The Gut Microbiome in Parkinson's Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies

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Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
Authors
Lubomski M, Xu X, Holmes AJ, Muller S, Yang JYH, Davis RL, Sue CM
Journal
Frontiers in aging neuroscience
Year
2022
Keywords:
Parkinson’s disease, deep brain stimulation, device-assisted therapies, gastrointestinal microbiome, gut microbiota, levodopa-carbidopa intestinal gel, longitudinal, progression
BACKGROUND: Altered gut microbiome (GM) composition has been established in Parkinson's disease (PD). However, few studies have longitudinally investigated the GM in PD, or the impact of device-assisted therapies. OBJECTIVES: To investigate the temporal stability of GM profiles from PD patients on standard therapies and those initiating device-assisted therapies (DAT) and define multivariate models of disease and progression. METHODS: We evaluated validated clinical questionnaires and stool samples from 74 PD patients and 74 household controls (HCs) at 0, 6, and 12 months. Faster or slower disease progression was defined from levodopa equivalence dose and motor severity measures. 19 PD patients initiating Deep Brain Stimulation or Levodopa-Carbidopa Intestinal Gel were separately evaluated at 0, 6, and 12 months post-therapy initiation. RESULTS: Persistent underrepresentation of short-chain fatty-acid-producing bacteria, Butyricicoccus, Fusicatenibacter, Lachnospiraceae ND3007 group, and Erysipelotrichaceae UCG-003, were apparent in PD patients relative to controls. A sustained effect of DAT initiation on GM associations with PD was not observed. PD progression analysis indicated that the genus Barnesiella was underrepresented in faster progressing PD patients at t = 0 and t = 12 months. Two-stage predictive modeling, integrating microbiota abundances and nutritional profiles, improved predictive capacity (change in Area Under the Curve from 0.58 to 0.64) when assessed at Amplicon Sequence Variant taxonomic resolution. CONCLUSION: We present longitudinal GM studies in PD patients, showing persistently altered GM profiles suggestive of a reduced butyrogenic production potential. DATs exerted variable GM influences across the short and longer-term. We found that specific GM profiles combined with dietary factors improved prediction of disease progression in PD patients.

Experiment 1


Needs review

Curated date: 2024/03/13

Curator: Bolanle

Revision editor(s): Bolanle

Subjects

Location of subjects
Australia
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
Blood , Feces Portion of blood,Vertebrate blood,Whole blood,Blood,blood,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
Household Control
Group 1 name Corresponds to the case (exposed) group for case-control studies
Parkinson's diease (PD) patients
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
PD patients on standard therapies
Group 0 sample size Number of subjects in the control (unexposed) group
74
Group 1 sample size Number of subjects in the case (exposed) group
74
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

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
centered log-ratio
Statistical test
ANOVA
T-Test
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
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, diet, sex, constipation

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/13

Curator: Bolanle

Revision editor(s): Bolanle

Source: Result, Figure 2

Description: Differentially abundant taxa between the PD and HC groups across the three timepoints; bacteria that produce short chain fatty-acids in PD patients compared to healthy controls

Abundance in Group 1: decreased abundance in Parkinson's diease (PD) patients

NCBI Quality ControlLinks
Butyricicoccus
Fusicatenibacter
Lachnospiraceae
erysipelotrichaceae UCG-003erysipelotrichaceae UCG-003

Revision editor(s): Bolanle

Experiment 2


Needs review

Curated date: 2024/03/13

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Patients with Slow progressing Parkinson's disease
Group 1 name Corresponds to the case (exposed) group for case-control studies
Patients with Faster progressing Parkinson's disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Patients with faster progressing parkinson's disease over a 12 month period
Group 0 sample size Number of subjects in the control (unexposed) group
40
Group 1 sample size Number of subjects in the case (exposed) group
34
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
All participants had not received antibiotics supplements for at least 1 month prior sample collection

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/13

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 4

Description: Differential abundance of taxa between faster progressing and slower progressing PD patients within 12 months, specifically at two-time intervals(t=0, t=12)

Abundance in Group 1: decreased abundance in Patients with Faster progressing Parkinson's disease

NCBI Quality ControlLinks
Barnesiellaceae

Revision editor(s): Bolanle

Experiment 3


Needs review

Curated date: 2024/03/13

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre DAT(device assisted therapy)
Group 1 name Corresponds to the case (exposed) group for case-control studies
DBS(deep brain stimulation)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
initiation of DBS therapy on parkinson's disease patients at 0 month
Group 0 sample size Number of subjects in the control (unexposed) group
74
Group 1 sample size Number of subjects in the case (exposed) group
9
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

Statistical Analysis

Statistical test
ANOVA
Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.01
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, diet, sex, constipation

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Experiment 4


Needs review

Curated date: 2024/03/13

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre DAT(device assisted therapy) PD patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
LCIG(Levodopa-Carbidopa Intestinal Gel)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
initiation of LCIG therapy on parkinson's disease patients at 0 month
Group 1 sample size Number of subjects in the case (exposed) group
10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Experiment 5


Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Household Control
Group 1 name Corresponds to the case (exposed) group for case-control studies
Parkinson's diease patients at 6 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
PD patients on standard therapies at 6months
Group 1 sample size Number of subjects in the case (exposed) group
74

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.05
Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, body mass index, sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/18

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 2 text

Description: There was statistically significant underrepresentation of the bacterial signatures in the gut microbiota of PD patients at 6months time point compared to healthy controls

Abundance in Group 1: decreased abundance in Parkinson's diease patients at 6 months

NCBI Quality ControlLinks
Agathobacter
Butyricicoccus
Eubacterium
Faecalibacterium
Firmicutes bacterium CAG:56
Fusicatenibacter
Ruminococcus
lachnospiraceae ND3007lachnospiraceae ND3007
erysipelotrichaceae UGC-003erysipelotrichaceae UGC-003
lachnospiraceae FCS020lachnospiraceae FCS020

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/18

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 7 text

Description: There was statistically significant overrepresentation of the bacterial signatures in the gut microbiota of PD patients at 6months time point compared to healthy controls

Abundance in Group 1: increased abundance in Parkinson's diease patients at 6 months

NCBI Quality ControlLinks
Enterobacteriaceae
unclassified Lactobacillaceae

Revision editor(s): Bolanle

Experiment 6


Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 name Corresponds to the case (exposed) group for case-control studies
Parkinson's diease patients at 12 months
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
Parkinson's disease patients samples collected at 12months

Lab analysis

Statistical Analysis

Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
age, diet, sex, constipation

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/18

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 2 text

Description: There was statistically significant overrepresentation of the bacterial signatures in the gut microbiota of PD patients at 12months time point compared to healthy control

Abundance in Group 1: decreased abundance in Parkinson's diease patients at 12 months

NCBI Quality ControlLinks
Anaerostipes
Butyricicoccaceae

Revision editor(s): Bolanle

Signature 3

Needs review

Curated date: 2024/03/18

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 2 text

Description: There was statistically significant overrepresentation of the bacterial signatures in the gut microbiota of PD patients at 12months time point compared to healthy control

Abundance in Group 1: increased abundance in Parkinson's diease patients at 12 months

NCBI Quality ControlLinks
unclassified Lactobacillaceae

Revision editor(s): Bolanle

Experiment 7


Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre DAT(device assisted therapy)
Group 1 name Corresponds to the case (exposed) group for case-control studies
DBS(deep brain stimulation)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
initiation of DBS therapy on parkinson's disease patients at 6 month
Group 1 sample size Number of subjects in the case (exposed) group
9

Lab analysis

Statistical Analysis

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
0.01

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Source: figure 7

Description: the most differentially abbundant taxa after the initiation of DS therapy at 0-6months timepoint included overrepresentation of the geus level

Abundance in Group 1: increased abundance in DBS(deep brain stimulation)

NCBI Quality ControlLinks
Prevotella

Revision editor(s): Bolanle

Experiment 8


Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
initiation of DBS therapy on parkinson's disease patients at 12 month

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 7

Description: DBS therapy patients showed overrepresentation of these taxa (t=12moths)

Abundance in Group 1: increased abundance in DBS(deep brain stimulation)

NCBI Quality ControlLinks
Bacillaceae
Bacillus
Citrobacter
Faecalicoccus
Methanobacteriaceae
Methanobrevibacter
Morganella
Prevotella
Spirochaetaceae
Treponema
Veillonella

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 7

Description: DBS therapy patients showed uderrepresentation of these taxa after 12 months initiation

Abundance in Group 1: decreased abundance in DBS(deep brain stimulation)

NCBI Quality ControlLinks
Acetanaerobacterium
Anaerotruncus
Flavonifractor
Hespellia
Howardella

Revision editor(s): Bolanle

Experiment 9


Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies
Pre DAT(device assisted therapy) PD patients
Group 1 name Corresponds to the case (exposed) group for case-control studies
LCIG(Levodopa-Carbidopa Intestinal Gel)
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
initiation of LCIG therapy on parkinson's disease patients at 6 month
Group 1 sample size Number of subjects in the case (exposed) group
10

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 7

Description: Gut microbiome compositional differences in response to the initiation and continuation Levodopa-Carbidopa Intestinal gel (LCIG) therapies at 6months

Abundance in Group 1: increased abundance in LCIG(Levodopa-Carbidopa Intestinal Gel)

NCBI Quality ControlLinks
Prevotellaceae
Roseburia

Revision editor(s): Bolanle

Signature 2

Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 7

Description: Gut microbiome compositional differences in response to the initiation and continuation Levodopa-Carbidopa Intestinal gel (LCIG) therapies at 6months

Abundance in Group 1: decreased abundance in LCIG(Levodopa-Carbidopa Intestinal Gel)

NCBI Quality ControlLinks
Acetanaerobacterium
Eggerthella
Gordonibacter
Hespellia
Holdemania

Revision editor(s): Bolanle

Experiment 10


Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
initiation of LCIG therapy on parkinson's disease patients at 12 month

Lab analysis

Statistical Analysis

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness
decreased
Simpson Estimator of species richness and species evenness: more weight on species evenness
decreased

Signature 1

Needs review

Curated date: 2024/03/16

Curator: Bolanle

Revision editor(s): Bolanle

Source: Figure 7

Description: Gut microbiome compositional differences in response to the initiation and continuation Levodopa-Carbidopa Intestinal gel (LCIG) therapies at 12months

Abundance in Group 1: increased abundance in LCIG(Levodopa-Carbidopa Intestinal Gel)

NCBI Quality ControlLinks
Bacillus
Prevotella

Revision editor(s): Bolanle