Publicaties

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

Li R, Kurilshikov A, Yang S, van Oortmerssen JAE, van Hilten A, Ahmadizar F, Roshchupkin G, Kraaij R, Duijts L, Fu J, Ikram MK, Jaddoe VWV, Uitterlinden AG, Rivadeneira F, Kavousi M, Zhernakova A, Medina-Gomez C.
Lancet Reg Health Eur (2024)

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)

The gut microbiome across the cardiovascular risk spectrum

Prins FM, Collij V, Groot HE, Björk JR, Swarte JC, Andreu-Sánchez S, Jansen BH, Fu J, Harmsen HJM, Zhernakova A, Lipsic E, van der Harst P, Weersma RK, Gacesa R.
Eur J Prev Cardiol (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)

Rome III Criteria Capture Higher Irritable Bowel Syndrome SNP-Heritability and Highlight a Novel Genetic Link With Cardiovascular Traits

Camargo Tavares L, Lopera-Maya EA, Bonfiglio F, Zheng T, Sinha T, Zanchetta Marques F, Zhernakova A, Sanna S, D'Amato M.
Cell Mol Gastroenterol Hepatol (2024)

Unraveling interindividual variation of trimethylamine N-oxide and its precursors at the population level

Andreu-Sánchez S, Ahmad S, Kurilshikov A, Beekman M, Ghanbari M, van Faassen M, van den Munckhof ICL, Steur M, Harms A, Hankemeier T, Ikram MA, Kavousi M, Voortman T, Kraaij R, Netea MG, Rutten JHW, Riksen NP, Zhernakova A, Kuipers F, Slagboom PE, van Duijn CM, Fu J, Vojinovic D.
Imeta (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)

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)

Gut feelings: the relations between depression, anxiety, psychotropic drugs and the gut microbiome

Brushett S, Gacesa R, Vich Vila A, Brandao Gois MF, Andreu-Sánchez S, Swarte JC, Klaassen MAY, Collij V, Sinha T, Bolte LA, Wu J, Swertz M, de Kroon MLA, Reijneveld SA, Wijmenga C, Weersma RK, Fu J, van Loo HM, Kurilshikov A, Zhernakova A.
Gut Microbes (2023)

Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques

Spreckels JE, Fernández-Pato A, Kruk M, Kurilshikov A, Garmaeva S, Sinha T, Ghosh H, Harmsen H, Fu J, Gacesa R, Zhernakova A.
ISME Commun (2023)

Gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV

Zhang Y, Andreu-Sánchez S, Vadaq N, Wang D, Matzaraki V, van der Heijden WA, Gacesa R, Weersma RK, Zhernakova A, Vandekerckhove L, de Mast Q, Joosten LAB, Netea MG, van der Ven AJAM, Fu J.
Front Cell Infect Microbiol (2023)

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)

The maternal gut microbiome during pregnancy and its role in maternal and infant health

Sinha T, Brushett S, Prins J, Zhernakova A.
Curr Opin Microbiol (2023)

Diversity and Ecology of Caudoviricetes Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts

Gulyaeva A, Garmaeva S, Kurilshikov A, Vich Vila A, Riksen NP, Netea MG, Weersma RK, Fu J, Zhernakova A.
Viruses (2022)

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)

The Gut Microbiome Composition Is Altered in Long-standing Type 1 Diabetes and Associates With Glycemic Control and Disease-Related Complications

van Heck JIP, Gacesa R, Stienstra R, Fu J, Zhernakova A, Harmsen HJM, Weersma RK, Joosten LAB, Tack CJ.
Diabetes Care (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)

Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome

Le Roy CI, Kurilshikov A, Leeming ER, Visconti A, Bowyer RCE, Menni C, Falchi M, Koutnikova H, Veiga P, Zhernakova A, Derrien M, Spector TD.
BMC Microbiol (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)

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)

Characterization of gut microbial structural variations as determinants of human bile acid metabolism

Wang D, Doestzada M, Chen L, Andreu-Sánchez S, van den Munckhof ICL, Augustijn HE, Koehorst M, Ruiz-Moreno AJ, Bloks VW, Riksen NP, Rutten JHW, Joosten LAB, Netea MG, Wijmenga C, Zhernakova A, Kuipers F, Fu J.
Cell Host Microbe (2021)

An association between chronic widespread pain and the gut microbiome

Freidin MB, Stalteri MA, Wells PM, Lachance G, Baleanu AF, Bowyer RCE, Kurilshikov A, Zhernakova A, Steves CJ, Williams FMK.
Rheumatology (Oxford) (2021)

A combination of fecal calprotectin and human beta-defensin 2 facilitates diagnosis and monitoring of inflammatory bowel disease

Gacesa R, Vich Vila A, Collij V, Mujagic Z, Kurilshikov A, Voskuil MD, Festen EAM, Wijmenga C, Jonkers DMAE, Dijkstra G, Fu J, Zhernakova A, Imhann F, Weersma RK.
Gut Microbes (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)

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)

The Composition and Metabolic Potential of the Human Small Intestinal Microbiota Within the Context of Inflammatory Bowel Disease

Ruigrok RAAA, Collij V, Sureda P, Klaassen MAY, Bolte LA, Jansen BH, Voskuil MD, Fu J, Wijmenga C, Zhernakova A, Weersma RK, Vich Vila A.
J Crohns Colitis (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)

Lifelines COVID-19 cohort: investigating COVID-19 infection and its health and societal impacts in a Dutch population-based cohort

Mc Intyre K, Lanting P, Deelen P, Wiersma HH, Vonk JM, Ori APS, Jankipersadsing SA, Warmerdam R, van Blokland I, Boulogne F, Dijkema MXL, Herkert JC, Claringbould A, Bakker O, Lopera Maya EA, Bültmann U, Zhernakova A, Reijneveld SA, Zijlstra E, Swertz MA, Brouwer S, van Ooijen R, Angelini V, Dekker LH, Sijtsma A, Scherjon SA, Wijmenga C, Dekens JAM, Mierau J, Boezen HM, Franke L.
BMJ Open (2021)

Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals

Folkersen L, Gustafsson S, Wang Q, Hansen DH, Hedman ÅK, Schork A, Page K, Zhernakova DV, Wu Y, Peters J, Eriksson N, Bergen SE, Boutin TS, Bretherick AD, Enroth S, Kalnapenkis A, Gådin JR, Suur BE, Chen Y, Matic L, Gale JD, Lee J, Zhang W, Quazi A, Ala-Korpela M, Choi SH, Claringbould A, Danesh J, Davey Smith G, de Masi F, Elmståhl S, Engström G, Fauman E, Fernandez C, Franke L, Franks PW, Giedraitis V, Haley C, Hamsten A, Ingason A, Johansson Å, Joshi PK, Lind L, Lindgren CM, Lubitz S, Palmer T, Macdonald-Dunlop E, Magnusson M, Melander O, Michaelsson K, Morris AP, Mägi R, Nagle MW, Nilsson PM, Nilsson J, Orho-Melander M, Polasek O, Prins B, Pålsson E, Qi T, Sjögren M, Sundström J, Surendran P, Võsa U, Werge T, Wernersson R, Westra HJ, Yang J, Zhernakova A, Ärnlöv J, Fu J, Smith JG, Esko T, Hayward C, Gyllensten U, Landen M, Siegbahn A, Wilson JF, Wallentin L, Butterworth AS, Holmes MV, Ingelsson E, Mälarstig A.
Nature Metabolism (2020)

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)