate these discoveries and may evaluate targeted microbiota shifts to improve outcomes in GC patients.

Experiment 1


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): WikiWorks, Rimsha, Claregrieve1, 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 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
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 cancer patients
Group 0 sample size Number of subjects in the control (unexposed) group
22
Group 1 sample size Number of subjects in the case (exposed) group
20
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
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).
raw counts
Statistical test
T-Test
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
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: Valentina Pineda

Revision editor(s): WikiWorks

Source: Figure 2, Sup. figure 2A, Sup. figure 2B

Description: Comparision of gut microbiota between Gastric Cancer patients and Healthy Controls

Abundance in Group 1: increased abundance in gastric cancer

NCBI Quality ControlLinks
Pseudomonadota
Enterobacteriaceae
Escherichia
Shigella
Clostridium
Veillonella
Gammaproteobacteria
Enterobacterales

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: Valentina Pineda

Revision editor(s): WikiWorks

Source: Figure 2, Sup. figure 2A, Sup. figure 2B

Description: Comparision of gut microbiota between Gastric Cancer patients and Healthy Controls

Abundance in Group 1: decreased abundance in gastric cancer

NCBI Quality ControlLinks
Bacteroidota
Bacteroidaceae
Bacteroides
Bacteroidia
Bacteroidales

Revision editor(s): WikiWorks

Experiment 2


Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: WikiWorks

Revision editor(s): Claregrieve1, WikiWorks, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
healthy gastric cancer (post surgery)
Group 0 sample size Number of subjects in the control (unexposed) group
6

Lab analysis

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
LEfSe
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
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: Valentina Pineda

Revision editor(s): WikiWorks

Source: Figure 5

Description: LEfSe analysis of enriched bacterial taxa in gut microbiota between gastric cancer group and healthy gastric cancer group

Abundance in Group 1: increased abundance in gastric cancer

NCBI Quality ControlLinks
Synergistota
Lachnospiraceae
Klebsiella

Revision editor(s): WikiWorks

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/1

Curated date: 2021/01/10

Curator: Valentina Pineda

Revision editor(s): WikiWorks

Source: Figure 5

Description: LEfSe analysis of enriched bacterial taxa in gut microbiota between gastric cancer group and healthy gastric cancer group

Abundance in Group 1: decreased abundance in gastric cancer

NCBI Quality ControlLinks
Verrucomicrobiia
Verrucomicrobiales
Verrucomicrobiaceae
Verrucomicrobiota
Akkermansia
Shigella
Candidatus Saccharibacteria
Selenomonadales
Negativicutes
Veillonellaceae
Lactobacillaceae
Lactobacillus
Dialister
Prevotellaceae

Revision editor(s): WikiWorks