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

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

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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 Control	Links
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

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Edit History Delete

Flag for review

Your review change was submitted

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 Control	Links
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