Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Svetlana up on 2025-3-26

Curated date: 2025/03/24

Curator: Miss Lulu

Revision editor(s): Miss Lulu

Subjects

Location of subjects
Taiwan
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
Treatment outcome measurement Treatment outcome measurement,treatment outcome measurement
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Partial response group- PR
Group 1 name Corresponds to the case (exposed) group for case-control studies
Progressive disease group- PD
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients who had a progressive disease (PD) for at least 12 cycles of therapy
Group 0 sample size Number of subjects in the control (unexposed) group
31
Group 1 sample size Number of subjects in the case (exposed) group
24

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).
raw counts
Statistical test
DESeq2
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

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-26

Curated date: 2025/03/24

Curator: Miss Lulu

Revision editor(s): Miss Lulu

Source: Figure 4A

Description: Results of the log2 fold change in the disease progression and partial response groups

Abundance in Group 1: increased abundance in Progressive disease group- PD

NCBI Quality ControlLinks
Veillonella orientalis
Veillonella nakazawae
Veillonella dispar
Veillonella atypica
Streptococcus sp. HSISS3
Limosilactobacillus vaginalis
Limosilactobacillus mucosae
Ligilactobacillus salivarius
Lactobacillus crispatus
Lacticaseibacillus paracasei
Klebsiella quasipneumoniae
Fusobacterium nucleatum
Bifidobacterium dentium
Bifidobacterium breve
Bifidobacterium bifidum

Revision editor(s): Miss Lulu

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-26

Curated date: 2025/03/24

Curator: Miss Lulu

Revision editor(s): Miss Lulu

Source: Figure 4A

Description: Results of the log2 fold change in the disease progression and partial response groups

Abundance in Group 1: decreased abundance in Progressive disease group- PD

NCBI Quality ControlLinks
Prevotella dentalis
Segatella copri
Phascolarctobacterium sp. Marseille-Q4147
Klebsiella aerogenes
Fusobacterium mortiferum
Desulfovibrio fairfieldensis
Adlercreutzia equolifaciens

Revision editor(s): Miss Lulu