Long-term follow-up of colorectal cancer screening attendees identifies differences in Phascolarctobacterium spp. using 16S rRNA and metagenome sequencing/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
Subjects
- Location of subjects
- Norway
- 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
- Colorectal adenoma adenoma of large bowel,adenoma of large intestine,adenoma of the large bowel,adenoma of the large intestine,colorectal adenoma,colorectum adenoma,large bowel adenoma,large intestine adenoma,Colorectal adenoma
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- HRA (high-risk adenoma)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals selected from available archive of fresh-frozen stool samples with high-risk adenomas were defined as those presenting with one or more adenomas of ≥10 mm, with high-grade dysplasia or villous components regardless of polyp size, or those with three or more adenomas regardless of size, dysplasia, and villosity.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 53
- Group 1 sample size Number of subjects in the case (exposed) group
- 63
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).
- raw counts
- Statistical test
- Negative Binomial Regression
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, time, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- sex, geographic area
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by Folakunmi on 2024-1-24
Source: Table 2
Description: Differential abundance analyses of taxa and pathways between CRC, HRA, and healthy controls.
Abundance in Group 1: decreased abundance in HRA (high-risk adenoma)
| NCBI | Quality Control | Links |
|---|---|---|
| Azospirillum sp. 47_25 | ||
| Escherichia/Shigella sp. | ||
| Pseudomonadota |
