Targeted Analysis of the Gut Microbiome for Diagnosis, Prognosis and Treatment Individualization in Pediatric Inflammatory Bowel Disease/Experiment 3

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Reviewed Marked as Reviewed by Chloe on 2023-12-14

Curated date: 2023/12/10

Curator: Yjung24

Revision editor(s): Yjung24

Subjects

Location of subjects
Norway
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
Inflammatory bowel disease autoimmune bowel disorder,Bowel Diseases, Inflammatory,IBD,INFLAMM BOWEL DIS,inflammatory bowel disease,Inflammatory Bowel Diseases,Inflammatory bowel disease
Group 0 name Corresponds to the control (unexposed) group for case-control studies
non-inflammatory bowel disease symptomatic controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
inflammatory bowel disease patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
patients under 18 diagnosed with inflammatory bowel disease (Crohn's Disease or ulcerative colitis) from the catchment areas of two university hospitals in three population-based prospective epidemiological studies of treatment-naïve pediatric IBD in South-Eastern Norway between 2005-2015.
Group 0 sample size Number of subjects in the control (unexposed) group
50
Group 1 sample size Number of subjects in the case (exposed) group
110
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
antibiotics use within the last six months of study for healthy controls (group 0)

Lab analysis

Sequencing type
PCR
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
Not specified
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
RT-qPCR

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
relative abundances
Statistical test
Mann-Whitney (Wilcoxon)
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


Signature 1

Reviewed Marked as Reviewed by Chloe on 2023-12-14

Curated date: 2023/12/10

Curator: Yjung24

Revision editor(s): Yjung24

Source: Table 2

Description: Bacterial species exhibiting deviating abundances between patient and control groups.

Abundance in Group 1: decreased abundance in inflammatory bowel disease patients

NCBI Quality ControlLinks
Paraprevotella clara
Bifidobacterium adolescentis
Bifidobacterium angulatum
Bifidobacterium bifidum
Christensenella minuta
[Clostridium] leptum
Desulfovibrio piger
Agathobacter rectalis
[Eubacterium] siraeum
Eubacterium ventriosum
Lactobacillus acidophilus
Lacticaseibacillus paracasei
Roseburia intestinalis
Roseburia inulinivorans
Roseburia hominis
Ruminococcus bromii
Alistipes finegoldii
Phocaeicola plebeius
Bacteroides stercoris
Akkermansia muciniphila

Revision editor(s): Yjung24

Signature 2

Reviewed Marked as Reviewed by Chloe on 2023-12-14

Curated date: 2023/12/10

Curator: Yjung24

Revision editor(s): Yjung24

Source: Table 2

Description: Bacterial species exhibiting deviating abundances between patient and control groups. IBD vs. Non-IBD.

Abundance in Group 1: increased abundance in inflammatory bowel disease patients

NCBI Quality ControlLinks
Haemophilus parainfluenzae

Revision editor(s): Yjung24