Associations between bacterial and fungal communities in the human gut microbiota and their implications for nutritional status and body weight/Experiment 3

From BugSigDB


Needs review

Curated date: 2025/03/08

Curator: Tosin

Revision editor(s): Tosin

Subjects

Location of subjects
Mexico
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
Obesity Adiposis,Adiposity,Obese,Obese (finding),obesity,Obesity (disorder),Obesity [Ambiguous],obesity disease,obesity disorder,Obesity NOS,Obesity, unspecified,Overweight and obesity,Obesity
Group 0 name Corresponds to the control (unexposed) group for case-control studies
Overweight group
Group 1 name Corresponds to the case (exposed) group for case-control studies
Obese group
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Individuals with BMIs (body mass index) in the range of 30.0–34.9.
Group 0 sample size Number of subjects in the control (unexposed) group
10
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)
3 months

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
Linear Discriminant Analysis
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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
unchanged
Chao1 Abundance-based estimator of species richness
unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness
unchanged

Signature 1

Needs review

Curated date: 2025/03/08

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 3c

Description: Statistically significant bacterial genera between the obese and overweight groups by Volcano plots.

Abundance in Group 1: increased abundance in Obese group

NCBI Quality ControlLinks
Clostridium
Romboutsia

Revision editor(s): Tosin

Signature 2

Needs review

Curated date: 2025/03/08

Curator: Tosin

Revision editor(s): Tosin

Source: Figure 3c

Description: Statistically significant bacterial genera between the obese and overweight groups by Volcano plots.

Abundance in Group 1: decreased abundance in Obese group

NCBI Quality ControlLinks
Alloprevotella
Eggerthella
Flavonifractor

Revision editor(s): Tosin