Differential human gut microbiome assemblages during soil-transmitted helminth infections in Indonesia and Liberia/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- Liberia
- 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
- Helminthiasis helminth infection,helminthiasis,helminthosis,parasitic helminthiasis infectious disease,worm infection,Helminthiasis
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Zero Soil Transmitted Helminth infection (Zero STH infection)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- High Soil Transmitted Helminth infection (High STH infection)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- High Soil Transmitted Helminth infection (High STH infection) refers to individuals found with eggs from Ascaris helminth; when their feces was measured by the Kato-Katz smear in eggs per gram (EPG).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 26
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V1-V3
- 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)?
- Yes
- 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
- increased
- Richness Number of species
- increased
Signature 1
Needs review
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of eggs in feces for Ascaris helminth).
Abundance in Group 1: decreased abundance in High Soil Transmitted Helminth infection (High STH infection)
| NCBI | Quality Control | Links |
|---|---|---|
| Eubacteriales | ||
| Bacteria | ||
| Cellulosilyticum | ||
| Clostridium_XIXClostridium_XIX |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Table S5
Description: Differential abundance in the gut microbiota between infected and uninfected groups in Liberia (based on the presence of eggs in feces for Ascaris helminth).
Abundance in Group 1: increased abundance in High Soil Transmitted Helminth infection (High STH infection)
| NCBI | Quality Control | Links |
|---|---|---|
| Solobacterium | ||
| unclassified Bacteria |
Revision editor(s): KateRasheed
