Gut microbiota in Parkinson's disease: Temporal stability and relations to disease progression

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/02/02

Curator: Fcuevas3

Revision editor(s): Fcuevas3, Aiyshaaaa, ChiomaBlessing, Folakunmi

Subjects

Location of subjects: Finland

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Parkinson's disease IDIOPATHIC PARKINSON DIS,Idiopathic Parkinson Disease,Idiopathic Parkinson's Disease,IDIOPATHIC PARKINSONS DIS,Idiopathic PD,LEWY BODY PARKINSON DIS,Lewy Body Parkinson Disease,Lewy Body Parkinson's Disease,Paralysis agitans,paralysis agitans,PARKINSON DIS,PARKINSON DIS IDIOPATHIC,Parkinson disease,Parkinson Disease, Idiopathic,Parkinson syndrome,Parkinson's,Parkinson's disease,Parkinson's disease (disorder),Parkinson's disease NOS,Parkinson's disease NOS (disorder),Parkinson's Disease, Idiopathic,Parkinson's Disease, Lewy Body,Parkinson's syndrome,Parkinsonian disorder,Parkinsonism, Primary,Parkinsons,PARKINSONS DIS,PARKINSONS DIS IDIOPATHIC,PARKINSONS DIS LEWY BODY,Parkinsons disease,Primary Parkinsonism,parkinson's disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy controls at baseline

Group 1 name Corresponds to the case (exposed) group for case-control studies: Participants with Parkinson's Disease at baseline

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with Parkinson's disease at baseline.

Group 0 sample size Number of subjects in the control (unexposed) group: 64

Group 1 sample size Number of subjects in the case (exposed) group: 64

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None.

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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: raw counts

Statistical test: ANCOM; DESeq2

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Matched on Factors on which subjects have been matched on in a case-control study: age, sex

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: body mass index, irritable bowel syndrome

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/02/02

Curator: Fcuevas3

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Source: Table 8, Supplemental. Table S4C

Description: Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Baseline

Abundance in Group 1: increased abundance in Participants with Parkinson's Disease at baseline

NCBI	Quality Control	Links
Alistipes
Bifidobacteriaceae
Bifidobacterium
Romboutsia
Clostridium_XIVaClostridium_XIVa

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/02/02

Curator: Fcuevas3

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Source: Table 8, Supplemental. Table S4C

Description: Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Baseline

Abundance in Group 1: decreased abundance in Participants with Parkinson's Disease at baseline

NCBI	Quality Control	Links
Blautia
Butyricimonas
Porphyromonadaceae
Prevotella
Veillonellaceae
Clostridium_XVIIIClostridium_XVIII
Dialister

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Experiment 2

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/02/02

Curator: Fcuevas3

Revision editor(s): LGeistlinger, Fcuevas3, ChiomaBlessing, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Stable PD patients at follow up

Group 1 name Corresponds to the case (exposed) group for case-control studies: Progressed PD patients at follow up

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with progressed Parkinson's disease, defined based on between-timepoint change in Unified Parkinson's Disease Rating Scale (UPDRS) I-III sum and total medication load calculated using the Levodopa Equivalent Dose (LED).

Group 0 sample size Number of subjects in the control (unexposed) group: 41

Group 1 sample size Number of subjects in the case (exposed) group: 15

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "COMT inhibitor use" 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.COMT inhibitor use

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/02/02

Curator: Fcuevas3

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Source: Table 9: Follow up.

Description: Summary of differential abundance results contrasting follow-up progressed and stable PD patients

Abundance in Group 1: increased abundance in Progressed PD patients at follow up

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Bifidobacterium
Anaeroplasmataceae
Asteroleplasma
unclassified Lachnospiraceae
unclassified Eubacteriales
Clostridium IVClostridium IV

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2024/01/10

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Table 9: Follow-up

Description: Summary of differential abundance results contrasting follow-up progressed and stable PD patients

Abundance in Group 1: decreased abundance in Progressed PD patients at follow up

NCBI	Quality Control	Links
Prevotella
Phascolarctobacterium
Coprococcus
Desulfovibrio

Revision editor(s): ChiomaBlessing

Experiment 3

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/02/02

Curator: Fcuevas3

Revision editor(s): Lwaldron, Fcuevas3, ChiomaBlessing, Folakunmi

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Healthy controls at time of follow-up

Group 1 name Corresponds to the case (exposed) group for case-control studies: Participants with Parkinson's Disease at time of follow-up

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Participants with Parkinson's Disease at time of follow-up

Group 0 sample size Number of subjects in the control (unexposed) group: 64

Group 1 sample size Number of subjects in the case (exposed) group: 64

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None.

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: body mass index, irritable bowel syndrome

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/02/02

Curator: Fcuevas3

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Source: Table 8, Supplemental. Table S4C

Description: Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Follow-up.

Abundance in Group 1: increased abundance in Participants with Parkinson's Disease at time of follow-up

NCBI	Quality Control	Links
Bifidobacteriaceae
Bifidobacterium
Clostridium_IVClostridium_IV
Clostridium_XIVaClostridium_XIVa
Romboutsia

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-10

Curated date: 2023/02/02

Curator: Fcuevas3

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Source: Table 8, Supplemental. Table S4C

Description: Taxa that are differentially abundant between control and PD groups, according to ANCOM and DESeq2 at Follow-up.

Abundance in Group 1: decreased abundance in Participants with Parkinson's Disease at time of follow-up

NCBI	Quality Control	Links
Bacteroides
Prevotella
Prevotellaceae
Puniceicoccaceae
Roseburia
Ruminococcus
Clostridium_XIVaClostridium_XIVa
Porphyromonadaceae
Dialister
Veillonellaceae

Revision editor(s): Fcuevas3, Folakunmi, ChiomaBlessing

Experiment 4

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2023/10/16

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Tremor-dominant phenotype (TD) at baseline

Group 1 name Corresponds to the case (exposed) group for case-control studies: Postural instability and gait difficulty (PIGD) phenotype at baseline

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Parkinson's disease patients with PIGD phenotype at baseline.

Group 0 sample size Number of subjects in the control (unexposed) group: 21

Group 1 sample size Number of subjects in the case (exposed) group: 28

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): none

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Not specified

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2023/10/16

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing, MyleeeA

Source: Table S8 (B) in supplementary results.

Description: Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at baseline.

Abundance in Group 1: decreased abundance in Postural instability and gait difficulty (PIGD) phenotype at baseline

NCBI	Quality Control	Links
Anaeroplasmataceae
Asteroleplasma
Bifidobacterium
Clostridium
Eisenbergiella
Enterobacteriaceae
Escherichia/Shigella sp.
Lactococcus
Prevotella
unclassified Deltaproteobacteria
unclassified Lachnospiraceae

Revision editor(s): Folakunmi, ChiomaBlessing, MyleeeA

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2023/10/16

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Source: Table S8 (B) in supplementary results.

Description: Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at baseline.

Abundance in Group 1: increased abundance in Postural instability and gait difficulty (PIGD) phenotype at baseline

NCBI	Quality Control	Links
Bacteroides
Butyrivibrio
Gemmiger
unclassified Acidaminococcaceae
unclassified Lachnospiraceae
unclassified Eubacteriales
unclassified Bacteria

Revision editor(s): Folakunmi, ChiomaBlessing

Experiment 5

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2023/10/16

Curator: Folakunmi

Revision editor(s): Folakunmi, ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Tremor-dominant phenotype (TD) at follow-up

Group 1 name Corresponds to the case (exposed) group for case-control studies: Postural instability and gait difficulty (PIGD) phenotype at follow-up

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Parkinson's disease patients with PIGD phenotype at follow-up

Group 0 sample size Number of subjects in the control (unexposed) group: 20

Group 1 sample size Number of subjects in the case (exposed) group: 35

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2023/10/16

Curator: Folakunmi

Revision editor(s): Peace Sandy, ChiomaBlessing, Folakunmi, Hodan Issah

Source: Table S8 (B) in supplementary results.

Description: Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group) at follow-up

Abundance in Group 1: decreased abundance in Postural instability and gait difficulty (PIGD) phenotype at follow-up

NCBI	Quality Control	Links
Barnesiella
Lactococcus
unclassified Clostridiaceae
unclassified Lachnospiraceae
unclassified Oscillospiraceae
unclassified Porphyromonadaceae
Clostridium XIVaClostridium XIVa
Anaeroplasmataceae
Asteroleplasma
unclassified Eubacteriales
unclassified Clostridia

Revision editor(s): Peace Sandy, ChiomaBlessing, Folakunmi, Hodan Issah

Signature 2

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2023/10/16

Curator: Folakunmi

Revision editor(s): Folakunmi

Source: Table S8 (B) in supplementary results.

Description: Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group)

Abundance in Group 1: increased abundance in Postural instability and gait difficulty (PIGD) phenotype at follow-up

NCBI	Quality Control	Links
Akkermansia
unclassified Oscillospiraceae

Revision editor(s): Folakunmi

Experiment 6

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2024/01/11

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Stable PD patients at baseline

Group 1 name Corresponds to the case (exposed) group for case-control studies: Progressed PD patients at baseline

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Patients with progressed Parkinson's disease, defined based on between-timepoint change in Unified Parkinson's Disease Rating Scale (UPDRS) I-III sum and total medication load calculated using the Levodopa Equivalent Dose (LED).

Group 0 sample size Number of subjects in the control (unexposed) group: 41

Group 1 sample size Number of subjects in the case (exposed) group: 15

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): None

Lab analysis

Statistical Analysis

Statistical test: DESeq2

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: No

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment: Confounders controlled for: "COMT inhibitor use" 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.COMT inhibitor use

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: unchanged

Inverse Simpson Modification of Simpsons index D as 1/D to obtain high values in datasets of high diversity and vice versa: unchanged

Richness Number of species: unchanged

Signature 1

Reviewed Marked as Reviewed by ChiomaBlessing on 2024-1-11

Curated date: 2024/01/11

Curator: ChiomaBlessing

Revision editor(s): ChiomaBlessing

Source: Table 9: Baseline

Description: Summary of differential abundance results contrasting follow-up progressed and stable PD patients

Abundance in Group 1: increased abundance in Progressed PD patients at baseline

NCBI	Quality Control	Links
Streptococcaceae
Streptococcus
unclassified Lachnospiraceae

Revision editor(s): ChiomaBlessing

Signature 2