Mucosal Microbiome in Patients with Early Bowel Polyps: Inferences from Short-Read and Long-Read 16S rRNA Sequencing/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
Subjects
- Location of subjects
- Australia
- 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
- Colonic mucosa Colon mucosa,Colon mucous membrane,Colonic mucosa,Colonic mucous membrane,Large bowel mucosa,Mucosa of colon,Mucosa of large bowel,colonic mucosa
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Intestinal polyp intestinal polyp,intestinal polyp (disease),Intestinal Polyps,Polyp, Intestinal,Polyps, Intestinal,Intestinal polyp
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Polyp-free control patients
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Patients with low-grade colorectal polyps cohort
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Colorectal polyps were removed as standard clinical care during the colonoscopy procedure. For each polyp removed, two further 2 mm mucosal biopsies 20 mm and 50 mm adjacent to the polyp were collected.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 27
- Group 1 sample size Number of subjects in the case (exposed) group
- 27
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Patients who had taken antibiotics up to four weeks before the colonoscopy.
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
- 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)?
- No
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index, sex
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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 Peace Sandy on 2024-2-3
Source: Figure 7a , 7c
Description: LEfSe differential abundance plot for short-read samples
Abundance in Group 1: increased abundance in Patients with low-grade colorectal polyps cohort
Revision editor(s): Yjung24, Peace Sandy
Signature 2
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-3
Source: Figure 7a , 7c
Description: LEfSe differential abundance plot for short read samples
Abundance in Group 1: decreased abundance in Patients with low-grade colorectal polyps cohort
Revision editor(s): Yjung24, Peace Sandy
