DOI: 10.5281/zenodo.10062077
title: Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

description: BACKGROUND: The datafiles deposited here are products of the research project "Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study"
Authors: Ayşe Demirkan1,2, Jenny van Dongen3,4, Casey T. Finnicum5, Harm-Jan Westra1, Soesma Jankipersadsing1, Gonneke Willemsen3,4, Richard G. Ijzerman6, Dorret I. Boomsma3,4, Erik A. Ehli5, Marc Jan Bonder1, Jingyuan Fu,1,7 Lude Franke1, Cisca Wijmenga1, Eco J.C. de Geus3,4, Alexander Kurilshikov1, Alexandra Zhernakova1
1 Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
2 Section of Statistical Multi-omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine & People-Centered AI institute University of Surrey, Guildford, United Kingdom
3 Biological Psychology, Vrije Universiteit, Amsterdam, the Netherlands
4 Amsterdam Public Health Research Institute, Amsterdam, the Netherlands
5 Avera Institute of Human Genetics, Avera McKennan Hospital & University Health Center, Sioux Falls, SD, USA
6 Department of Endocrinology, Amsterdam University Medical Center, location VUMC, Amsterdam, the Netherlands
7 Department of Pediatrics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
Corresponding Authors: Alexandra Zhernakova; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, the Netherlands
Ayse Demirkan; Section of Statistical Multi-omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine & People-Centered AI institute University of Surrey, Guildford, United Kingdom.
FILES: 
1-merged_lld16s.Rata: Epigenome-wide association of 16s microbial abundances in LifeLines-Deep (LLD, n = 616, 450k methylation array) 
2-lld_mgs.Rdata: Epigenome-wide association ofshotgun metagenomic sequencing derived taxa relative abundances (n = 683, 450k methylation array))
3-lld_mgs_pathways. Rdata: Epigenome-wide association ofshotgun metagenomic sequencing derived bacterial pathway relative abundances (n = 683, 450k methylation array)
FUNDING: The Lifelines initiative has been made possible by subsidy from the Dutch Ministry of Health, Welfare and Sport, the Dutch Ministry of Economic Affairs, the University Medical Center Groningen (UMCG), Groningen University and the Provinces in the North of the Netherlands (Drenthe, Friesland, Groningen). The Netherlands Twin Register acknowledges funding from the Netherlands Organization for Scientific Research (NWO): (NWO 911–09–032; NWO 480-04-004; 480-15-001/674, NWO 916-130-82), Biobanking and Biomolecular Research Infrastructure (184.033.111),  and the BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), NWO Large Scale infrastructures X-Omics (184.034.019), Genotype/phenotype database for behaviour genetic and genetic epidemiological studies (ZonMw Middelgroot 911-09-032); Netherlands Twin Registry Repository: researching the interplay between genome and environment (NWO-Groot 480-15-001/674); the Avera Institute, Sioux Falls (USA), the European Research Council (Genetics of Mental Illness 230374), the European Research Council (Genetics of Mental Illness 230374), and INRA-Pfizer. Pfizer provided support for data collection, but did not have any additional role in the study design, data analysis, decision to publish, or preparation of the manuscript.