IBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation/Experiment 3

From BugSigDB


Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): WikiWorks, LGeistlinger, Kwekuamoo, Atrayees

Subjects

Location of subjects
Italy
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
Irritable bowel syndrome [X]Psychogenic IBS,Adaptive colitis,Colitides, Mucous,Colitis, Mucous,Colon spasm,Colon, Irritable,Functional bowel disease,IBD,IBS,IBS - Irritable bowel syndrome,IC - Irritable colon,Irritable bowel,Irritable bowel - IBS,irritable bowel syndrome,Irritable Bowel Syndromes,Irritable Colon,irritable colon,Irritable colon (disorder),Irritable colon - Irritable bowel syndrome,Irritable colon syndrome,Membranous colitis,Mucous Colitides,Mucous colitis,mucus colitis,Nervous colitis,Psychogenic IBS,psychogenic IBS,Spastic colitis,Spastic colon,spastic colon,Syndrome, Irritable Bowel,Syndromes, Irritable Bowel,Irritable bowel syndrome
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy Control
Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS-D
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Fulfilled the Rome III criteria for the diagnosis of IBS. Diarrhea IBS (IBS-D).
Group 0 sample size Number of subjects in the control (unexposed) group
24
Group 1 sample size Number of subjects in the case (exposed) group
10
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
2 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V2-V3
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
HTF-Microbi.Array

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
Richness Number of species
unchanged

Signature 1

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo

Source: Table 1.

Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)

Abundance in Group 1: increased abundance in IBS-D

NCBI Quality ControlLinks
Shouchella clausii
Bacillus cereus
Bifidobacteriaceae
Bifidobacterium adolescentis
Bifidobacterium breve
Bifidobacterium longum
Clostridioides difficile
Enterobacteriaceae
Enterococcus faecium
Lactobacillaceae
Ligilactobacillus salivarius
Peptostreptococcaceae
Agathobacter rectalis

Revision editor(s): Kwekuamoo

Signature 2

Reviewed Marked as Reviewed by Atrayees on 2023-6-30

Curated date: 2021/07/18

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo, Atrayees

Source: Table 1.

Description: Bacterial groups significantly altered in IBS subjects (IBS; Constipation IBS, C-IBS; Diarrhea IBS, D-IBS; Mixed IBS, M-IBS), with respect to healthy subjects (HS)

Abundance in Group 1: decreased abundance in IBS-D

NCBI Quality ControlLinks
Bacteroides
Prevotella

Revision editor(s): Kwekuamoo, Atrayees