Gut microbiome signatures reflect different subtypes of irritable bowel syndrome/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Folakunmi on 2024-2-6

Curated date: 2023/10/26

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Folakunmi

Subjects

Location of subjects
United Kingdom
United States of America
Canada
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
Non-IBS2 (Non-irritable bowel syndrome 2)
Group 1 name Corresponds to the case (exposed) group for case-control studies
IBS-D (IBS-Diarrhea)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with IBS-D, a subtype of IBS characterized by diarrhea (watery stool)
Group 0 sample size Number of subjects in the control (unexposed) group
302
Group 1 sample size Number of subjects in the case (exposed) group
302
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
6 months

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V4
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).
relative abundances
Statistical test
LEfSe
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)?
No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
2
Matched on Factors on which subjects have been matched on in a case-control study
age, alcohol drinking, body mass index, diet, geographic area, sex
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, alcohol drinking, diet, sex

Alpha Diversity

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

Signature 1

Reviewed Marked as Reviewed by Folakunmi on 2024-2-5

Curated date: 2023/10/26

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Figure 2a, b and c and Supplemental. Table 4

Description: Differential microbial abundance between IBS-D and Non-IBS2

Abundance in Group 1: decreased abundance in IBS-D (IBS-Diarrhea)

NCBI Quality ControlLinks
Achromobacter
Akkermansia
Alistipes
Anaerostipes
Barnesiella
Bifidobacterium
Butyricimonas
Butyrivibrio
Campylobacter
Candidatus Izemoplasmatales
Christensenellaceae
Clostridiales Family XIII bacterium
Coprococcus
Cyanobacteriota
Dechloromonas
Desulfovibrio
Eubacterium ruminantium
Eubacterium xylanophilum
Faecalibacterium
Fenollaria
Hydrogenoanaerobacterium
Lentisphaerota
Muribaculaceae
Odoribacter
Oxalobacter
Parasutterella
Peptoniphilus
Porphyromonas
Prevotella
Ruminococcus
Sutterella
Varibaculum
Veillonella
Victivallis
[Eubacterium] siraeum
bacterium ND3007
candidate division VadinBE97
uncultured Erysipelotrichaceae bacterium
uncultured Lachnospiraceae bacterium
uncultured Oscillospiraceae bacterium
Bacilli_RF39Bacilli_RF39
Oscillospiraceae_NK4A21Oscillospiraceae_NK4A21
Incertae sedis DTU014Incertae sedis DTU014
Clostridia_vadinBB60Clostridia_vadinBB60
uncultured Clostridia bacterium

Revision editor(s): ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by Folakunmi on 2024-2-5

Curated date: 2023/10/26

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing, Iram jamshed, Folakunmi

Source: Figure 2a, b and c and Supplemental Table 4

Description: Differential microbial abundance between IBS-D and Non-IBS2

Abundance in Group 1: increased abundance in IBS-D (IBS-Diarrhea)

NCBI Quality ControlLinks
Abiotrophia
Dorea
Escherichia/Shigella sp.
Flavonifractor
Haemophilus
Mediterraneibacter gnavus
Subdoligranulum
Anaerobutyricum hallii
Brevundimonas
unclassified Defluviitaleaceae

Revision editor(s): ChiomaBlessing, Iram jamshed, Folakunmi