Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson's Disease from India

Study information

Reviewed Marked as Reviewed by Peace Sandy on 2024-4-15

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

38229613

DOI Digital object identifier for electronic documents.

10.4103/aian.aian_460_23

URI

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10789430/

Authors

Pavan S, Gorthi SP, Prabhu AN, Das B, Mutreja A, Vasudevan K, Shetty V, Ramamurthy T, Ballal M

Journal

Annals of Indian Academy of Neurology

Year

2023

Keywords:

16S rRNA gene sequencing, Parkinson's disease, dysbiosis, gut microbiota, neurodegenerative disease, stool

OBJECTIVES: Recent advancement in understanding neurological disorders has revealed the involvement of dysbiosis of the gut microbiota in the pathophysiology of Parkinson's disease (PD). We sequenced microbial DNA using fecal samples collected from PD cases and healthy controls (HCs) to evaluate the role of gut microbiota. METHODS: Full-length bacterial 16S rRNA gene sequencing of fecal samples was performed using amplified polymerase chain reaction (PCR) products on the GridION Nanopore sequencer. Sequenced data were analyzed using web-based tools BugSeq and MicrobiomeAnalyst. RESULTS: We found that certain bacterial families like Clostridia UCG 014, Cristensenellaceae, and Oscillospiraceae are higher in abundance, and Lachinospiracea, Coriobacteriaceae and genera associated with short-chain fatty acid production, Faecalibacterium, Fusicatenibacter, Roseburia and Blautia, are lower in abundance among PD cases when compared with the HC. Genus Akkermansia, Dialister, Bacteroides, and Lachnospiraceae NK4A136 group positively correlated with constipation in PD. CONCLUSION: Observations from this study support the other global research on the PD gut microbiome background and provide fresh insight into the gut microbial composition of PD patients from a south Indian population. We report a higher abundance of Clostridia UCG 014 group, previously not linked to PD.

Experiment 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-4-15

Curated date: 2024/03/18

Curator: Kaycee

Revision editor(s): Kaycee, Peace Sandy

Subjects

Location of subjects: India

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

Group 1 name Corresponds to the case (exposed) group for case-control studies: Parkinson's disease

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

Group 0 sample size Number of subjects in the control (unexposed) group: 13

Group 1 sample size Number of subjects in the case (exposed) group: 23

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 4 weeks

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Nanopore

Statistical Analysis

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

Statistical test: LEfSe

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

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

LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 2

Alpha Diversity

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

Chao1 Abundance-based estimator of species richness: unchanged

Simpson Estimator of species richness and species evenness: more weight on species evenness: increased

Richness Number of species: unchanged

Signature 1

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Reviewed Marked as Reviewed by Peace Sandy on 2024-4-15

Curated date: 2024/03/18

Curator: Kaycee

Revision editor(s): Kaycee, Peace Sandy

Source: Figure 5

Description: The differences between the groups were evaluated using the linear discrimination analysis effect size (LEfSe). The bar graph shows the LDA scores of significant bacteria. The colors (Healthy = red, Parkinson = blue) represent which group was more abundant compared with the other group at the genus and family level.

Abundance in Group 1: increased abundance in Parkinson's disease

NCBI	Quality Control	Links
Clostridia
Christensenellaceae
Oscillospiraceae

Revision editor(s): Kaycee, Peace Sandy

Signature 2

Edit History Delete

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Reviewed Marked as Reviewed by Peace Sandy on 2024-4-15

Curated date: 2024/03/18

Curator: Kaycee

Revision editor(s): Kaycee, Peace Sandy

Source: Figure 5

Description: The differences between the groups were evaluated using the linear discrimination analysis effect size (LEfSe). The bar graph shows the LDA scores of significant bacteria. The colors (Healthy = red, Parkinson = blue) represent which group was more abundant compared with the other group at the genus and family level.

Abundance in Group 1: decreased abundance in Parkinson's disease

NCBI	Quality Control	Links
Coriobacteriaceae
Lachnospiraceae
Collinsella
Roseburia
Fusicatenibacter
Blautia
Faecalibacterium
Lachnospiraceae bacterium

Revision editor(s): Kaycee, Peace Sandy