Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression/Experiment 3
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Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10
Curated date: 2023/02/02
Curator: Fcuevas3
Revision editor(s): Fcuevas3, Lwaldron, Folakunmi, ChiomaBlessing
Subjects
- Location of subjects
- Finland
- 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
- Parkinson's disease IDIOPATHIC PARKINSON DIS,Idiopathic Parkinson Disease,Idiopathic Parkinson's Disease,IDIOPATHIC PARKINSONS DIS,Idiopathic PD,LEWY BODY PARKINSON DIS,Lewy Body Parkinson Disease,Lewy Body Parkinson's Disease,Paralysis agitans,paralysis agitans,PARKINSON DIS,PARKINSON DIS IDIOPATHIC,Parkinson disease,Parkinson Disease, Idiopathic,Parkinson syndrome,Parkinson's,Parkinson's disease,Parkinson's disease (disorder),Parkinson's disease NOS,Parkinson's disease NOS (disorder),Parkinson's Disease, Idiopathic,Parkinson's Disease, Lewy Body,Parkinson's syndrome,Parkinsonian disorder,Parkinsonism, Primary,Parkinsons,PARKINSONS DIS,PARKINSONS DIS IDIOPATHIC,PARKINSONS DIS LEWY BODY,Parkinsons disease,Primary Parkinsonism,parkinson's disease
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy controls at time of follow-up
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Participants with Parkinson's Disease at time of follow-up
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants with Parkinson's Disease at time of follow-up
- Group 0 sample size Number of subjects in the control (unexposed) group
- 64
- Group 1 sample size Number of subjects in the case (exposed) group
- 64
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- None.
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
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .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, sex
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- body mass index, irritable bowel syndrome
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on 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
- Richness Number of species
- unchanged
Signature 1
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10
Source: Table 8, Supplemental. Table S4C
Description: Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Follow-up.
Abundance in Group 1: increased abundance in Participants with Parkinson's Disease at time of follow-up
| NCBI | Quality Control | Links |
|---|---|---|
| Bifidobacteriaceae | ||
| Bifidobacterium | ||
| Clostridium_IVClostridium_IV | ||
| Clostridium_XIVaClostridium_XIVa | ||
| Romboutsia |
Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing
Signature 2
Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10
Source: Table 8, Supplemental. Table S4C
Description: Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Follow-up.
Abundance in Group 1: decreased abundance in Participants with Parkinson's Disease at time of follow-up
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroides | ||
| Prevotella | ||
| Prevotellaceae | ||
| Puniceicoccaceae | ||
| Roseburia | ||
| Ruminococcus | ||
| Clostridium_XIVaClostridium_XIVa | ||
| Porphyromonadaceae | ||
| Dialister | ||
| Veillonellaceae |
Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing
