The link between increased Desulfovibrio and disease severity in Parkinson's disease

Study information

Reviewed Marked as Reviewed by Svetlana up on 2025-2-28

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

36995383

DOI Digital object identifier for electronic documents.

10.1007/s00253-023-12489-1

URI

Authors

Nie S, Jing Z, Wang J, Deng Y, Zhang Y, Ye Z, Ge Y

Journal

Applied microbiology and biotechnology

Year

2023

Keywords:

Desulfovibrio, Disease severity, Gut microbiome, Hydrogen sulfide, Parkinson’s disease

Parkinson's disease (PD), a progressive and incurable neurodegenerative disease, has taken a huge economic toll and medical burden on our society. Increasing evidence has shown a strong link between PD and the gut microbiome, but studies on the relationship between the gut microbiome and the severity of PD are limited. In this study, 90 fecal samples were collected from newly diagnosed and untreated patients with PD (n = 47) and matched healthy control subjects (n = 43). The 16S rRNA amplicon and shotgun metagenomic sequencing was performed, aiming to uncover the connection between the gut microbiome and disease severity in PD. The results showed that Desulfovibrio was significantly increased in PD compared to healthy controls and positively correlated with disease severity. The increase in Desulfovibrio was mainly driven by enhanced homogeneous selection and weakened drift. Moreover, through metagenome-assembled genomes (MAGs) analysis, a Desulfovibrio MAG (MAG58) was obtained which was also positively correlated with disease severity. MAG58 possesses a complete assimilatory sulfate reduction pathway and a near-complete dissimilatory sulfate reduction pathway to produce hydrogen sulfide which may influence the development of PD. Based on these results, a potential pathogenic mechanism was presented to illustrate how the increased Desulfovibrio accelerates the development of PD by producing excessive hydrogen sulfide. The present study highlighted the vital role of Desulfovibrio in the development of PD, which may provide a new target for the diagnosis and treatment of PD. KEY POINTS: • The evidence for the link between increased Desulfovibrio and disease severity in PD • A Desulfovibrio MAG was obtained which was correlated with PD • A model was presented to illustrate how increased Desulfovibrio causes PD.

Experiment 1

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Curated date: 2025/02/25

Curator: KateRasheed

Revision editor(s): KateRasheed

Subjects

Location of subjects: China

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: Untreated patients with Parkinson Disease (PD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Untreated patients with Parkinson Disease refers to patients with Parkinson’s disease (the second most common neurodegenerative disease with motor and non-motor symptoms).

Group 0 sample size Number of subjects in the control (unexposed) group: 43

Group 1 sample size Number of subjects in the case (exposed) group: 47

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).: relative abundances

Statistical test: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

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

Chao1 Abundance-based estimator of species richness: increased

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

Richness Number of species: increased

Signature 1

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Source: Table S3, Fig. S5

Description: Differential abundance of taxa with significant differences between PD and Healthy control

Abundance in Group 1: increased abundance in Untreated patients with Parkinson Disease (PD)

NCBI	Quality Control	Links
Bifidobacterium
Megasphaera
Lactobacillus
Desulfovibrio
Pseudomonadaceae
Streptococcus

Revision editor(s): KateRasheed

Signature 2

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Source: Table S3

Description: Differential abundance of taxa with significant differences between PD and Healthy control

Abundance in Group 1: decreased abundance in Untreated patients with Parkinson Disease (PD)

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Roseburia

Revision editor(s): KateRasheed

Experiment 2

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Differences from previous experiment shown

Subjects

Group 0 sample size Number of subjects in the control (unexposed) group: 8

Group 1 sample size Number of subjects in the case (exposed) group: 8

Lab analysis

Sequencing type: WMS

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

Statistical Analysis

Alpha Diversity

Pielou Quantifies how equal the community is numerically: unchanged

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

Chao1 Abundance-based estimator of species richness: increased

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

Richness Number of species: increased

Signature 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-2-28

Curated date: 2025/02/25

Curator: KateRasheed

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Source: Fig. S6

Description: Metagenome assembled genome (MAG58) was significantly increased in PD compared to healthy controls

Abundance in Group 1: increased abundance in Untreated patients with Parkinson Disease (PD)

NCBI	Quality Control	Links
Desulfovibrio

Revision editor(s): KateRasheed

Experiment 3

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Reviewed Marked as Reviewed by Svetlana up on 2025-2-28

Curated date: 2025/02/25

Curator: KateRasheed

Revision editor(s): KateRasheed

Differences from previous experiment shown

Subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Untreated patients with Parkinson Disease refers to patients with Parkinson’s disease (the second most common neurodegenerative disease with motor and non-motor symptoms). These patients were gotten from the National Center for Biotechnology Information (NCBI) SRA database (under project number PRJNA433459).