Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China

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Needs review

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3, Aiyshaaaa, WikiWorks

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

Needs review

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Needs review

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Needs review

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Needs review

Curated date: 2021/10/19

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Needs review

Curated date: 2021/10/19

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Needs review

Curated date: 2021/10/19

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Needs review

Curated date: 2021/10/19

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Needs review

Curated date: 2021/10/19

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

incomplete

Curated date: 2021/10/20

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

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

incomplete

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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

Your review change was submittedDuplicate this Experiment Add a new Signature

Needs review

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

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

incomplete

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3

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