Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/24

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp, UtibeIta

Subjects

Location of subjects: United States of America

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: HC (Healthy Control)

Group 1 name Corresponds to the case (exposed) group for case-control studies: IBS1 (Irritable Bowel Syndrome 1)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects

Group 0 sample size Number of subjects in the control (unexposed) group: 23

Group 1 sample size Number of subjects in the case (exposed) group: 13

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 3 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V3-V5

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Roche454

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

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

Richness Number of species: increased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/25

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Results text (Figure 4C - F)

Description: The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)

Abundance in Group 1: increased abundance in IBS1 (Irritable Bowel Syndrome 1)

NCBI	Quality Control	Links
Bacilli
Bacillota
Clostridia
Holdemania
Lactobacillales

Revision editor(s): Anne-mariesharp

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/25

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Results text (Figure 4C - F)

Description: The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)

Abundance in Group 1: decreased abundance in IBS1 (Irritable Bowel Syndrome 1)

NCBI	Quality Control	Links
Bacteroidales
Bacteroidia
Bacteroidota
Parabacteroides

Revision editor(s): Anne-mariesharp

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/25

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp, UtibeIta

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HC-like IBS(Healthy Control like Irritable Bowel Syndrome)

Group 0 sample size Number of subjects in the control (unexposed) group: 16

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

Richness Number of species: increased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/25

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Results text (Figure 4C - F)

Description: The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)

Abundance in Group 1: increased abundance in IBS1 (Irritable Bowel Syndrome 1)

NCBI	Quality Control	Links
Bacilli
Holdemania
Lactobacillales

Revision editor(s): Anne-mariesharp

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/25

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Results text (Figure 4C - F)

Description: The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)

Abundance in Group 1: decreased abundance in IBS1 (Irritable Bowel Syndrome 1)

NCBI	Quality Control	Links
Abiotrophia
Bacteroidales
Bacteroidia
Bacteroidota
Parabacteroides

Revision editor(s): Anne-mariesharp

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/25

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp, UtibeIta

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HC (Healthy Control)

Group 1 name Corresponds to the case (exposed) group for case-control studies: HC-like IBS (Healthy Control like Irritable Bowel Syndrome)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: A subgroup of irritable bowel syndrome (IBS) patients with similar microbial composition as healthy control (HC) subjects

Group 0 sample size Number of subjects in the control (unexposed) group: 23

Group 1 sample size Number of subjects in the case (exposed) group: 16

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Richness Number of species: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/25

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Results text (Figure 4C - F)

Description: The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)

Abundance in Group 1: increased abundance in HC-like IBS (Healthy Control like Irritable Bowel Syndrome)

NCBI	Quality Control	Links
Bacillota
Clostridia
Parabacteroides

Revision editor(s): Anne-mariesharp

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/25

Curator: Anne-mariesharp

Revision editor(s): Anne-mariesharp

Source: Results text (Figure 4C - F)

Description: The mean relative abundance for identifiable taxa demonstrating overall group differences at each taxonomic level (phylum, class, order, family, and genus)

Abundance in Group 1: decreased abundance in HC-like IBS (Healthy Control like Irritable Bowel Syndrome)

NCBI	Quality Control	Links
Bacteroidales
Bacteroidia
Bacteroidota

Revision editor(s): Anne-mariesharp

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/27

Curator: UtibeIta

Revision editor(s): UtibeIta

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies: IBS1 (Irritable Bowel Syndrome 1)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: A subgroup of irritable bowel syndrome (IBS) patients with microbial profiles distinct from healthy control (HC) subjects

Group 1 sample size Number of subjects in the case (exposed) group: 13

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

Richness Number of species: increased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/27

Curator: UtibeIta

Revision editor(s): UtibeIta, Anne-mariesharp

Source: Table S5

Description: Relative abundance of operational taxonomic units and taxa showing significant group differences

Abundance in Group 1: increased abundance in IBS1 (Irritable Bowel Syndrome 1)

NCBI	Quality Control	Links
Bacilli
Bacillota
Clostridia
Holdemania
Lactobacillales
unclassified Bacillota
unclassified Bacteria
unclassified Clostridia
unclassified Holdemania
unclassified Lachnospiraceae
unclassified Peptostreptococcaceae
unclassified Streptococcus

Revision editor(s): UtibeIta, Anne-mariesharp

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/27

Curator: UtibeIta

Revision editor(s): UtibeIta, Anne-mariesharp

Source: Table S5

Description: Relative abundance of operational taxonomic units and taxa showing significant group differences

Abundance in Group 1: decreased abundance in IBS1 (Irritable Bowel Syndrome 1)

NCBI	Quality Control	Links
Bacteroidales
Bacteroidia
Bacteroidota
Parabacteroides
Parabacteroides distasonis

Revision editor(s): UtibeIta, Anne-mariesharp

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/27

Curator: UtibeIta

Revision editor(s): UtibeIta

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HC-like IBS(Healthy Control like Irritable Bowel Syndrome)

Group 0 sample size Number of subjects in the control (unexposed) group: 16

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: increased

Richness Number of species: increased

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: increased

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/27

Curator: UtibeIta

Revision editor(s): UtibeIta, Anne-mariesharp

Source: Table S5

Description: Relative abundance of operational taxonomic units and taxa showing significant group differences

Abundance in Group 1: increased abundance in IBS1 (Irritable Bowel Syndrome 1)

NCBI	Quality Control	Links
Bacilli
Bacillota
Clostridia
Holdemania
Lactobacillales
unclassified Bacillota
unclassified Bacteria
unclassified Clostridia
unclassified Holdemania
unclassified Lachnospiraceae
unclassified Peptostreptococcaceae
unclassified Streptococcus

Revision editor(s): UtibeIta, Anne-mariesharp

Signature 2

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/27

Curator: UtibeIta

Revision editor(s): UtibeIta, Anne-mariesharp

Source: Table S5

Description: Relative abundance of operational taxonomic units and taxa showing significant group differences

Abundance in Group 1: decreased abundance in IBS1 (Irritable Bowel Syndrome 1)

NCBI	Quality Control	Links
Bacteroidales
Bacteroidia
Bacteroidota
Parabacteroides
Parabacteroides distasonis

Revision editor(s): UtibeIta, Anne-mariesharp

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/27

Curator: UtibeIta

Revision editor(s): UtibeIta

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: HC (Healthy Control)

Group 1 name Corresponds to the case (exposed) group for case-control studies: HC-like IBS (Healthy Control like Irritable Bowel Syndrome)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: A subgroup of irritable bowel syndrome (IBS) patients with similar microbial composition as healthy control (HC) subjects

Group 0 sample size Number of subjects in the control (unexposed) group: 23

Group 1 sample size Number of subjects in the case (exposed) group: 16

Lab analysis

Statistical Analysis

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Richness Number of species: unchanged

Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample: unchanged

Signature 1

Reviewed Marked as Reviewed by KateRasheed on 2025-7-7

Curated date: 2025/04/27

Curator: UtibeIta

Revision editor(s): UtibeIta, Anne-mariesharp

Source: Table S5

Description: Relative abundance of operational taxonomic units and taxa showing significant group differences

Abundance in Group 1: increased abundance in HC-like IBS (Healthy Control like Irritable Bowel Syndrome)

NCBI	Quality Control	Links
Bacillota
Clostridia
Parabacteroides
Parabacteroides distasonis
unclassified Clostridia

Revision editor(s): UtibeIta, Anne-mariesharp

Signature 2