Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms
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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
- 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.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Parkinson's Disease subjects.
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Potential PD cases for enrollment were identified via systematic pre-screening of electronic medical records (EMR) of patients with an upcoming appointment in the Movement Disorder Clinic at UAB. Subjects were invited to enroll in the study after their clinic visit if the attending specialist confirmed PD diagnosis and the patient was willing to hear about the study.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 234
- Group 1 sample size Number of subjects in the case (exposed) group
- 490
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 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
- 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
- Matched on: "Environmental effects" 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.Environmental effects
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "stool sample collection method" 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.stool sample collection method, Confounders controlled for: "total sequence count per sample" 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.total sequence count per sample
Signature 1
Source: Fig. 3
Description: Differential abundances and effect sizes of PD-associated species. Analysis included N = 724 biologically independent samples from 490 PD and 234 neurologically healthy control (NHC) subjects. Forty-six species that had at least 75% (and up to 750%) change in abundance in PD are shown here; for all 84 PD-associated species see Supplementary Fig. 3. a Distribution of relative abundances. Log2 transformed relative abundance values, as used in MaAsLin2, were used to generate the boxplots. Untransformed relative abundances, shown in parenthesis, are provided on the X-axis for easier interpretation of data. Boxplots show distribution of the data for PD (blue green) and NHC (orange). Each sample was plotted according to its abundance of the species. The left, middle, and right vertical boundaries of each box represents the first, second (median), and third quartiles of the data; that is, 25% of samples have abundance lower than the left border of the box, 25% of samples have abundances that are higher than the right border of the box. Absence of a box indicates 75% of samples had zero abundance. The lines extending from the two ends of each box represent 1.5x outside the interquartile range (range = (abundance value at 75% minus abundance value at 25%) x 1.5). Points beyond the lines are outlier samples.
Abundance in Group 1: increased abundance in Parkinson's Disease subjects.
Revision editor(s): Fcuevas3, Peace Sandy
Signature 2
Source: Fig. 3
Description: Differential abundances and effect sizes of PD-associated species. Analysis included N = 724 biologically independent samples from 490 PD and 234 neurologically healthy control (NHC) subjects. Forty-six species that had at least 75% (and up to 750%) change in abundance in PD are shown here; for all 84 PD-associated species see Supplementary Fig. 3. a Distribution of relative abundances. Log2 transformed relative abundance values, as used in MaAsLin2, were used to generate the boxplots. Untransformed relative abundances, shown in parenthesis, are provided on the X-axis for easier interpretation of data. Boxplots show distribution of the data for PD (blue green) and NHC (orange). Each sample was plotted according to its abundance of the species. The left, middle, and right vertical boundaries of each box represents the first, second (median), and third quartiles of the data; that is, 25% of samples have abundance lower than the left border of the box, 25% of samples have abundances that are higher than the right border of the box. Absence of a box indicates 75% of samples had zero abundance. The lines extending from the two ends of each box represent 1.5x outside the interquartile range (range = (abundance value at 75% minus abundance value at 25%) x 1.5). Points beyond the lines are outlier samples.
Abundance in Group 1: decreased abundance in Parkinson's Disease subjects.
Revision editor(s): Fcuevas3, Peace Sandy
