Altered gut microbial profile is associated with differentially expressed fecal microRNAs in patients with functional constipation/Experiment 2

From BugSigDB


Reviewed Marked as Reviewed by Svetlana up on 2025-3-29

Curated date: 2025/03/18

Curator: Tosin

Revision editor(s): Tosin

Subjects

Location of subjects
China
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
Chronic constipation Chronic constipation,Infrequent bowel movements,chronic constipation
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Healthy Controls
Group 1 name Corresponds to the case (exposed) group for case-control studies
Functional constipation (FC) group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with functional constipation (FC)
Group 0 sample size Number of subjects in the control (unexposed) group
30
Group 1 sample size Number of subjects in the case (exposed) group
30

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-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
3.5
Matched on Factors on which subjects have been matched on in a case-control study
age, sex, body mass index

Alpha Diversity

Pielou Quantifies how equal the community is numerically
increased
Shannon Estimator of species richness and species evenness: more weight on species richness
increased
Chao1 Abundance-based estimator of species richness
increased
Simpson Estimator of species richness and species evenness: more weight on species evenness
increased
Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
decreased
Richness Number of species
increased

Signature 1

Reviewed Marked as Reviewed by Svetlana up on 2025-3-29

Curated date: 2025/03/18

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 2B. 2C

Description: Differentially abundant taxa between Functional constipation (FC) group and Healthy Controls (HC)

Abundance in Group 1: increased abundance in Functional constipation (FC) group

NCBI Quality ControlLinks
Bacteroidaceae
Bacteroides
Bacteroides stercoris
Enterobacterales
Enterobacteriaceae
Escherichia/Shigella sp.
Eubacteriales
Eubacterium coprostanoligenes
Gammaproteobacteria
Lachnospira
Lachnospiraceae bacterium NK4A136
Oscillospiraceae
Parabacteroides
Phocaeicola coprocola
Phocaeicola dorei
Phocaeicola vulgatus
Pseudomonadota
Subdoligranulum
Tannerellaceae
CAG_352CAG_352
UCG_002UCG_002

Revision editor(s): Tosin

Signature 2

Reviewed Marked as Reviewed by Svetlana up on 2025-3-29

Curated date: 2025/03/18

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 2B, 2C

Description: Differentially abundant taxa between Functional constipation (FC) group and Healthy Controls (HC)

Abundance in Group 1: decreased abundance in Functional constipation (FC) group

NCBI Quality ControlLinks
Selenomonadaceae
Megamonas
Prevotellaceae bacterium
Megamonas funiformis
Coriobacteriia
Coriobacteriales

Revision editor(s): Tosin