Metagenome-assembled microbial genomes from Parkinson's disease fecal samples

Study information

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study design

case-control

Citation

PMID PubMed identifier for scientific articles.

39143178

DOI Digital object identifier for electronic documents.

10.1038/s41598-024-69742-4

URI

Authors

Duru IC, Lecomte A, Shishido TK, Laine P, Suppula J, Paulin L, Scheperjans F, Pereira PAB, Auvinen P

Journal

Scientific reports

Year

2024

Keywords:

Ruminococcus bromii, Metagenome, Microdiversity, Parkinson’s disease

The human gut microbiome composition has been linked to Parkinson's disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAGs) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different genomes of Collinsella and Prevotella, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.

Experiment 1

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-4

Curated date: 2025/02/27

Curator: An05hka

Revision editor(s): An05hka, KateRasheed

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: Control

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

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Parkinson’s disease (PD) patients refers to patients diagnosed of Parkinson’s disease (PD) - a common neurodegenerative disease.

Group 0 sample size Number of subjects in the control (unexposed) group: 68

Group 1 sample size Number of subjects in the case (exposed) group: 68

Lab analysis

Sequencing type: WMS

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: Illumina

Statistical Analysis

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

Statistical test: 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

Signature 1

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Curated date: 2025/03/03

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Supplementary Table 14

Description: Differential abundance of taxa between Control and PD patients using DESeq2

Abundance in Group 1: increased abundance in Parkinson’s disease (PD) patients

NCBI	Quality Control	Links
Methanobrevibacter smithii
Methanomethylophilus alvi

Revision editor(s): KateRasheed

Signature 2

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Reviewed Marked as Reviewed by Svetlana up on 2025-3-4

Curated date: 2025/03/03

Curator: KateRasheed

Revision editor(s): KateRasheed

Source: Supplementary Table 14

Description: Differential abundance of taxa between Control and PD patients using DESeq2

Abundance in Group 1: decreased abundance in Parkinson’s disease (PD) patients

NCBI	Quality Control	Links
Methanomethylophilaceae UBA71Methanomethylophilaceae UBA71
Candidatus Methanomassiliicoccus intestinalis

Revision editor(s): KateRasheed