The biogeography of the mucosa-associated microbiome in health and disease/Experiment 10
From BugSigDB
Reviewed Marked as Reviewed by KateRasheed on 2025-6-5
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
- Ileum , Right colon , Rectum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum,Proximal colon,Right colon,right colon,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
- Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls (lower gastrointestinal tract)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn’s disease (CD) (lower gastrointestinal tract)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals with the inflammatory bowel disease (IBD), Crohn’s disease (CD) across the lower gastrointestinal tract
- Group 0 sample size Number of subjects in the control (unexposed) group
- 16
- Group 1 sample size Number of subjects in the case (exposed) group
- 10
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 2 months
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V6-V8
- 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).
- arcsine square-root
- Statistical test
- MaAsLin2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "PPI usage" 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.PPI usage, Confounders controlled for: "disease status" 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.disease status
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Reviewed Marked as Reviewed by KateRasheed on 2025-6-5
Source: Figure 3C
Description: Significantly enriched and depleted bacterial genera in the Comparison of the microbiome composition of CD patients and controls, as measured by relative abundance (lower GI tract).
Abundance in Group 1: increased abundance in Crohn’s disease (CD) (lower gastrointestinal tract)
Revision editor(s): Tosin
Signature 2
Reviewed Marked as Reviewed by KateRasheed on 2025-6-5
Source: Figure 3C
Description: Significantly enriched and depleted bacterial genera in the Comparison of the microbiome composition of CD patients and controls, as measured by relative abundance (lower GI tract).
Abundance in Group 1: decreased abundance in Crohn’s disease (CD) (lower gastrointestinal tract)
| NCBI | Quality Control | Links |
|---|---|---|
| uncultured Clostridium sp. | ||
| Adlercreutzia | ||
| Coprococcus | ||
| Phascolarctobacterium | ||
| Christensenellaceae | ||
| Collinsella | ||
| Blautia | ||
| Anaerostipes | ||
| Prevotella | ||
| Subdoligranulum | ||
| Faecalibacterium |
Revision editor(s): Tosin
