Publications

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)

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)

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)

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)

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)

Impact of occupational pesticide exposure on the human gut microbiome

Milla F Brandao Gois, Asier Fernández-Pato, Anke Huss, Ranko Gacesa, Cisca Wijmenga, Rinse K Weersma, Jingyuan Fu, Roel C H Vermeulen, Alexandra Zhernakova, Virissa C Lenters, Alexander Kurilshikov
Front. 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)

Integrated fecal microbiome-metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome

Zlatan Mujagic, Melpomeni Kasapi, Daisy Mae Jonkers, Isabel Garcia-Perez, Lisa Vork, Zsa Zsa R M Weerts, Jose Ivan Serrano-Contreras, Alexandra Zhernakova, Alexander Kurilshikov, Jamie Scotcher, Elaine Holmes, Cisca Wijmenga, Daniel Keszthelyi, Jeremy K Nicholson, Joram M Posma, Ad Am Masclee
Gut Microbes (2022)

Systematic analysis of relationships between plasma branched-chain amino acid concentrations and cardiometabolic parameters: an association and Mendelian randomization study

Marwah Doestzada, Daria V. Zhernakova, Inge C. L. van den Munckhof, Daoming Wang, Alexander Kurilshikov, Lianmin Chen,Vincent W. Bloks, Martijn van Faassen, Joost H. W. Rutten, Leo A. B. Joosten, Mihai G. Netea, Cisca Wijmenga, Niels P. Riksen, Alexandra Zhernakova, Folkert Kuipers, and Jingyuan Fu
BMC Medicine (2022)

Influence of the microbiome, diet and genetics on inter-individual variation in the human plasma metabolome

Lianmin Chen, Daria V Zhernakova, Alexander Kurilshikov, Sergio Andreu-Sánchez, Daoming Wang, Hannah E Augustijn, Arnau Vich Vila; Lifelines Cohort Study; Rinse K Weersma, Marnix H Medema, Mihai G Netea, Folkert Kuipers, Cisca Wijmenga, Alexandra Zhernakova, Jingyuan Fu
Nature medicine (2022)

Role of the gut microbiome in mediating lactose intolerance symptoms

Brandao Gois MF, Sinha T, Spreckels JE et al.
Gut (2022)

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)

Environmental factors shaping the gut microbiome in a Dutch population

R. Gacesa, A. Kurilshikov, A. Vich Vila, T. Sinha, M.A.Y. Klaassen L.A. Bolte, S. Andreu-Sánchez, L. Chen, V. Collij, S. Hu, J.A.M. Dekens, V.C. Lenters, J.R. Björk, J.C. Swarte, M.A. Swertz, B.H. Jansen, J. Gelderloos-Arends, S. Jankipersadsing, M. Hofker, R.C.H. Vermeulen, S. Sanna, H.J.M. Harmsen, C. Wijmenga, J. Fu, A. Zhernakova, R.K. Weersma
Nature (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)

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)