What is the microbiome dataset?

The microbiome dataset was generated through EPND’s third biomarker case study. The study investigates the taxonomic and functional profiles of the gut microbiome in Alzheimer’s disease and Parkinson’s disease, and aims to identify microbial gene biomarkers.

The dataset comprises two parts: a shotgun metagenomics part, based on newly generated sequencing data, and a 16S rRNA part, based on existing sequencing data. Together, they bring together gut microbiome data from Alzheimer’s disease, Parkinson’s disease and control groups across three European studies.

What does the dataset contain?

Both parts contain taxonomic profiling output tables, including feature counts and associated metadata, derived from stool samples.

Shotgun metagenomics part: Taxonomic profiling outputs derived from newly generated shotgun metagenomic sequencing of the University of Geneva’s Alzheimer’s disease cohort and the University of Luxembourg’s Parkinson’s disease cohort. Samples were processed using a unified laboratory protocol.

16S rRNA part: Taxonomic profiling outputs derived from existing 16S rRNA gene sequencing data from the Amsterdam Dementia Cohort at Amsterdam University Medical Center, the University of Geneva’s Alzheimer’s disease cohort and the University of Luxembourg’s Parkinson’s disease cohort.

Version 1 of the dataset is described in the AD Workbench catalogue as containing baseline data, with study data in English. The listing records clinical, genomics and other data types, and includes female and male participants.

Which cohorts were involved in the microbiome case study?

The dataset draws on three European studies: the COSCODE-gMAD cohort at the University of Geneva, the NCER-PD cohort at the University of Luxembourg, and the Amsterdam Dementia Cohort at Amsterdam UMC.

The observational, multi-site EPND Microbiome Study began in 2023. Its study overview lists 275 participants: 109 with Alzheimer’s disease, 54 with Parkinson’s disease and 112 cognitively normal controls. Separately, the AD Workbench dataset listing reports 1,152 research participants across the dataset resource. The study’s primary investigators are Professor Giovanni Frisoni at the University of Geneva, Professor Rejko Kruger at the University of Luxembourg and Professor Naama Geva-Zatorsky at Technion. The dataset publishers are the University of Luxembourg, Amsterdam University Medical Center, the University of Geneva and Technion.

How can researchers access and analyse the microbiome dataset?

The microbiome dataset is hosted by the AD Data Initiative and is discoverable through the EPND Hub. Its EPND listing describes the use conditions as unconditionally free and unrestricted. Through EPND’s interoperability with the AD Workbench, registered users can access its data analysis infrastructure using a unified login and work in secure, cloud-based workspaces.

What is the EPND Hub and how can it support collaborative research?

The EPND Hub supports the discovery of neurodegenerative disease datasets and biosample collections, alongside data access and collaborative analysis through its interoperability with the AD Workbench. Its ELSI Support Desk provides guidance on data protection, research ethics and contractual arrangements for researchers collaborating through the platform.

Explore the EPND Hub to find the microbiome dataset listing and information on the contributing studies.

Click here to access the microbiome dataset listing on the EPND Hub.