Preliminary characterization of gut mycobiome enterotypes reveals the correlation trends between host metabolic parameter and diet: a case study in the Thai Cohort/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- Thailand
- 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
- Gut microbiome measurement Gut microbiome measurement,gut microbiome measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Saccharomyces enterotype (enterotype SA)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Aspergillus/Penicillium enterotype (enterotype AP/Pe)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals whose gut mycobiome composition was dominated by Aspergillus and Penicillium genera, identified through hierarchical clustering of ITS2 fungal profiles.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 111
- Group 1 sample size Number of subjects in the case (exposed) group
- 191
- 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
- ITS / ITS2
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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
- 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, Matched on: "BMI" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.BMI
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
- decreased
Signature 1
Source: Figure 1b
Description: Lesfe analysis showing specific taxa significantly abundant between Saccharomyces enterotype (enterotype SA) and Aspergillus/Penicillium enterotype (enterotype AP/Pe)
Abundance in Group 1: increased abundance in Aspergillus/Penicillium enterotype (enterotype AP/Pe)
| NCBI | Quality Control | Links |
|---|---|---|
| Agaricomycetes | ||
| Aspergillus | ||
| Basidiomycota | ||
| Cystobasidiomycetes | ||
| Dothideomycetes | ||
| Eurotiomycetes | ||
| Penicillium | ||
| Sordariomycetes | ||
| Tremellomycetes | ||
| Ustilaginomycetes |
Revision editor(s): Ese
Signature 2
Source: Figure 1b
Description: Lesfe analysis showing specific taxa significantly abundant between Saccharomyces enterotype (enterotype SA) and Aspergillus/Penicillium enterotype (enterotype AP/Pe)
Abundance in Group 1: decreased abundance in Aspergillus/Penicillium enterotype (enterotype AP/Pe)
| NCBI | Quality Control | Links |
|---|---|---|
| Saccharomyces | ||
| Saccharomycetes |
Revision editor(s): Ese
