Unraveling gut microbiota in Parkinson's disease and atypical parkinsonism

From BugSigDB
Reviewed Marked as Reviewed by Fatima on 2021/10/20
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Barichella M, Severgnini M, Cilia R, Cassani E, Bolliri C, Caronni S, Ferri V, Cancello R, Ceccarani C, Faierman S, Pinelli G, De Bellis G, Zecca L, Cereda E, Consolandi C, Pezzoli G
Journal
Movement disorders : official journal of the Movement Disorder Society
Year
2019
BACKGROUND: Although several studies have suggested that abnormalities in gut microbiota may play a critical role in the pathogenesis of PD, data are still extremely heterogeneous. METHODS: 16S gene ribosomal RNA sequencing was performed on fecal samples of 350 individuals, subdivided into idiopathic PD (n = 193, of whom 39 were drug naïve) stratified by disease duration, PSP (n = 22), MSA (n = 22), and healthy controls (HC; n = 113). Several confounders were taken into account, including dietary habits. RESULTS: Despite the fact that unadjusted comparison of PD and HC showed several differences in relative taxa abundances, the significant results were greatly reduced after adjusting for confounders. Although most of these differences were associated with disease duration, lower abundance in Lachnospiraceae was the only difference between de novo PD and HC (remaining lower across almost all PD duration strata). Decreased Lachnospiraceae and increased Lactobacillaceae and Christensenellaceae were associated with a worse clinical profile, including higher frequencies of cognitive impairment, gait disturbances, and postural instability. When compared with HC, MSA and PSP patients shared the changes in PD, with a few exceptions: in MSA, Lachnospiraceae were not lower, and Prevotellaceae were reduced; in PSP, Lactobacillaceae were similar, and Streptococcaceae were reduced. CONCLUSIONS: Gut microbiota may be an environmental modulator of the pathogenesis of PD and contribute to the interindividual variability of clinical features. Data are influenced by PD duration and several confounders that need to be taken into account in future studies. Prospective studies in de novo PD patients are needed to elucidate the net effect of dysbiosis on the progression of the disease. © 2018 International Parkinson and Movement Disorder Society.

Experiment 1


Reviewed Marked as Reviewed by Fatima on 2021/10/20

Curated date: 2021/09/19

Curator: Fcuevas3

Revision editor(s): Fatima, Fcuevas3, WikiWorks

Subjects

Location of subjects
Italy
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 idiopathic parkinson's disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with idiopathic parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996)
Group 0 sample size Number of subjects in the control (unexposed) group
113
Group 1 sample size Number of subjects in the case (exposed) group
193
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
1 month

Lab analysis

Sequencing type
16S
16S variable region One or more hypervariable region(s) of the bacterial 16S gene
V3-V4
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
Matched on Factors on which subjects have been matched on in a case-control study
age, geographic area, 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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, breast feeding, smoking status, Confounders controlled for: "use of catechol-O-methyltransferase inhibitors" 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.use of catechol-O-methyltransferase inhibitors, Confounders controlled for: "genetic status (recessive)" 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.genetic status (recessive), Confounders controlled for: "gender" 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.gender, Confounders controlled for: "constipation" 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.constipation, Confounders controlled for: "protein intake" 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.protein intake, Confounders controlled for: "animal vegetal protein ratio" 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.animal vegetal protein ratio, Confounders controlled for: "alcohol intake" 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.alcohol intake, Confounders controlled for: "fibers intake" 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.fibers intake, Confounders controlled for: "insoluble-soluble fiber ratio" 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.insoluble-soluble fiber ratio, Confounders controlled for: "water intake [mL/day]" 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.water intake [mL/day], Confounders controlled for: "coffee intake" 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.coffee intake

Alpha Diversity

Chao1 Abundance-based estimator of species richness
increased
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2021/09/19

Curator: Fcuevas3

Revision editor(s): Fatima, Fcuevas3

Source: Supplementary table 3, Signature 1 is for increased abundance in those with Parkinson's

Description: Analysis of relative taxa abundance in controls and different disease groups.

Abundance in Group 1: increased abundance in patients with idiopathic parkinson's disease

NCBI Links
Akkermansia
Bifidobacteriaceae
Bifidobacterium
Christensenellaceae
Coriobacteriaceae
Enterobacteriaceae
Lactobacillaceae
Oscillospira
Parabacteroides
Pseudomonadota
Verrucomicrobiota
Verrucomicrobiaceae
unclassified Bacillota

Revision editor(s): Fatima, Fcuevas3

Signature 2

Needs review

Curated date: 2021/09/28

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 3, Signature 2 is for decreased abundance in those with Parkinson's

Description: Analysis of relative taxa abundance in controls and different disease groups.

Abundance in Group 1: decreased abundance in patients with idiopathic parkinson's disease

NCBI Links
Lachnospiraceae
Roseburia
Ruminococcus

Revision editor(s): Fcuevas3

Experiment 2


Needs review

Curated date: 2021/09/20

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

Subjects

Location of subjects
Italy
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
the trend over Parkinson's disease progression
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with idiopathic Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996)
Group 0 sample size Number of subjects in the control (unexposed) group
113
Group 1 sample size Number of subjects in the case (exposed) group
193

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
Matched on Factors on which subjects have been matched on in a case-control study
age, geographic area, 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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, breast feeding, smoking status, Confounders controlled for: "use of catechol-O-methyltransferase inhibitors" 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.use of catechol-O-methyltransferase inhibitors, Confounders controlled for: "genetic status (recessive)" 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.genetic status (recessive), Confounders controlled for: "gender" 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.gender, Confounders controlled for: "constipation" 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.constipation, Confounders controlled for: "protein intake" 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.protein intake, Confounders controlled for: "animal vegetal protein ratio" 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.animal vegetal protein ratio, Confounders controlled for: "alcohol intake" 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.alcohol intake, Confounders controlled for: "fibers intake" 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.fibers intake, Confounders controlled for: "insoluble-soluble fiber ratio" 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.insoluble-soluble fiber ratio, Confounders controlled for: "water intake [mL/day]" 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.water intake [mL/day], Confounders controlled for: "coffee intake" 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.coffee intake, Confounders controlled for: "use of protein pump inhibitors" 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.use of protein pump inhibitors


Signature 1

Needs review

Curated date: 2021/09/20

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 1 is for increased taxa abundance in different groups of Parkinson's disease patients.

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.

Abundance in Group 1: increased abundance in the trend over Parkinson's disease progression

NCBI Links
Akkermansia
Lactobacillaceae
Lactobacillus
Verrucomicrobiota
Verrucomicrobiaceae

Revision editor(s): Fcuevas3

Signature 2

Needs review

Curated date: 2021/09/28

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 2 is for decreased taxa abundance in different groups of Parkinson's disease patients.

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.

Abundance in Group 1: decreased abundance in the trend over Parkinson's disease progression

NCBI Links
Lachnospiraceae

Revision editor(s): Fcuevas3

Experiment 3


Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

Subjects

Location of subjects
Italy
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 MSA(multiple system atrophy) disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with synucleinopathy multiple system atrophy (MSA)
Group 0 sample size Number of subjects in the control (unexposed) group
113
Group 1 sample size Number of subjects in the case (exposed) group
22

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
Matched on Factors on which subjects have been matched on in a case-control study
age, geographic area, 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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, breast feeding, smoking status, Confounders controlled for: "use of catechol-O-methyltransferase inhibitors" 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.use of catechol-O-methyltransferase inhibitors, Confounders controlled for: "genetic status (recessive)" 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.genetic status (recessive), Confounders controlled for: "gender" 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.gender, Confounders controlled for: "constipation" 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.constipation, Confounders controlled for: "protein intake" 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.protein intake, Confounders controlled for: "animal vegetal protein ratio" 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.animal vegetal protein ratio, Confounders controlled for: "alcohol intake" 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.alcohol intake, Confounders controlled for: "fibers intake" 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.fibers intake, Confounders controlled for: "insoluble-soluble fiber ratio" 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.insoluble-soluble fiber ratio, Confounders controlled for: "water intake [mL/day]" 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.water intake [mL/day], Confounders controlled for: "coffee intake" 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.coffee intake

Alpha Diversity

Chao1 Abundance-based estimator of species richness
increased
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 3, signature 1 is for increased abundance in those with MSA

Description: Analysis of relative taxa abundance in controls and different disease groups.

Abundance in Group 1: increased abundance in patients with MSA(multiple system atrophy) disease

NCBI Links
Akkermansia
Lactobacillaceae
Parabacteroides
Verrucomicrobiota
Verrucomicrobiaceae

Revision editor(s): Fcuevas3

Signature 2

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 3, Signature 2 is for decreased abundance in those with MSA

Description: Analysis of relative taxa abundance in controls and different disease groups.

Abundance in Group 1: decreased abundance in patients with MSA(multiple system atrophy) disease

NCBI Links
Faecalibacterium
Prevotellaceae

Revision editor(s): Fcuevas3

Experiment 4


Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

Subjects

Location of subjects
Italy
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 PSP(progressive supranuclear palsy) disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients diagnosed with tauopathy progressive supranuclear palsy (PSP)
Group 0 sample size Number of subjects in the control (unexposed) group
113
Group 1 sample size Number of subjects in the case (exposed) group
22

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
Matched on Factors on which subjects have been matched on in a case-control study
age, geographic area, 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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, breast feeding, smoking status, Confounders controlled for: "use of catechol-O-methyltransferase inhibitors" 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.use of catechol-O-methyltransferase inhibitors, Confounders controlled for: "genetic status (recessive)" 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.genetic status (recessive), Confounders controlled for: "gender" 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.gender, Confounders controlled for: "constipation" 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.constipation, Confounders controlled for: "protein intake" 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.protein intake, Confounders controlled for: "animal vegetal protein ratio" 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.animal vegetal protein ratio, Confounders controlled for: "alcohol intake" 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.alcohol intake, Confounders controlled for: "fibers intake" 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.fibers intake, Confounders controlled for: "insoluble-soluble fiber ratio" 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.insoluble-soluble fiber ratio, Confounders controlled for: "water intake [mL/day]" 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.water intake [mL/day], Confounders controlled for: "coffee intake" 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.coffee intake

Alpha Diversity

Chao1 Abundance-based estimator of species richness
increased
Richness Number of species
increased

Signature 1

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 3, Signature 1 is for increased abundance in those with PSP

Description: Analysis of relative taxa abundance in controls and different disease groups

Abundance in Group 1: increased abundance in patients with PSP(progressive supranuclear palsy) disease

NCBI Links
Akkermansia
Christensenellaceae
Oscillospira
Parabacteroides
Verrucomicrobiota
Verrucomicrobiaceae

Revision editor(s): Fcuevas3

Signature 2

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 3, Signature 2 is for decreased abundance in those with PSP

Description: Analysis of relative taxa abundance in controls and different disease groups

Abundance in Group 1: decreased abundance in patients with PSP(progressive supranuclear palsy) disease

NCBI Links
Lachnospiraceae
Roseburia
Streptococcaceae
Streptococcus

Revision editor(s): Fcuevas3

Experiment 5


Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

Subjects

Location of subjects
Italy
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 De-novo Parkinson's disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with de novo Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996)
Group 0 sample size Number of subjects in the control (unexposed) group
113
Group 1 sample size Number of subjects in the case (exposed) group
39

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
Matched on Factors on which subjects have been matched on in a case-control study
age, geographic area, 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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, breast feeding, smoking status, Confounders controlled for: "use of catechol-O-methyltransferase inhibitors" 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.use of catechol-O-methyltransferase inhibitors, Confounders controlled for: "genetic status (recessive)" 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.genetic status (recessive), Confounders controlled for: "gender" 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.gender, Confounders controlled for: "constipation" 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.constipation, Confounders controlled for: "protein intake" 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.protein intake, Confounders controlled for: "animal vegetal protein ratio" 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.animal vegetal protein ratio, Confounders controlled for: "alcohol intake" 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.alcohol intake, Confounders controlled for: "fibers intake" 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.fibers intake, Confounders controlled for: "insoluble-soluble fiber ratio" 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.insoluble-soluble fiber ratio, Confounders controlled for: "water intake [mL/day]" 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.water intake [mL/day], Confounders controlled for: "coffee intake" 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.coffee intake, Confounders controlled for: "use of protein pump inhibitors" 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.use of protein pump inhibitors


Signature 1

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 1 is for decreased taxa abundance in patients with De novo parkinson's

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.

Abundance in Group 1: decreased abundance in patients with De-novo Parkinson's disease

NCBI Links
Lachnospiraceae

Revision editor(s): Fcuevas3

Experiment 6


Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

Subjects

Location of subjects
Italy
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 early Parkinson's disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with early Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996)
Group 0 sample size Number of subjects in the control (unexposed) group
113
Group 1 sample size Number of subjects in the case (exposed) group
57

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
Matched on Factors on which subjects have been matched on in a case-control study
age, geographic area, 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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, breast feeding, smoking status, Confounders controlled for: "use of catechol-O-methyltransferase inhibitors" 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.use of catechol-O-methyltransferase inhibitors, Confounders controlled for: "genetic status (recessive)" 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.genetic status (recessive), Confounders controlled for: "gender" 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.gender, Confounders controlled for: "constipation" 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.constipation, Confounders controlled for: "protein intake" 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.protein intake, Confounders controlled for: "animal vegetal protein ratio" 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.animal vegetal protein ratio, Confounders controlled for: "alcohol intake" 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.alcohol intake, Confounders controlled for: "fibers intake" 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.fibers intake, Confounders controlled for: "insoluble-soluble fiber ratio" 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.insoluble-soluble fiber ratio, Confounders controlled for: "water intake [mL/day]" 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.water intake [mL/day], Confounders controlled for: "coffee intake" 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.coffee intake, Confounders controlled for: "use of protein pump inhibitors" 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.use of protein pump inhibitors


Signature 1

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 1 is for increased taxa abundance among patients with early Parkinson's

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients

Abundance in Group 1: increased abundance in patients with early Parkinson's disease

NCBI Links
Akkermansia
Christensenellaceae
Enterobacteriaceae
Verrucomicrobiota
Verrucomicrobiaceae

Revision editor(s): Fcuevas3

Signature 2

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 2 is for decreased taxa abundance among participants with early Parkinson's

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients.

Abundance in Group 1: decreased abundance in patients with early Parkinson's disease

NCBI Links
Lachnospiraceae

Revision editor(s): Fcuevas3

Experiment 7


Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

Subjects

Location of subjects
Italy
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 mid stage Parkinson's
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with mid stage Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996)
Group 0 sample size Number of subjects in the control (unexposed) group
113
Group 1 sample size Number of subjects in the case (exposed) group
53

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
Matched on Factors on which subjects have been matched on in a case-control study
age, geographic area, 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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, breast feeding, smoking status, Confounders controlled for: "use of catechol-O-methyltransferase inhibitors" 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.use of catechol-O-methyltransferase inhibitors, Confounders controlled for: "genetic status (recessive)" 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.genetic status (recessive), Confounders controlled for: "gender" 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.gender, Confounders controlled for: "constipation" 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.constipation, Confounders controlled for: "protein intake" 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.protein intake, Confounders controlled for: "animal vegetal protein ratio" 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.animal vegetal protein ratio, Confounders controlled for: "alcohol intake" 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.alcohol intake, Confounders controlled for: "fibers intake" 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.fibers intake, Confounders controlled for: "insoluble-soluble fiber ratio" 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.insoluble-soluble fiber ratio, Confounders controlled for: "water intake [mL/day]" 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.water intake [mL/day], Confounders controlled for: "coffee intake" 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.coffee intake, Confounders controlled for: "use of protein pump inhibitors" 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.use of protein pump inhibitors


Signature 1

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 1 is for increased taxa abundance among participants w/mid stage Parkinson's Analysis of relative taxa abundance in different groups of Parkinson’s disease patients

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients

Abundance in Group 1: increased abundance in patients with mid stage Parkinson's

NCBI Links
Akkermansia
Christensenellaceae
Enterobacteriaceae
Pseudomonadota
Verrucomicrobiota
Verrucomicrobiaceae

Revision editor(s): Fcuevas3

Signature 2

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 2 is for decreased taxa abundance among those w/ mid stage Parkinson's

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients

Abundance in Group 1: decreased abundance in patients with mid stage Parkinson's

NCBI Links
Lachnospiraceae

Revision editor(s): Fcuevas3

Experiment 8


Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3, WikiWorks

Subjects

Location of subjects
Italy
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 advanced stage Parkinson's
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with advanced stage Parkinson's disease with stage diagnosed according to UK Brain Bank Criteria(1996)
Group 0 sample size Number of subjects in the control (unexposed) group
113
Group 1 sample size Number of subjects in the case (exposed) group
44

Lab analysis

Sequencing type
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Illumina

Statistical Analysis

Statistical test
Negative Binomial Regression
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
.05
Matched on Factors on which subjects have been matched on in a case-control study
age, geographic area, 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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, breast feeding, smoking status, Confounders controlled for: "use of catechol-O-methyltransferase inhibitors" 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.use of catechol-O-methyltransferase inhibitors, Confounders controlled for: "genetic status (recessive)" 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.genetic status (recessive), Confounders controlled for: "gender" 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.gender, Confounders controlled for: "constipation" 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.constipation, Confounders controlled for: "protein intake" 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.protein intake, Confounders controlled for: "animal vegetal protein ratio" 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.animal vegetal protein ratio, Confounders controlled for: "alcohol intake" 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.alcohol intake, Confounders controlled for: "fibers intake" 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.fibers intake, Confounders controlled for: "insoluble-soluble fiber ratio" 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.insoluble-soluble fiber ratio, Confounders controlled for: "water intake [mL/day]" 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.water intake [mL/day], Confounders controlled for: "coffee intake" 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.coffee intake, Confounders controlled for: "use of protein pump inhibitors" 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.use of protein pump inhibitors


Signature 1

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 1 is for increased taxa abundance among those with advanced Parkinson's

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients

Abundance in Group 1: increased abundance in patients with advanced stage Parkinson's

NCBI Links
Akkermansia
Enterobacteriaceae
Pseudomonadota
Verrucomicrobiota
Verrucomicrobiaceae

Revision editor(s): Fcuevas3

Signature 2

Needs review

Curated date: 2021/09/30

Curator: Fcuevas3

Revision editor(s): Fcuevas3

Source: Supplementary table 4, Signature 2 is for decreased taxa abundance among those with advanced Parkinson's

Description: Analysis of relative taxa abundance in different groups of Parkinson’s disease patients

Abundance in Group 1: decreased abundance in patients with advanced stage Parkinson's

NCBI Links
Bacillota
Lachnospiraceae

Revision editor(s): Fcuevas3