Differences in the gut microbiome by physical activity and BMI among colorectal cancer patients/Experiment 4
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-3
Subjects
- Location of subjects
- Germany
- United States of America
- 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
- Body mass index , Physical activity BMI,Quetelet's Index,Body mass index,body mass index,Activities, Locomotor,Activities, Motor,Activities, Physical,Activity, Locomotor,Activity, Motor,Activity, Physical,Locomotor Activities,Locomotor Activity,Motor Activities,Motor Activity,Physical Activities,Physical activity,physical activity
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Normal weight/active patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Normal weight/inactive patients
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patient that has a BMI greater than 18.5 kg/m2 but less than 25 kg/m2 and engaged in little to no physical activity on a regular basis.
- 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
- 33
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 4 weeks
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
- Wald 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)?
- Yes
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, Confounders controlled for: "stage at diagnosis" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.stage at diagnosis, Confounders controlled for: "neoadjuvant treatment" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.neoadjuvant treatment, Confounders controlled for: "study site" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.study site
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- decreased
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-2-4
Source: Table 3
Description: Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in normal weight/ inactive group compared to normal weight/ active group
Abundance in Group 1: decreased abundance in Normal weight/inactive patients
| NCBI | Quality Control | Links |
|---|---|---|
| Succiniclasticum | ||
| Succinivibrio |
Revision editor(s): ChiomaBlessing
Signature 2
Needs review
Source: Table 3
Description: Differential abundance (mean normalized counts) at genus level (by individual BMI and physical activity groups) in normal weight/ inactive group compared to normal weight/ active group
Abundance in Group 1: increased abundance in Normal weight/inactive patients
| NCBI | Quality Control | Links |
|---|---|---|
| Pyramidobacter |
Revision editor(s): ChiomaBlessing
