The biogeography of the mucosa-associated microbiome in health and disease/Experiment 8

From BugSigDB


Reviewed Marked as Reviewed by KateRasheed on 2025-6-5

Curated date: 2025/05/02

Curator: Tosin

Revision editor(s): Tosin

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
Right colon Proximal colon,Right colon,right colon
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 (right colon)
Group 1 name Corresponds to the case (exposed) group for case-control studies
Crohn’s disease (CD) (right colon)
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)
Group 0 sample size Number of subjects in the control (unexposed) group
21
Group 1 sample size Number of subjects in the case (exposed) group
3
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

Reviewed Marked as Reviewed by KateRasheed on 2025-6-5

Curated date: 2025/05/02

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 2A, Supplementary Table 3

Description: Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [right colon (RC) samples]

Abundance in Group 1: increased abundance in Crohn’s disease (CD) (right colon)

NCBI Quality ControlLinks
Anaerococcus
Bilophila
Coprobacter
Moryella
[Ruminococcus] torques

Revision editor(s): Tosin

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-6-5

Curated date: 2025/05/02

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 2A, Supplementary Table 3

Description: Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [right colon (RC) 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 Crohn’s disease (CD) (right colon)

NCBI Quality ControlLinks
Anaerostipes
Faecalibacterium

Revision editor(s): Tosin