The treatment-naive microbiome in new-onset Crohn's disease/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Curated date: 2023/03/13
Curator: Khadeeejah
Revision editor(s): Chloe, Claregrieve1, Khadeeejah, Atrayees, Aiyshaaaa, Victoria
Subjects
- Location of subjects
- China
- 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 , Rectum Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,ileum,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
- Healthy control
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Treatment-naive pediatric patients (ages 3-17) with new-onset Crohn's disease
- Group 0 sample size Number of subjects in the control (unexposed) group
- 221
- Group 1 sample size Number of subjects in the case (exposed) group
- 447
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Linear Regression
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, antibiotic exposure, race, sex, Confounders controlled for: "subject" 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.subject, Confounders controlled for: "diagnosis" 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.diagnosis, Confounders controlled for: "ulcering" 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.ulcering, Confounders controlled for: "PCDAI" 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.PCDAI, Confounders controlled for: "biopsy location" 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.biopsy location, Confounders controlled for: "ileal involvement" 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.ileal involvement
Alpha Diversity
- Richness Number of species
- decreased
Signature 1
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Curated date: 2023/03/13
Curator: Khadeeejah
Revision editor(s): Chloe, Khadeeejah, Atrayees, Aiyshaaaa
Source: Table S2A
Description: Alteration in the abundance of several taxa in the ileal and rectal samples, in the diagnosis variable.
Abundance in Group 1: increased abundance in Crohn's disease
Revision editor(s): Chloe, Khadeeejah, Atrayees, Aiyshaaaa
Signature 2
Reviewed Marked as Reviewed by Atrayees on 2023-6-16
Curated date: 2023/03/13
Curator: Khadeeejah
Revision editor(s): Chloe, Khadeeejah, Atrayees, Aiyshaaaa
Source: Table S2A
Description: Alteration in the abundance of several taxa in the ileal and rectal samples, in the diagnosis variable.
Abundance in Group 1: decreased abundance in Crohn's disease
Revision editor(s): Chloe, Khadeeejah, Atrayees, Aiyshaaaa
