Environmental, socioeconomic, and health factors associated with gut microbiome species and strains in isolated Honduras villages/Experiment 1
From BugSigDB
Needs review
Subjects
- Location of subjects
- Honduras
- 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
- Health-related quality of life measurement HRQOL,Health-related quality of life measurement,health-related quality of life measurement
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Health associated(Healthy)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Disease associated(Chronically diseased individuals)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Disease associated has to do with chronically diseased individuals who had at least one chronic condition. Examples of the chronic conditions include: diabetes, asthma, heart disease, arthritis, etc
- Group 1 sample size Number of subjects in the case (exposed) group
- 468
Lab analysis
- Sequencing type
- WMS
- 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).
- centered log-ratio
- Statistical test
- MaAsLin2
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, sex, Confounders controlled for: "DNA concentration" 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.DNA concentration, Confounders controlled for: "sequencing batch" 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.sequencing batch, Confounders controlled for: "sampling date" 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.sampling date, Confounders controlled for: "Bristol stool scale" 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.Bristol stool scale
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
Signature 1
Needs review
Source: Fig. S4B
Description: Differential abundance in healthy vs chronically diseased individuals using MaAsLin2.
Abundance in Group 1: decreased abundance in Disease associated(Chronically diseased individuals)
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospiraceae bacterium |
Revision editor(s): KateRasheed
Signature 2
Needs review
Source: Fig. S4B
Description: Differential abundance in healthy vs chronically diseased individuals using MaAsLin2
Abundance in Group 1: increased abundance in Disease associated(Chronically diseased individuals)
| NCBI | Quality Control | Links |
|---|---|---|
| unclassified Clostridia | ||
| Coprococcus | ||
| Spirochaetia bacterium | ||
| uSGB1663uSGB1663 | ||
| uSGB27424uSGB27424 |
Revision editor(s): KateRasheed
