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The Dutch Microbiome Project: Defining the (un)healthy gut microbiome

The Dutch Microbiome Project (DMP) data includes raw data generated by shotgun metagenomic sequencing of faecal samples of 8,208 Dutch individuals, processed microbiome data analysed using Biobakery2 tools (including taxonomy, pathway, virulence factors and antibiotic resistance gene profiles), and basic phenotypes (age and sex, BMI). Data is made available in two randomly assigned batches to facilitate the data access and maintenance. Access to this dataset requires a minimal access procedure (data access form at or email request to the data access committee (DAC) of this study, listed at DAC EGAC00001001996, This access procedure is to ensure that the data is being requested for research/scientific purposes only and thus complies with the informed consent signed by Lifelines participants, which specifies that the collected data will not be used for commercial purposes. Submitted data access forms will be evaluated by the DAC and Lifelines, and a response to requests will be given within two weeks. For requests from verified academic parties, access will be given without further delay. For requests from commercial parties, Lifelines will perform a pre-DPIA (Data Privacy Impact Assessment) to assess the risks of the proposed processing of personal data (e.g. purpose, storage, access, archiving, etc.) with respect to the GDPR (EU privacy laws) subject rights. Based on the outcome of the pre-DPIA, Lifelines will decide whether sharing data with the commercial entity is allowed and/or whether additional measures have to be taken.

Click on a Dataset ID in the table below to learn more, and to find out who to contact about access to these data

Dataset ID Description Technology Samples
EGAD00001007027 Illumina HiSeq 2000 4396
EGAD00001007501 Illumina HiSeq 2000 3848
Publications Citations
The genomic landscape of reference genomes of cultivated human gut bacteria.
Nat Commun 14: 2023 1663
Gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV.
Front Cell Infect Microbiol 13: 2023 1202035
Impact of occupational pesticide exposure on the human gut microbiome.
Front Microbiol 14: 2023 1223120
Host genetic regulation of human gut microbial structural variation.
Nature 625: 2024 813-821