Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China
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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
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls without any form of Parkinson's Disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with parkinson's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotic use for at least 3 months prior to the study.
Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.
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
- Statistical test
- T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age, body mass index
Alpha Diversity
- Shannon Estimator of species richness and species evenness: more weight on species richness
- increased
- Chao1 Abundance-based estimator of species richness
- increased
- Simpson Estimator of species richness and species evenness: more weight on species evenness
- increased
- Richness Number of species
- decreased
Signature 1
Source: Figure 2A: Phylum
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.
Abundance in Group 1: increased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Verrucomicrobiota |
Revision editor(s): Fcuevas3
Signature 2
Source: Figure 2B: Class
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.
Abundance in Group 1: increased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Clostridia | |
Negativicutes | |
Verrucomicrobiae |
Revision editor(s): Fcuevas3
Signature 3
Source: Figure 2B: Class
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels
Abundance in Group 1: decreased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Bacilli |
Revision editor(s): Fcuevas3
Signature 4
Source: Figure 2C: Order
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.
Abundance in Group 1: increased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Clostridiales Family XIII bacterium | |
Selenomonadales | |
Verrucomicrobiales |
Revision editor(s): Fcuevas3
Signature 5
Source: Figure 2C: Order
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.
Abundance in Group 1: decreased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Lactobacillales |
Revision editor(s): Fcuevas3
Signature 6
Source: Figure 2D: Family
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.
Abundance in Group 1: increased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Oscillospiraceae | |
Veillonellaceae | |
Verrucomicrobiaceae | |
Porphyromonadaceae | |
Rikenellaceae | |
Acidaminococcaceae |
Revision editor(s): Fcuevas3
Signature 7
Source: Figure 2D: Family
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.
Abundance in Group 1: decreased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Lactobacillaceae | |
Bacteroidales |
Revision editor(s): Fcuevas3
Signature 8
Source: Figure 2E: Genus
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.
Abundance in Group 1: increased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Ruminococcus | |
Akkermansia | |
Eubacterium | |
Parabacteroides | |
Coprococcus | |
Phascolarctobacterium | |
Methanobrevibacter | |
Alistipes | |
Roseburia | |
Lachnospiraceae | |
Eubacterium ventriosum | |
Lachnospira |
Revision editor(s): Fcuevas3
Signature 9
Source: Figure 2E: Genus
Description: Gut microbiota differences between PD patients and controls detected by t-tests. Gut microbiota is compared between PD patients and healthy control subjects at phylum (A), class (B), order (C), family (D), genus (E), and species (F) levels.
Abundance in Group 1: decreased abundance in patients with parkinson's disease
NCBI | Links |
---|---|
Lactobacillus | |
Streptococcus | |
Anaerobutyricum hallii |
Revision editor(s): Fcuevas3
Experiment 2
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- healthy controls without any form of Parkinson's Disease, with Wexner scores < 3 using Wilcoxon rank sum test.
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with Parkinson's disease with Wexner scores < 3
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients with Parkinson's disease with Wexner scores < 3.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 25
- Group 1 sample size Number of subjects in the case (exposed) group
- 13
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotic use for at least 3 months prior to the study.
Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .01
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age, Matched on: "bmi" 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.bmi
Alpha Diversity
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Source: Supplemental Figure 5
Description: Comparison of microbiota abundances between PD and controls with constipation Wexner score less than or equal to 3.
Abundance in Group 1: decreased abundance in patients with Parkinson's disease with Wexner scores < 3
NCBI | Links |
---|---|
Bacilli | |
Lactobacillales | |
Bacteroidales | |
Lactobacillaceae | |
Lactobacillus |
Revision editor(s): Fcuevas3
Experiment 3
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls without any form of Parkinson's
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with Parkinson's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotic use for at least 3 months prior to the study.
Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- ANOVA
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- .05
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age, Matched on: "bmi" 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.bmi
Signature 1
Source: Supplemental Figure 7
Description: Two-way ANOVA analysis to assess the impact of gender and PD on gut microbiota taxa identified by LDA scores>4 in LEfSe analysis.
Abundance in Group 1: increased abundance in patients with Parkinson's disease
NCBI | Links |
---|---|
Revision editor(s): Fcuevas3
Signature 2
Source: Supplemental Figure 7
Description: Two-way ANOVA analysis to assess the impact of gender and PD on gut microbiota taxa identified by LDA scores>4 in LEfSe analysis.
Abundance in Group 1: decreased abundance in patients with Parkinson's disease
NCBI | Links |
---|---|
Bacteroidales | |
Lactobacillaceae | |
Lactobacillales | |
Lactobacillus | |
Bacilli |
Revision editor(s): Fcuevas3
Experiment 4
Subjects
- Location of subjects
- China
- Host species Species from which microbiome was sampled (if applicable)
- 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
- 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
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- controls without any form of Parkinson's disease
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- patients with Parkinson's disease
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 48
- Group 1 sample size Number of subjects in the case (exposed) group
- 51
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- No antibiotic use for at least 3 months prior to the study.
Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.
Lab analysis
- Sequencing type
- 16S
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Statistical test
- LEfSe
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 4
- Matched on Factors on which subjects have been matched on in a case-control study
- age, Matched on: "bmi" 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.bmi
Signature 1
Source: Figure 3
Description: Gut microbiota differences between PD patients and controls detected by LEfSe analysis.
Abundance in Group 1: increased abundance in patients with Parkinson's disease
NCBI | Links |
---|---|
Revision editor(s): Fcuevas3