Gut microbiota composition differences are associated with geographic location and age in malaria-endemic regions of Rwanda/Experiment 2
From BugSigDB
Subjects
- Location of subjects
- Rwanda
- 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
- Western Province
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Eastern Province
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants from the Eastern province of Rwanda
- Group 0 sample size Number of subjects in the control (unexposed) group
- 50
- Group 1 sample size Number of subjects in the case (exposed) group
- 73
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Yes
Lab analysis
- Sequencing type
- 16S
- 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).
- raw counts
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, diet
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- 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
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
- Richness Number of species
- unchanged
- Faith Phylogenetic diversity, takes into account phylogenetic distance of all taxa identified in a sample
- unchanged
Signature 1
Source: Figure 2B
Description: Phylum enriched in Eastern province compared to Western province, identified by ANCOM-BC
Abundance in Group 1: increased abundance in Eastern Province
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteria | ||
| Sutterellaceae | ||
| Tyzzerella | ||
| Verrucomicrobiota | ||
| Eubacterium xylanophilum | ||
| lachnospiraceae NK4B4lachnospiraceae NK4B4 |
Revision editor(s): Martha KJ
Signature 2
Source: Figure 2B
Description: Taxa depleted in Eastern province compared to Western province, identified by ANCOM-BC analysis
Abundance in Group 1: decreased abundance in Eastern Province
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Coriobacteriaceae | ||
| Erysipelotrichaceae |
Revision editor(s): Martha KJ
