Gegen Qinlian decoction enhances the effect of PD-1 blockade in colorectal cancer with microsatellite stability by remodelling the gut microbiota and the tumour microenvironment/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/18

Curated date: 2022/09/04

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Claregrieve1, WikiWorks

Subjects

Location of subjects
China
Host species Species from which microbiome was sampled. Contact us to have more species added.
Mus musculus
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
Colorectal cancer cancer of colorectum,cancer of large bowel,cancer of large intestine,cancer of the large bowel,colon cancer,colorectal cancer,colorectum cancer,CRC,large intestine cancer,malignant colorectal neoplasm,malignant colorectal tumor,malignant colorectum neoplasm,malignant large bowel neoplasm,malignant large bowel tumor,malignant large intestine neoplasm,malignant large intestine tumor,malignant neoplasm of colorectum,malignant neoplasm of large bowel,malignant neoplasm of large intestine,malignant neoplasm of the large bowel,malignant neoplasm of the large intestine,malignant tumor of large bowel,malignant tumor of large intestine,malignant tumor of the large bowel,malignant tumor of the large intestine,Colorectal cancer
Group 0 name Corresponds to the control (unexposed) group for case-control studies
non-GQD
Group 1 name Corresponds to the case (exposed) group for case-control studies
low-dose GQD (300 mg/kg)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
BALB/c mice (male, ~20 g, aged 5 weeks) were fed adaptively for 1 week under specific pathogen-free conditions with food and water provided ad libitum. Then the mice were orally lavaged with 300 mg/kg Gegen Qinlian decoction (GQD), a classical traditional Chinese medicine (TCM) formula, once a day for 10 days. The mouse colorectal carcinoma cell line CT26 (~2.5 × 106 cells/mouse) were transplanted subcutaneously into the left axillary region of each mouse and allowed ~1 week to establish tumours.
Group 0 sample size Number of subjects in the control (unexposed) group
20
Group 1 sample size Number of subjects in the case (exposed) group
23

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/18

Curated date: 2022/09/04

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Claregrieve1

Source: Figure 3d

Description: Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on LefSe analysis (LDA > 2)

Abundance in Group 1: increased abundance in low-dose GQD (300 mg/kg)

NCBI Quality ControlLinks
Stoquefichus
Clostridiales bacterium CIEAF 012
Erysipelotrichaceae
Erysipelotrichales
Erysipelotrichia
Ligilactobacillus murinus
Proteus
Proteus mirabilis
[Clostridium] innocuum
unclassified Erysipelotrichaceae
unclassified Parasutterella
uncultured Roseburia sp.

Revision editor(s): Mary Bearkland, Claregrieve1

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2022/11/18

Curated date: 2022/09/04

Curator: Mary Bearkland

Revision editor(s): Mary Bearkland, Claregrieve1

Source: Figure 3D

Description: Differential microbial abundance between the GQD (300 mg/kg) vs. the non-GQD groups based on LefSe analysis (LDA > 2)

Abundance in Group 1: decreased abundance in low-dose GQD (300 mg/kg)

NCBI Quality ControlLinks
uncultured Bacteroidales bacterium
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Peptococcaceae
Bacillales
Staphylococcus
Candidatus Saccharimonas
Candidatus Saccharibacteria
Turicibacter
Tyzzerella
Oscillibacter sp.

Revision editor(s): Mary Bearkland, Claregrieve1