Deep nasal sinus cavity microbiota dysbiosis in Parkinson's disease
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Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Experiment 1
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
- Nasal cavity Cavitas nasalis,Cavitas nasi,Cavity of nose,Cavity of olfactory apparatus,Cavum nasi,Nasal canal,Nasal conduit space,Nasal fossa,Nasal pit,Olfactory cavity,Olfactory chamber,Olfactory chamber cavity,Olfactory pit,Nasal cavity,nasal cavity
- 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
- rHC (Random non-household healthy controls)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- PD (Parkinson's Disease)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of 30 Parkinson's disease subjects.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 17
- Group 1 sample size Number of subjects in the case (exposed) group
- 30
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 12 weeks
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).
- 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
- Matched on Factors on which subjects have been matched on in a case-control study
- age, race, sex
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
- Richness Number of species
- decreased
Signature 1
Source: Supplementary figure 2 and Supplementary table 10 & 11.
Description: Nasal microbial differences between rHC and PD subjects. Differential abundance differences were measured using DESeq2 within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.
Abundance in Group 1: increased abundance in PD (Parkinson's Disease)
Signature 2
Source: Supplementary figure 2 and Supplementary table 10 & 11.
Description: Nasal microbial differences between rHC and PD subjects. Differential abundance differences were measured using DESeq2 within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.
Abundance in Group 1: decreased abundance in PD (Parkinson's Disease)
Experiment 2
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
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
- Richness Number of species
- decreased
Signature 1
Source: Supplementary table 10 & 11.
Description: Nasal microbial differences between rHC and PD subjects. The differential abundance differences were measured using ANCOM within PD (n=30) subjects compared to rHC (n=17) subjects. At the genus and species taxonomic level.
Abundance in Group 1: increased abundance in PD (Parkinson's Disease)
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter | ||
| Acinetobacter guillouiae | ||
| Desulfuromusa |
Revision editor(s): Victoria
Experiment 3
Subjects
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SpHC (Spousal household healthy controls)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of 11 spousal healthy controls of Parkinson's disease subjects.
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- Statistical test
- DESeq2
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
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary Figure 1 and Supplementary table 6 & 7.
Description: Nasal microbial differences between rHC and SpHC subjects. The differential abundance differences were measured using DESeq2 within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.
Abundance in Group 1: increased abundance in SpHC (Spousal household healthy controls)
Revision editor(s): Victoria
Signature 2
Source: Supplementary Figure 1 and Supplementary table 6 & 7.
Description: Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using DESeq2 within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.
Abundance in Group 1: decreased abundance in SpHC (Spousal household healthy controls)
Revision editor(s): Victoria
Experiment 4
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- centered log-ratio
- Statistical test
- ANCOM
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
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary table 6 & 7.
Description: Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using ANCOM within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.
Abundance in Group 1: increased abundance in SpHC (Spousal household healthy controls)
| NCBI | Quality Control | Links |
|---|---|---|
| Acinetobacter guillouiae | ||
| Acinetobacter |
Revision editor(s): Victoria
Signature 2
Source: Supplementary table 6 & 7.
Description: Nasal microbial differences between rHC and SpHC subjects. Differential abundance differences were measured using ANCOM within SpHC (n=11) compared to rHC (n=17) subjects. At the genus and species taxonomic level.
Abundance in Group 1: decreased abundance in SpHC (Spousal household healthy controls)
| NCBI | Quality Control | Links |
|---|---|---|
| Paraburkholderia xenovorans |
Revision editor(s): Victoria
Experiment 5
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- SpHC (Spousal household Healthy Control)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- SpPD (Spousal household Parkinson's Disease)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- This group consists of Parkinson's Disease subjects living in the same household as their healthy control spouses.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 11
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Mann-Whitney (Wilcoxon)
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
- Richness Number of species
- unchanged
Signature 1
Source: Supplementary table 13 and Fig. 2b
Description: Significant differential abundance analysis values of the microbial profiles between spousal household (SpHC) healthy control subjects and their corresponding household PD (SpPD) subjects. At the genus and species taxonomic level.
Abundance in Group 1: increased abundance in SpPD (Spousal household Parkinson's Disease)
| NCBI | Quality Control | Links |
|---|---|---|
| Chromobacterium | ||
| Moraxella | ||
| Corynebacterium bovis | ||
| Moraxella catarrhalis |
Revision editor(s): Victoria
Signature 2
Source: Supplementary table 13 and Fig. 2b
Description: Significant differential abundance analysis values of the microbial profiles between spousal household (SpHC) healthy control subjects and their corresponding household PD (SpPD) subjects. At the genus and species taxonomic level.
Abundance in Group 1: decreased abundance in SpPD (Spousal household Parkinson's Disease)
Revision editor(s): Victoria
