Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls/Experiment 2
From BugSigDB
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-25
Subjects
- Location of subjects
- South Africa
- 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
- Clinical treatment Clinical treatment,clinical treatment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Individuals not using psychotropic medication
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Individuals using psychotropic medication
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Individuals using psychotropic medication that may associate with the gut microbiome of the sample.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 21
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- Antibiotic use within 4 weeks before stool sampling.
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- 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
- Linear Regression
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.1
- 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: "gastrointestinal diseases" 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.gastrointestinal diseases, Confounders controlled for: "unidentified bowel diseases" 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.unidentified bowel diseases
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-25
Source: Figure 4A, C and D
Description: Relative abundance (clr-transformed and filtered) of specific taxa at the genus and phylum level in individuals who were using psychotropic medication at the time of sample collection compared to individuals not using psychotropic medication
Abundance in Group 1: increased abundance in Individuals using psychotropic medication
| NCBI | Quality Control | Links |
|---|---|---|
| Bacillota | ||
| Bacteroidota | ||
| Ruminococcus |
Revision editor(s): Keamy, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-3-25
Source: Figure 4B and 4E
Description: Relative abundance (clr-transformed and filtered) of specific taxa at the genus and phylum level in individuals who were using psychotropic medication at the time of sample collection compared to individuals not using psychotropic medication
Abundance in Group 1: decreased abundance in Individuals using psychotropic medication
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia | ||
| Verrucomicrobiota |
Revision editor(s): Keamy, ChiomaBlessing
