Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice/Experiment 3
From BugSigDB
Subjects
- Location of subjects
- Cambodia
- 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
- Vitamin A deficiency deficiencies, vitamin A,deficiency, vitamin A,vitamin A deficiencies,Vitamin A Deficiency,vitamin A deficiency,vitamin A deficiency (disease),Vitamin A deficiency
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Sufficient vitamin A
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Vitamin A deficiency
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group includes children diagnosed with Vitamin A deficiency with level less than 20 micrograms per deciliter [mcg/dL]
- Group 0 sample size Number of subjects in the control (unexposed) group
- 350
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 30 days
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)?
- Yes
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2.0
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- decreased
- Shannon Estimator of species richness and species evenness: more weight on species richness
- decreased
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- decreased
Signature 1
Source: Figure 2 C
Description: Differential ASVs between the children grouped according to Vitamin A deficiency.
Abundance in Group 1: increased abundance in Vitamin A deficiency
Revision editor(s): Joiejoie
Signature 2
Source: Figure 2 C
Description: Differential ASVs between the children grouped according to Vitamin A deficiency
Abundance in Group 1: decreased abundance in Vitamin A deficiency
| NCBI | Quality Control | Links |
|---|---|---|
| Gordonibacter | ||
| Romboutsia | ||
| unidentified | ||
| LactobacillaceaeLactobacillaceae |
Revision editor(s): Joiejoie
