The biogeography of the mucosa-associated microbiome in health and disease/Experiment 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
- Mucosa of pyloric antrum Antral mucosa,Antrum of stomach mucosa,Antrum of stomach mucosa of organ,Antrum of stomach mucous membrane,Antrum of stomach organ mucosa,Gastric antrum mucosa,Mucosa of antrum of stomach,Mucosa of organ of antrum of stomach,Mucosa of organ of pyloric antrum,Mucosa of organ of stomach pyloric antrum,Mucosa of stomach pyloric antrum,Mucous membrane of antrum of stomach,Mucous membrane of pyloric antrum,Mucous membrane of stomach pyloric antrum,Organ mucosa of antrum of stomach,Organ mucosa of pyloric antrum,Organ mucosa of stomach pyloric antrum,Pyloric antrum mucosa,Pyloric antrum mucosa of organ,Pyloric antrum mucous membrane,Pyloric antrum organ mucosa,Stomach pyloric antrum mucosa,Stomach pyloric antrum mucosa of organ,Stomach pyloric antrum mucous membrane,Stomach pyloric antrum organ mucosa,Mucosa of pyloric antrum,mucosa of pyloric antrum
- 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 (gastric antrum)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Crohn’s disease (CD) (gastric antrum)
- 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
- 32
- Group 1 sample size Number of subjects in the case (exposed) group
- 20
- 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 2A, Supplementary Table 3
Description: Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [gastric antrum (G) 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 Crohn’s disease (CD) (gastric antrum)
NCBI | Quality Control | Links |
---|---|---|
Megasphaera | ||
Neisseriaceae | ||
Tannerella |
Revision editor(s): Tosin
Signature 2
Source: Figure 2A, Supplementary Table 3
Description: Biogeography of significantly enriched and depleted bacterial genera in Crohn’s disease (CD) patients [gastric antrum (G) 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) (gastric antrum)
NCBI | Quality Control | Links |
---|---|---|
Helicobacter |
Revision editor(s): Tosin