Gut microbiome is not associated with mild cognitive impairment in Parkinson's disease/Experiment 2
From BugSigDB
Needs review
Subjects
- Location of subjects
- Luxembourg
- 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 Unimpaired-PD (PD-NC)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Mild Cognitive Impairment-PD
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease (PD) patients with mild cognitive impairment (MCI).
- 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
- 58
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- N/A
Lab analysis
- Sequencing type
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-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).
- raw counts
- Statistical test
- DESeq2
- 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
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- unchanged
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- unchanged
Signature 1
Needs review
Source: Supplementary Figure 1d and table 3c
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: increased abundance in Mild Cognitive Impairment-PD
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillales | ||
| Streptococcaceae | ||
| Streptococcus |
Revision editor(s): Aleru Divine
Signature 2
Needs review
Source: Supplementary Figure 1d and table 3c
Description: Heatmap summarizing differentially abundant taxa.
Abundance in Group 1: decreased abundance in Mild Cognitive Impairment-PD
| NCBI | Quality Control | Links |
|---|---|---|
| Akkermansia muciniphila | ||
| Asteroleplasma |
Revision editor(s): Aleru Divine
