Relationships between the Microbiome and Response to Neoadjuvant Chemoradiotherapy in Locally Advanced Rectal Cancer/Experiment 3

From BugSigDB


Needs review

Curated date: 2025/05/07

Curator: Tosin

Revision editor(s): Tosin

Subjects

Location of subjects
South Korea
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
Rectum Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum,rectum
Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
Response to platinum-based neoadjuvant chemotherapy Response to platinum-based neoadjuvant chemotherapy,response to platinum-based neoadjuvant chemotherapy
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre-nCRT (Pre-neoadjuvant chemoradiotherapy)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Post-nCRT (Post-neoadjuvant chemoradiotherapy)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients during post-neoadjuvant chemoradiotherapy
Group 0 sample size Number of subjects in the control (unexposed) group
26
Group 1 sample size Number of subjects in the case (exposed) group
26
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

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)
1
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
2

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
decreased
Richness Number of species
decreased

Signature 1

Needs review

Curated date: 2025/05/07

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 3A

Description: Differentially abundant taxa before and after nCRT: red nodes indicate increased abundance post-nCRT; green nodes show decreased abundance

Abundance in Group 1: increased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy)

NCBI Quality ControlLinks
Enterobacterales
Halomonadaceae
Halomonas
Mycobacteriaceae
Mycobacteriales
Mycobacterium
Oceanospirillales
Pseudomonadaceae
Pseudomonadales
Pseudomonas
Thermaceae
Thermales
Thermus

Revision editor(s): Tosin

Signature 2

Needs review

Curated date: 2025/05/07

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 3A

Description: Differentially abundant taxa before and after nCRT (Neo-adjuvant chemoradiotherapy) : red nodes indicate increased abundance post-nCRT (Neo-adjuvant chemoradiotherapy) : green nodes show decreased abundance

Abundance in Group 1: decreased abundance in Post-nCRT (Post-neoadjuvant chemoradiotherapy)

NCBI Quality ControlLinks
Aeromonadaceae
Aeromonadales
Aeromonas
Alloprevotella
Bacteroidaceae
Bacteroidales
Bacteroides
Eubacteriales
Lachnospiraceae
Prevotella
Prevotellaceae

Revision editor(s): Tosin