Compositional changes in fecal microbiota associated with clinical phenotypes and prognosis in Korean patients with inflammatory bowel disease/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26

Curated date: 2023/11/24

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

Subjects

Location of subjects
South Korea
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 control individual
Group 1 name Corresponds to the case (exposed) group for case-control studies
Crohn's disease patient
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with Crohn's disease from 3 different academic hospitals in Korea.
Group 0 sample size Number of subjects in the control (unexposed) group
100
Group 1 sample size Number of subjects in the case (exposed) group
39
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
Patients who used drugs can affect intestinal microbial community, such as probiotics and antibiotics, within a month were excluded.

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
LEfSe
MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
3.0

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26

Curated date: 2023/11/24

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

Source: Figure 4b

Description: Taxa list according to linear discriminate analysis values determined from comparisons between HC and CD patients. HC, healthy control individuals; CD, Crohn’s disease.

Abundance in Group 1: increased abundance in Crohn's disease patient

NCBI Quality ControlLinks
Bifidobacterium dentium
Bilophila wadsworthia
Enterocloster clostridioformis
Escherichia coli
Faecalimonas umbilicata
Lactobacillus gasseri
Leuconostoc lactis
Mediterraneibacter gnavus
Megasphaera elsdenii
Pseudomonas fragi
Streptococcus gallolyticus
Veillonella parvula
Veillonella dispar

Revision editor(s): Yjung24, Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-1-26

Curated date: 2023/11/24

Curator: Yjung24

Revision editor(s): Yjung24, Peace Sandy

Source: Figure 4b

Description: Taxa list according to linear discriminate analysis values determined from comparisons between HC and CD patients. HC, healthy control individuals; CD, Crohn’s disease.

Abundance in Group 1: decreased abundance in Crohn's disease patient

NCBI Quality ControlLinks
Alistipes putredinis
Bifidobacterium pseudolongum
Bifidobacterium pullorum subsp. gallinarum
Collinsella aerofaciens
Dorea longicatena
Faecalibacterium prausnitzii
Holdemanella biformis
Mediterraneibacter faecis
Parabacteroides merdae
Romboutsia timonensis
Roseburia cecicola
Roseburia inulinivorans
Ruminococcus bromii
Subdoligranulum variabile
[Eubacterium] siraeum

Revision editor(s): Yjung24, Peace Sandy