Gut Microbiota Differs Between Parkinson's Disease Patients and Healthy Controls in Northeast China

Study information

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Reviewed Marked as Reviewed by Fatima on 2023-6-15

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

31354427

DOI Digital object identifier for electronic documents.

10.3389/fnmol.2019.00171

URI

https://www.frontiersin.org/articles/10.3389/fnmol.2019.00171/full

Authors

Li C, Cui L, Yang Y, Miao J, Zhao X, Zhang J, Cui G, Zhang Y

Journal

Frontiers in molecular neuroscience

Year

2019

Keywords:

Akkermansia, Lactobacillus, Parkinson’s disease, dysbiosis, gut microbiota

Background: There is accumulating evidence suggesting a connection between the gut and Parkinson's disease (PD). Gut microbiota may play an important role in the intestinal lesions in PD patients. Objective: This study aims to determine whether gut microbiota differs between PD patients and healthy controls in Northeast of China, and to identify the factors that influence the changes in the gut microbiota. Methods: We enrolled 51 PD patients and 48 healthy controls in this study. Microbial species in stool samples were determined through 16S-rRNA gene sequencing. Dietary intakes were collected from a subset of 42 patients and 23 controls using a food frequency questionnaire (FFQ). Gut microbiota species richness, diversity, differential abundance of individual taxa between PD patients and controls, and the relationship between the gut microbiota abundance and the dietary and clinical factors were analyzed. Results: PD patients showed decreased species richness, phylogenetic diversity, β- diversity, and altered relative abundance in several taxa compared to the controls. PD- associated clinical scores appeared to be the most influential factors that correlated with the abundance of a variety of taxa. The most consistent findings suggested by multiple analyses used in this study were the increase of Akkermansia and the decrease of Lactobacillus in PD patients in Northeast China. Conclusion: Gut microbiota significantly differed between a group of PD patients and healthy controls in Northeast China, with decreased species richness, phylogenetic diversity, β-diversity, and altered relative abundance in several taxa compared to the controls.

Experiment 1

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Reviewed Marked as Reviewed by Fatima on 2023-6-15

Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): WikiWorks, Lwaldron, Fatima, Fcuevas3, Aiyshaaaa

Subjects

Location of subjects

China

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(HC)

Group 1 name Corresponds to the case (exposed) group for case-control studies

patients with parkinson's disease

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

The patients who have been diagnosed with Parkinson's Disease(PD). Parkinson’s disease (PD) is a common neurodegenerative disorder characterized by motor and non-motor symptoms.

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

48

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

51

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

3 months

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

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

LEfSe

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

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

4

Matched on Factors on which subjects have been matched on in a case-control study

age, body mass index

Alpha Diversity

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

increased

Chao1 Abundance-based estimator of species richness

decreased

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

increased

Richness Number of species

decreased

Signature 1

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Curated date: 2021/10/18

Curator: Fcuevas3

Revision editor(s): Fcuevas3, Lwaldron, Aiyshaaaa

Source: Figure 3

Description: Using LEfSe analysis we identified one class, four orders, three families, and two genera that showed significant different abundances between the PD and control groups

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

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Prevotella
Oscillospiraceae

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Source: Figure 3

Description: Using LEfSe analysis we identified one class, four orders, three families, and two genera that showed significant different abundances between the PD and control groups.

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

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Bacilli
Lactobacillaceae
Lactobacillales
Lactobacillus
Muribaculaceae

Revision editor(s): Fcuevas3, Lwaldron, Aiyshaaaa

Experiment 2

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Curated date: 2023/05/24

Curator: Fcuevas3

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Differences from previous experiment shown

Subjects

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 subjects

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Patients who had been diagnosed with PD according to the diagnostic criteria proposed by the International Parkinson Disease and Movement Disorder Society in 2015 (Postuma et al., 2015) in the First Hospital of Jilin University.

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

Subjects with a history of using medications that have been shown to affect gut microbiota, including COMT inhibitors, anticholinergics, anti-secretory drugs, or cardiological drugs within the 3 months before the start of the study were excluded.

Lab analysis

Statistical Analysis

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

Not specified

Statistical test

T-Test

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

Not specified

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

Not specified

Alpha Diversity

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

increased

Chao1 Abundance-based estimator of species richness

decreased

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

increased

Richness Number of species

decreased

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.

Description: 2A. Phylum, increased abundances.

Abundance in Group 1: increased abundance in Parkinson's Disease subjects

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Verrucomicrobiota

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.

Description: 2B. Class. Increased abundances.

Abundance in Group 1: increased abundance in Parkinson's Disease subjects

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Clostridia
Negativicutes
Verrucomicrobiae

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.

Description: 2B. Class, decreased abundances.

Abundance in Group 1: decreased abundance in Parkinson's Disease subjects

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Bacilli

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.

Description: 2C. Order, increased abundances.

Abundance in Group 1: increased abundance in Parkinson's Disease subjects

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Eubacteriales
Selenomonadales
Verrucomicrobiales

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.

Description: 2C. Order, decreased abundances.

Abundance in Group 1: decreased abundance in Parkinson's Disease subjects

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Lactobacillales

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.

Description: 2D. Family, increased abundances.

Abundance in Group 1: increased abundance in Parkinson's Disease subjects

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Acidaminococcaceae
Oscillospiraceae
Porphyromonadaceae
Rikenellaceae
Veillonellaceae
Verrucomicrobiaceae

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.

Description: 2D. Family, decreased abundances.

Abundance in Group 1: decreased abundance in Parkinson's Disease subjects

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Lactobacillaceae
Muribaculaceae

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests

Description: 2E. Genus, increased abundances.

Abundance in Group 1: increased abundance in Parkinson's Disease subjects

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Akkermansia
Alistipes
Coprococcus
Eubacterium coprostanoligenes
Eubacterium ventriosum
Lachnospira
Lachnospiraceae
Methanobrevibacter
Oscillospiraceae
Parabacteroides
Phascolarctobacterium
Roseburia
Ruminococcus

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests

Description: 2E. Genus, decreased abundances.

Abundance in Group 1: decreased abundance in Parkinson's Disease subjects

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Anaerobutyricum hallii
Lactobacillus
Streptococcus

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests.

Description: 2F. Species, increased abundances.

Abundance in Group 1: increased abundance in Parkinson's Disease subjects

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Methanobrevibacter smithii
Parabacteroides merdae
Segatella copri
Roseburia inulinivorans
Ruminococcus callidus
[Ruminococcus] torques

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Source: FIGURE 2. Gut microbiota differences between PD patients and controls detected by t-tests

Description: 2F. Species, decreased abundances.

Abundance in Group 1: decreased abundance in Parkinson's Disease subjects

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Lactobacillus gasseri

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