The biogeography of the mucosa-associated microbiome in health and disease/Experiment 1
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
- 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
- Ulcerative colitis colitis ulcerative,Colitis, Ulcerative,Left-sided ulcerative (chronic) colitis,Left-sided ulcerative colitis,left-sided ulcerative colitis,Other ulcerative colitis,Other ulcerative colitis (disorder),UC - ulcerative colitis,ulcerative colitis,ulcerative colitis (disease),ulcerative colitis (disorder),Ulcerative colitis, unspecified,ULCERATVE COLITIS UNSPCF,Ulcerative colitis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Controls (rectum)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Ulcerative colitis patients (UC) (rectum)
- 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), Ulcerative colitis patients (UC).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 22
- Group 1 sample size Number of subjects in the case (exposed) group
- 28
- 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
Signature 1
Source: Figure 2B, Supplementary Table 3
Description: Biogeography of significantly enriched and depleted bacterial genera in (ulcerative colitis) UC patients (rectum samples) relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]
Abundance in Group 1: increased abundance in Ulcerative colitis patients (UC) (rectum)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerococcus |
Revision editor(s): Tosin
Signature 2
Source: Figure 2B, Supplementary Table 3
Description: Biogeography of significantly enriched and depleted bacterial genera in (ulcerative colitis) UC patients (rectum samples) relative to controls, across the lower (gastrointestinal) GI tract, measured in terms of relative abundance [upper and lower gastrointestinal (GI) tract]
Abundance in Group 1: decreased abundance in Ulcerative colitis patients (UC) (rectum)
| NCBI | Quality Control | Links |
|---|---|---|
| Phascolarctobacterium | ||
| Prevotella | ||
| Ruminococcus |
Revision editor(s): Tosin
