Fecal microbial dysbiosis in Chinese patients with inflammatory bowel disease/Experiment 1

From BugSigDB


Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Peace Sandy, LGeistlinger

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
Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
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 controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Patients with Crohn's disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with Crohn's disease (11 with as active disease defined by CDAI > 150, 4 with inactive disease)
Group 0 sample size Number of subjects in the control (unexposed) group
29
Group 1 sample size Number of subjects in the case (exposed) group
15
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
3 months

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
Kruskall-Wallis
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)?
Yes
Matched on Factors on which subjects have been matched on in a case-control study
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1, Suwaiba

Source: Table 2

Description: Differential microbial abundance between Crohn's patients and healthy controls

Abundance in Group 1: increased abundance in Patients with Crohn's disease

NCBI Quality ControlLinks
Abiotrophia
Escherichia
Pseudomonadota
Pseudoramibacter
unidentified rumen bacterium RFN20

Revision editor(s): Claregrieve1, Suwaiba

Signature 2

Reviewed Marked as Reviewed by Claregrieve1 on 2023-4-16

Curated date: 2022/10/20

Curator: Claregrieve1

Revision editor(s): Claregrieve1

Source: Table 2

Description: Differential microbial abundance between Crohn's patients and healthy controls

Abundance in Group 1: decreased abundance in Patients with Crohn's disease

NCBI Quality ControlLinks
Butyricicoccus
Mitsuokella
Haemophilus
Victivallis

Revision editor(s): Claregrieve1