Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (P<sub>meta-analysis</sub> = 3.21 × 10<sup>-11</sup>) and cg12234533 (P<sub>meta-analysis</sub> = 4.29 × 10<sup>-10</sup>). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.

Authors

Institutions

Publication Details

Journal
BMC Genomics
Published
2024-12-19
DOI
https://doi.org/10.1186/s12864-024-11136-x
Citations
6
Primary Topic
Epigenetics and DNA Methylation
Type
article
Field-Weighted Citation Impact
1.40
Controls
|||
ALL TIME
JAN
FEB
MAR
APR
MAY
JUN
JUL
AUG
SEP
OCT
article

Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

Ayşe Demirkan, Jingyuan Fu, Marc Jan Bonder, Soesma A. Jankipersadsing et al.
6 citations
BMC Genomics
Epigenetics and DNA Methylation
1.40
article

Linking the gut microbiome to host DNA methylation by a discovery and replication epigenome-wide association study

Ayşe Demirkan, Jingyuan Fu, Marc Jan Bonder, Soesma A. Jankipersadsing, Erik A. Ehli, Richard G. IJzerman, Cisca Wijmenga, Gonneke Willemsen, Alexander Kurilshikov, Harm-Jan Westra, Alexandra Zhernakova, Jenny van Dongen, Eco J. C. de Geus, Dorret Irene Boomsma, Casey T. Finnicum, Lude Franke
article en
6 citations

Abstract

Microbiome influences multiple human systems, but its effects on gene methylation is unknown. We investigated the relations between gene methylation in blood and the abundance of common gut bacteria profiled by 16s rRNA gene sequencing in two population-based Dutch cohorts: LifeLines-Deep (LLD, n = 616, discovery) and the Netherlands Twin Register (NTR, n = 296, replication). In LLD, we also explored microbial pathways using data generated by shotgun metagenomic sequencing (n = 683). Methylation in both cohorts was profiled in blood samples using the Illumina 450K array. Discovery and replication analysis identified two independent CpGs associated with the genus Eggerthella: cg16586104 (P<sub>meta-analysis</sub> = 3.21 × 10<sup>-11</sup>) and cg12234533 (P<sub>meta-analysis</sub> = 4.29 × 10<sup>-10</sup>). We also show that microbiome can mediate the effect of environmental factors on host gene methylation. In this first association study linking epigenome to microbiome, we found and replicated the associations of two CpGs to the abundance of genus Eggerthella and identified microbiome as a mediator of the exposome. These associations are observational and suggest further investigation in larger and longitudinal set-ups.

BMC GenomicsVol. 25(1)
University Medical Center Groningen (NL), University of Groningen (NL), University of Surrey (GB), Amsterdam University Medical Centers (NL), Avera McKennan Hospital & University Health Center (US), Vrije Universiteit Amsterdam (NL)
Life in Land
Openalex Percentile: Top 18%
Epigenetics and DNA Methylation
1.40
DOIOpen Access PDFOpenAlex
AI Navigator

Ask Laika to Summarize, Analyze, and Connect papers live on the map.

Summarize Papers & Methodologies

Extract key findings, datasets, and comparative methods across publications.

Benchmark Rankings & Visual Analytics

Rank top research institutions, authors, funders, topics, and journals by Field-Weighted Citation Impact (FWCI) and paper volume with instant charts.

Connect Distant Disciplines

Bridge topological clusters on the map to find hidden collaborative intersections.