Household environment and animal fecal contamination are critical modifiers of the gut microbiome and resistome in young children from rural Nicaragua/Experiment 1
From BugSigDB
Subjects
- Location of subjects
- Nicaragua
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Infants
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Children
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants between 2.0–6.0 years
- Group 0 sample size Number of subjects in the control (unexposed) group
- 26
- Group 1 sample size Number of subjects in the case (exposed) group
- 31
Lab analysis
- 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
- Nanopore
Statistical Analysis
- Statistical test
- Kruskall-Wallis
- PERMANOVA
- Spearman Correlation
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body height, body weight, breast feeding, mode of birth, sex
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
Signature 1
Source: Figure 2b
Description: Bacterial families with different abundances in children and infants identified with linear discriminant analysis effect size (LEfSe)
Abundance in Group 1: increased abundance in Children
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae | ||
| Prevotellaceae | ||
| Spirochaetaceae | ||
| RuminococcaceaeRuminococcaceae |
Revision editor(s): Aishat
Signature 2
Source: Figure 2b
Description: Bacterial families with different abundances in children and infants identified with linear discriminant analysis effect size (LEfSe)
Abundance in Group 1: decreased abundance in Children
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidaceae | ||
| Bifidobacteriaceae | ||
| Enterobacteriaceae |
Revision editor(s): Aishat
