Oral and gut microbiome profiles in people with early idiopathic 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
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Parkinson disease, mitochondrial Parkinson disease, mitochondrial,parkinson disease, mitochondrial
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Healthy Controls
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson’s disease patients (PD patients)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 220
- Group 1 sample size Number of subjects in the case (exposed) group
- 438
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 6 months
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- 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).
- centered log-ratio
- Statistical test
- ANCOM
- 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, sex
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
Signature 1
Source: Figure 6b, Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using ANCOM statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
Signature 2
Source: Figure 6b, Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using ANCOM statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
Experiment 2
Subjects
- 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 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 221
- Group 1 sample size Number of subjects in the case (exposed) group
- 445
Lab analysis
Statistical Analysis
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Supplementary Data 2
Description: Significantly differentially abundant OTU-level microbial taxa in the gut microbiota between controls and PD cases identified using the ANCOM statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
Signature 2
Source: Supplementary Data 2
Description: Significantly differentially abundant OTU-level microbial taxa in the gut microbiota between controls and PD cases identified using the ANCOM statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
Experiment 3
Subjects
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Saliva Sailva normalis,Saliva atomaris,Saliva molecularis,Salivary gland secretion,Saliva,saliva
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Parkinson disease, mitochondrial Parkinson disease, mitochondrial,parkinson disease, mitochondrial
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease patients (PD patients) refers to patients with Parkinson disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 220
- Group 1 sample size Number of subjects in the case (exposed) group
- 438
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, smoking status, Confounders controlled for: "dessert consumption frequency" 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.dessert consumption frequency, Confounders controlled for: "flossing teeth frequency" 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.flossing teeth frequency, Confounders controlled for: "laxative use in the past month" 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.laxative use in the past month, Confounders controlled for: "number of weekly bowel movements" 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.number of weekly bowel movements, Confounders controlled for: "US census region" 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.US census region
Alpha Diversity
- 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
Source: Supplementary Data 2
Description: Significantly differentially abundant OTU-level microbial taxa (oral microbiota) between controls and PD cases (after adjustment for covariates) identified using the ANCOM statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
Signature 2
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases (after adjustment for covariates) using ANCOM statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Experiment 4
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Linear Regression
Alpha Diversity
- 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
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa (oral microbiota) between controls and PD cases (after adjustment for covariates) using linear models statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa (oral microbiota) between controls and PD cases (after adjustment for covariates) using linear models statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Experiment 5
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa
- increased
Signature 1
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using linear models statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(oral microbiota) between controls and PD cases using linear models statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Experiment 6
Subjects
- 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
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Parkinson’s disease patients (PD patients) refer to patients with Parkinson's disease - a neurodegenerative disease that is characterized by both motor symptoms, such as tremors, and non-motor symptoms, such as constipation.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 221
- Group 1 sample size Number of subjects in the case (exposed) group
- 445
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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, smoking status, Confounders controlled for: "dessert consumption frequency" 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.dessert consumption frequency, Confounders controlled for: "flossing teeth frequency" 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.flossing teeth frequency, Confounders controlled for: "laxative use in the past month" 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.laxative use in the past month, Confounders controlled for: "number of weekly bowel movements" 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.number of weekly bowel movements, Confounders controlled for: "US census region" 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.US census region
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Supplementary Data 2
Description: Significantly differentially abundant OTU-level microbial taxa (gut microbiota) between controls and PD cases (after adjustment for covariates) were identified using the ANCOM statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed, Chrisawoke
Signature 2
Source: Supplementary Data 2
Description: Significantly differentially abundant OTU-level microbial taxa (gut microbiota) between controls and PD cases (after adjustment for covariates) were identified using the ANCOM statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides distasonis CL03T12C09 |
Revision editor(s): KateRasheed, Chrisawoke
Experiment 7
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Linear Regression
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Not specified
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(gut microbiota) between controls and PD cases using linear models statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa(gut microbiota) between controls and PD cases using linear models statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Experiment 8
Subjects
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, body mass index, smoking status, Confounders controlled for: "dessert consumption frequency" 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.dessert consumption frequency, Confounders controlled for: "flossing teeth frequency" 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.flossing teeth frequency, Confounders controlled for: "laxative use in the past month" 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.laxative use in the past month, Confounders controlled for: "number of weekly bowel movements" 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.number of weekly bowel movements, Confounders controlled for: "US census region" 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.US census region
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- increased
Signature 1
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa (gut microbiota) between controls and PD cases (after adjustment for covariates) using linear models statistical test.
Abundance in Group 1: increased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
Signature 2
Source: Supplementary Data 2
Description: Significant differentially abundant OTU-level microbial taxa (gut microbiota) between controls and PD cases (after adjustment for covariates) using linear models statistical test.
Abundance in Group 1: decreased abundance in Parkinson’s disease patients (PD patients)
Revision editor(s): KateRasheed
