The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults/Experiment 1
From BugSigDB
Reviewed Marked as Reviewed by Svetlana up on 2024-10-23
Subjects
- Location of subjects
- United States of America
- 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
- Cognitive impairment Abnormality of cognition,Cognitive abnormality,Cognitive defects,Cognitive deficits,Cognitive impairment,Intellectual impairment,cognitive impairment
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Cognitively Intact Group
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Cognitively Impaired Group
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of 23 patients with cognitive impairment.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 60
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
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
- 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
- 4
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- unchanged
Signature 1
Reviewed Marked as Reviewed by Svetlana up on 2024-10-23
Source: Figure 2C
Description: Cladogram and linear discriminant analysis of effect size (Lefse) showing biomarker taxa associated with cognitively intact and impaired individuals. The Lefse analysis included non-probiotic groups only.
Abundance in Group 1: increased abundance in Cognitively Impaired Group
Signature 2
Reviewed Marked as Reviewed by Svetlana up on 2024-10-23
Source: Figure 2C
Description: Cladogram and linear discriminant analysis of effect size (Lefse) showing biomarker taxa associated with cognitively intact and impaired individuals. The Lefse analysis included non-probiotic groups only.
Abundance in Group 1: decreased abundance in Cognitively Impaired Group
| NCBI | Quality Control | Links |
|---|---|---|
| Pseudomonadota | ||
| Phocaeicola vulgatus |
