Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn's Disease

From BugSigDB
Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Journal
Year
Pages:
30
First page:
Keywords:
pouchitis, UC, CD, mucin, butyrate, bile acids, oxidative stress, classifier, Crohn's disease, microbiome, ulcerative colitis

Experiment 1


Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

Curated date: 2023/11/18

Curator: MyleeeA

Revision editor(s): MyleeeA, Peace Sandy

Subjects

Location of subjects
Israel
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
Normal pouch
Group 1 name Corresponds to the case (exposed) group for case-control studies
Pouchitis
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with a pouch that developed inflammation
Group 0 sample size Number of subjects in the control (unexposed) group
35
Group 1 sample size Number of subjects in the case (exposed) group
34
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month (recent use) or 6 months off antibiotics

Lab analysis

Sequencing type
WMS
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
Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
raw counts
Statistical test
Linear Regression
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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, Confounders controlled for: "antibiotic use" 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.antibiotic use

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased

Signature 1

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

Curated date: 2024/02/17

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: FIG 7

Description: Highest-scoring microbiome features identified by the classification models as the most informative for distinguishing between patients with a normal pouch and pouchitis and thus possibly predictive of pouchitis. The feature importance scores (averaged across 5-fold cross-validation) for (A) species.

Abundance in Group 1: increased abundance in Pouchitis

NCBI Quality ControlLinks
Acinetobacter
Akkermansia muciniphila
Blautia hydrogenotrophica
Burkholderiales bacterium 1_1_47
Cellvibrio
Enterococcus faecium
Erysipelotrichaceae bacterium 21_3
Erysipelotrichaceae bacterium 6_1_45
Escherichia coli
Lachnospiraceae bacterium 5_1_63FAA
Mediterraneibacter gnavus
Megasphaera micronuciformis
Parasutterella excrementihominis
Streptococcus agalactiae
Veillonella dispar
Yersinia
[Clostridium] innocuum
unclassified Coprobacillus
unclassified Escherichia
unclassified Providencia
unclassified Slackia
unclassified Veillonella

Revision editor(s): Peace Sandy

Signature 2

Reviewed Marked as Reviewed by Peace Sandy on 2024-2-17

Curated date: 2024/02/17

Curator: Peace Sandy

Revision editor(s): Peace Sandy

Source: FIG 7

Description: Highest-scoring microbiome features identified by the classification models as the most informative for distinguishing between patients with a normal pouch and pouchitis and thus possibly predictive of pouchitis. The feature importance scores (averaged across 5-fold cross-validation) for (A) species.

Abundance in Group 1: decreased abundance in Pouchitis

NCBI Quality ControlLinks
Bifidobacterium pseudocatenulatum
Blautia obeum
Dorea formicigenerans
Dorea longicatena
Erysipelotrichaceae bacterium 2_2_44A
Faecalibacterium prausnitzii
Haemophilus pittmaniae
Phocaeicola massiliensis
Roseburia inulinivorans
Ruminococcus sp. 5_1_39BFAA
Solobacterium moorei
Stomatobaculum longum
Streptococcus parasanguinis
Streptococcus pasteurianus
Streptococcus vestibularis
Veillonella dispar
[Ruminococcus] lactaris
[Ruminococcus] torques
unclassified Bartonella
unclassified Dorea
unclassified Halomonas
unclassified Pediococcus
unclassified Peptostreptococcaceae

Revision editor(s): Peace Sandy