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

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).
relative abundances
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): Khadeeejah, Atrayees, Chloe, 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

NCBI Quality ControlLinks
Micrococcaceae
Campylobacterales
Neisseria
Veillonella parvula
Actinobacillus
Aggregatibacter
Aggregatibacter segnis
Neisseriaceae
Veillonella dispar
Fusobacteriales
Fusobacteriaceae
Burkholderiaceae
Veillonellaceae
Betaproteobacteria
Haemophilus
Haemophilus parainfluenzae
Pasteurellaceae
Enterobacteriaceae

Revision editor(s): Khadeeejah, Atrayees, Chloe, Aiyshaaaa

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-16

Curated date: 2023/03/13

Curator: Khadeeejah

Revision editor(s): Khadeeejah, Aiyshaaaa, Chloe, Atrayees

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

NCBI Quality ControlLinks
Bacillota
Clostridia
Eubacteriales
Lachnospiraceae
Faecalibacterium
Faecalibacterium prausnitzii
Erysipelotrichaceae
Parabacteroides
Porphyromonadaceae
Roseburia
Coprococcus
Blautia
Clostridiaceae
Ruminococcus
Bacteroides uniformis
Eubacterium
Bifidobacterium
Amedibacillus dolichus
Bifidobacteriaceae
Actinomycetota
Holdemanella biformis
Clostridium
Bifidobacterium adolescentis
Coprococcus catus
Verrucomicrobiaceae
Roseburia faecis
Christensenellaceae
Ruminococcus bromii
Akkermansia muciniphila

Revision editor(s): Khadeeejah, Aiyshaaaa, Chloe, Atrayees