Publications

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

Demirkan A, van Dongen J, Finnicum CT, Westra HJ, Jankipersadsing S, Willemsen G, Ijzerman RG, Boomsma DI, Ehli EA, Bonder MJ, Fu J, Franke L, Wijmenga C, de Geus EJC, Kurilshikov A, Zhernakova A.
BMC Genomics (2024)

Epigenome-wide association study on the plasma metabolome suggests self-regulation of the glycine and serine pathway through DNA methylation

Wu J, Palasantzas V, Andreu-Sánchez S, Plösch T, Leonard S, Li S, Bonder MJ, Westra HJ, van Meurs J, Ghanbari M, Franke L, Zhernakova A, Fu J, Hoogerland JA, Zhernakova DV.
Clinical Epigenetics (2024)

Maternal antibiotic prophylaxis during cesarean section has a limited impact on the infant gut microbiome

Sinha T, Prins JR, Fernández-Pato A, Kruk M, Dierikx T, de Meij T, de Boer M, de Boer JF, Scherjon S, Kurilshikov A, Zhernakova A.
Cell Host Microbe (2024)

Intestinal Blastocystis is linked to healthier diets and more favorable cardiometabolic outcomes in 56,989 individuals from 32 countries

Piperni E, Nguyen LH, Manghi P, Kim H, Pasolli E, Andreu-Sánchez S, Arrè A, Bermingham KM, Blanco-Míguez A, Manara S, Valles-Colomer M, Bakker E, Busonero F, Davies R, Fiorillo E, Giordano F, Hadjigeorgiou G, Leeming ER, Lobina M, Masala M, Maschio A, McIver LJ, Pala M, Pitzalis M, Wolf J, Fu J, Zhernakova A, Cacciò SM, Cucca F, Berry SE, Ercolini D, Chan AT, Huttenhower C, Spector TD, Segata N, Asnicar F.
Cell (2024)

Antibody signatures against viruses and microbiome reflect past and chronic exposures and associate with aging and inflammation

Andreu-Sánchez S, Ripoll-Cladellas A, Culinscaia A, Bulut O, Bourgonje AR, Netea MG, Lansdorp P, Aubert G, Bonder MJ, Franke L, Vogl T, van der Wijst MGP, Melé M, Van Baarle D, Fu J, Zhernakova A.
iScience (2024)

Genome-wide characterization of circulating metabolic biomarkers

Karjalainen MK, Karthikeyan S, Oliver-Williams C, Sliz E, Allara E, Fung WT, Surendran P, Zhang W, Jousilahti P, Kristiansson K, Salomaa V, Goodwin M, Hughes DA, Boehnke M, Fernandes Silva L, Yin X, Mahajan A, Neville MJ, van Zuydam NR, de Mutsert R, Li-Gao R, Mook-Kanamori DO, Demirkan A, Liu J, Noordam R, Trompet S, Chen Z, Kartsonaki C, Li L, Lin K, Hagenbeek FA, Hottenga JJ, Pool R, Ikram MA, van Meurs J, Haller T, Milaneschi Y, Kähönen M, Mishra PP, Joshi PK, Macdonald-Dunlop E, Mangino M, Zierer J, Acar IE, Hoyng CB, Lechanteur YTE, Franke L, Kurilshikov A, Zhernakova A, Beekman M, van den Akker EB, Kolcic I, Polasek O, Rudan I, Gieger C, Waldenberger M, Asselbergs FW; China Kadoorie Biobank Collaborative Group; Estonian Biobank Research Team; FinnGen; Hayward C, Fu J, den Hollander AI, Menni C, Spector TD, Wilson JF, Lehtimäki T, Raitakari OT, Penninx BWJH, Esko T, Walters RG, Jukema JW, Sattar N, Ghanbari M, Willems van Dijk K, Karpe F, McCarthy MI, Laakso M, Järvelin MR, Timpson NJ, Perola M, Kooner JS, Chambers JC, van Duijn C, Slagboom PE, Boomsma DI, Danesh J, Ala-Korpela M, Butterworth AS, Kettunen J.
Nature (2024)

Transmission and dynamics of mother-infant gut viruses during pregnancy and early life

Garmaeva S, Sinha T, Gulyaeva A, Kuzub N, Spreckels JE, Andreu-Sánchez S, Gacesa R, Vich Vila A, Brushett S, Kruk M; Lifelines NEXT cohort study; Dekens J, Sikkema J, Kuipers F, Shkoporov AN, Hill C, Scherjon S, Wijmenga C, Fu J, Kurilshikov A, Zhernakova A.
Nature Communications (2024)

Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses

Fernández-Pato A, Sinha T, Gacesa R, Andreu-Sánchez S, Gois MFB, Gelderloos-Arends J, Jansen DBH, Kruk M, Jaeger M, Joosten LAB, Netea MG, Weersma RK, Wijmenga C, Harmsen HJM, Fu J, Zhernakova A, Kurilshikov A.
Scientific Reports (2024)

Association between gut microbiome profiles and host metabolic health across the life course: a population-based study

Fernández-Pato A, Sinha T, Gacesa R, Andreu-Sánchez S, Gois MFB, Gelderloos-Arends J, Jansen DBH, Kruk M, Jaeger M, Joosten LAB, Netea MG, Weersma RK, Wijmenga C, Harmsen HJM, Fu J, Zhernakova A, Kurilshikov A.
Scientific Reports (2024)

PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs

Vochteloo M, Deelen P, Vink B; BIOS Consortium; Tsai EA, Runz H, Andreu-Sánchez S, Fu J, Zhernakova A, Westra HJ, Franke L.
Genome Biology (2024)

Host genetic regulation of human gut microbial structural variation

Zhernakova DV, Wang D, Liu L, Andreu-Sánchez S, Zhang Y, Ruiz-Moreno AJ, Peng H, Plomp N, Del Castillo-Izquierdo Á, Gacesa R, Lopera-Maya EA, Temba GS, Kullaya VI, van Leeuwen SS; Lifelines Cohort Study; Xavier RJ, de Mast Q, Joosten LAB, Riksen NP, Rutten JHW, Netea MG, Sanna S, Wijmenga C, Weersma RK, Zhernakova A, Harmsen HJM, Fu J.
Nature (2024)

Phage display sequencing reveals that genetic, environmental, and intrinsic factors influence variation of human antibody epitope repertoire

Andreu-Sánchez S, Bourgonje AR, Vogl T, Kurilshikov A, Leviatan S, Ruiz-Moreno AJ, Hu S, Sinha T, Vich Vila A, Klompus S, Kalka IN, de Leeuw K, Arends S, Jonkers I, Withoff S; Lifelines Cohort Study; Brouwer E, Weinberger A, Wijmenga C, Segal E, Weersma RK, Fu J, Zhernakova A.
Immunity (2023)

Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures

Bourgonje AR, Andreu-Sánchez S, Vogl T, Hu S, Vich Vila A, Gacesa R, Leviatan S, Kurilshikov A, Klompus S, Kalka IN, van Dullemen HM, Weinberger A, Visschedijk MC, Festen EAM, Faber KN, Wijmenga C, Dijkstra G, Segal E, Fu J, Zhernakova A, Weersma RK.
Immunity (2023)

Age-dependent sex differences in cardiometabolic risk factors

Zhernakova DV, Sinha T, Andreu-Sánchez S, Prins JR, Kurilshikov A, Balder JW, Sanna S; Lifelines Cohort Study; Franke L, Kuivenhoven JA, Zhernakova A, Fu J.
Nat Cardiovasc Res (2022)

Challenges and future directions for studying effects of host genetics on the gut microbiome

Sanna S, Kurilshikov A, van der Graaf A, Fu J, Zhernakova A.
Nature Genetics (2022)

Genetic, parental and lifestyle factors influence telomere length

Andreu-Sánchez S, Aubert G, Ripoll-Cladellas A, Henkelman S, Zhernakova DV, Sinha T, Kurilshikov A, Cenit MC, Jan Bonder M, Franke L, Wijmenga C, Fu J, van der Wijst MGP, Melé M, Lansdorp P, Zhernakova A.
Communications Biology (2022)

Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project

Lopera-Maya EA, Kurilshikov A, van der Graaf A, Hu S, Andreu-Sánchez S, Chen L, Vila AV, Gacesa R, Sinha T, Collij V, Klaassen MAY, Bolte LA, Gois MFB, Neerincx PBT, Swertz MA; LifeLines Cohort Study; Harmsen HJM, Wijmenga C, Fu J, Weersma RK, Zhernakova A, Sanna S.
Nature Genetics (2022)

Large HDL particles negatively associate with leukocyte counts independent of cholesterol efflux capacity: A cross sectional study in the population-based LifeLines DEEP cohort

Groenen AG, Bazioti V, van Zeventer IA, Chen L, Groot HE, Balder JW, Zhernakova A, van der Harst P, Rimbert A, Kuivenhoven JA, Fu J, Westerterp M.
Atherosclerosis (2022)

Discovery, diversity, and functional associations of crAss-like phages in human gut metagenomes from four Dutch cohorts: Cell Reports

Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A.
Cell Reports (2022)

GWAS of stool frequency provides insights into gastrointestinal motility and irritable bowel syndrome

Bonfiglio F, Liu X, Smillie C, Pandit A, Kurilshikov A, Bacigalupe R, Zheng T, Nim H, Garcia-Etxebarria K, Bujanda L, Andreasson A, Agreus L, Walter S, Abecasis G, Eijsbouts C, Jostins L, Parkes M, Hughes DA, Timpson N, Raes J, Franke A, Kennedy NA, Regev A, Zhernakova A, Simren M, Camilleri M, D'Amato M.
Cell Genomics (2021)

Circulating miRNAs as Potential Biomarkers for Celiac Disease Development

Tan IL, Coutinho de Almeida R, Modderman R, Stachurska A, Dekens J, Barisani D, Meijer CR, Roca M, Martinez-Ojinaga E, Shamir R, Auricchio R, Korponay-Szabó IR, Castillejo G, Szajewska H, Koletzko S, Zhernakova A, Kumar V, Li Y, Visschedijk MC, Weersma RK, Troncone R, Mearin ML, Wijmenga C, Jonkers I, Withoff S.
Frontiers in Immunology (2021)

Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders

Eijsbouts C, Zheng T, Kennedy NA, Bonfiglio F, Anderson CA, Moutsianas L, Holliday J, Shi J, Shringarpure S; 23andMe Research Team; Voda AI; Bellygenes Initiative; Farrugia G, Franke A, Hübenthal M, Abecasis G, Zawistowski M, Skogholt AH, Ness-Jensen E, Hveem K, Esko T, Teder-Laving M, Zhernakova A, Camilleri M, Boeckxstaens G, Whorwell PJ, Spiller R, McVean G, D'Amato M, Jostins L, Parkes M.
Nature Genetics (2021)

Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota

Vogl T, Klompus S, Leviatan S, Kalka IN, Weinberger A, Wijmenga C, Fu J, Zhernakova A, Weersma RK, Segal E.
Nature Medicine (2021)

Stability of the human gut virome and effect of gluten-free diet

Garmaeva S, Gulyaeva A, Sinha T, Shkoporov AN, Clooney AG, Stockdale SR, Spreckels JE, Sutton TDS, Draper LA, Dutilh BE, Wijmenga C, Kurilshikov A, Fu J, Hill C, Zhernakova A.
Cell Reports (2021)

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing

Andreu-Sánchez S, Chen L, Wang D, Augustijn HE, Zhernakova A, Fu J.
Frontiers in Genetics (2021)

The long-term genetic stability and individual specificity of the human gut microbiome

Chen L, Wang D, Garmaeva S, Kurilshikov A, Vich Vila A, Gacesa R, Sinha T; Lifelines Cohort Study; Segal E, Weersma RK, Wijmenga C, Zhernakova A, Fu J.
Cell (2021)

Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome

Bolte LA, Vich Vila A, Imhann F, Collij V, Gacesa R, Peters V, Wijmenga C, Kurilshikov A, Campmans-Kuijpers MJE, Fu J, Dijkstra G, Zhernakova A, Weersma RK.
Gut (2021)

Large-scale association analyses identify host factors influencing human gut microbiome composition

Kurilshikov A, Medina-Gomez C, Bacigalupe R, Radjabzadeh D, Wang J, Demirkan A, Le Roy CI, Raygoza Garay JA, Finnicum CT, Liu X, Zhernakova DV, Bonder MJ, Hansen TH, Frost F, Rühlemann MC, Turpin W, Moon JY, Kim HN, Lüll K, Barkan E, Shah SA, Fornage M, Szopinska-Tokov J, Wallen ZD, Borisevich D, Agreus L, Andreasson A, Bang C, Bedrani L, Bell JT, Bisgaard H, Boehnke M, Boomsma DI, Burk RD, Claringbould A, Croitoru K, Davies GE, van Duijn CM, Duijts L, Falony G, Fu J, van der Graaf A, Hansen T, Homuth G, Hughes DA, Ijzerman RG, Jackson MA, Jaddoe VWV, Joossens M, Jørgensen T, Keszthelyi D, Knight R, Laakso M, Laudes M, Launer LJ, Lieb W, Lusis AJ, Masclee AAM, Moll HA, Mujagic Z, Qibin Q, Rothschild D, Shin H, Sørensen SJ, Steves CJ, Thorsen J, Timpson NJ, Tito RY, Vieira-Silva S, Völker U, Völzke H, Võsa U, Wade KH, Walter S, Watanabe K, Weiss S, Weiss FU, Weissbrod O, Westra HJ, Willemsen G, Payami H, Jonkers DMAE, Arias Vasquez A, de Geus EJC, Meyer KA, Stokholm J, Segal E, Org E, Wijmenga C, Kim HL, Kaplan RC, Spector TD, Uitterlinden AG, Rivadeneira F, Franke A, Lerch MM, Franke L, Sanna S, D'Amato M, Pedersen O, et al.
Nature Genetics (2021)

Genetic and Microbial Associations to Plasma and Fecal Bile Acids in Obesity Relate to Plasma Lipids and Liver Fat Content

Chen L, van den Munckhof ICL, Schraa K, Ter Horst R, Koehorst M, van Faassen M, van der Ley C, Doestzada M, Zhernakova DV, Kurilshikov A, Bloks VW, Groen AK; Human Functional Genomics Project; Riksen NP, Rutten JHW, Joosten LAB, Wijmenga C, Zhernakova A, Netea MG, Fu J, Kuipers F.
Cell Reports (2020)

Lack of Association Between Genetic Variants at ACE2 and TMPRSS2 Genes Involved in SARS-CoV-2 Infection and Human Quantitative Phenotypes

Lopera Maya EA, van der Graaf A, Lanting P, van der Geest M, Fu J, Swertz M, Franke L, Wijmenga C, Deelen P, Zhernakova A, Sanna S; Lifelines Cohort Study.
Frontiers in Genetics (2020)