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

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

Curated date: 2021/07/17

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

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.

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: 19

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: sex, age

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

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Shouchella clausii
Bacillus cereus
Bifidobacteriaceae
Bifidobacterium adolescentis
Bifidobacterium breve
Bifidobacterium longum
Campylobacter
Clostridioides difficile
Enterobacteriaceae
Enterococcus faecium
Lactobacillaceae
Lentilactobacillus buchneri
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

NCBI	Quality Control	Links
Bacteroides
Veillonella
Prevotella

Revision editor(s): Kwekuamoo, Atrayees

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/18

Curator: Kwekuamoo

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

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: IBS-C

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. Constipation IBS (IBS-C)

Group 1 sample size Number of subjects in the case (exposed) group: 4

Lab analysis

Statistical Analysis

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-C

NCBI	Quality Control	Links
Shouchella clausii
Bifidobacteriaceae

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-C

NCBI	Quality Control	Links
Bacteroides
Prevotella

Revision editor(s): Kwekuamoo, Atrayees

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/18

Curator: Kwekuamoo

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

Differences from previous experiment shown

Subjects

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 1 sample size Number of subjects in the case (exposed) group: 10

Lab analysis

Statistical Analysis

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 Control	Links
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 Control	Links
Bacteroides
Prevotella

Revision editor(s): Kwekuamoo, Atrayees

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

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

Curated date: 2021/07/18

Curator: Kwekuamoo

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

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: IBS-M

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. Mixed IBS (IBS-M).

Group 1 sample size Number of subjects in the case (exposed) group: 5

Lab analysis

Statistical Analysis

Alpha Diversity

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

Richness Number of species: unchanged

Signature 1