The role of the virome in shaping the gut ecosystem during the first year of life

Project Information

BabyVir

Grant agreement ID: 715772

DOI

10.3030/715772

Project closed

EC signature date 20 February 2017

Start date 1 April 2017

End date 30 June 2023

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 499 881,00

EU contribution

€ 1 499 881,00

Coordinated by

ACADEMISCH ZIEKENHUIS GRONINGEN
Netherlands

CORDIS provides links to public deliverables and publications of HORIZON projects.

Links to deliverables and publications from FP7 projects, as well as links to some specific result types such as dataset and software, are dynamically retrieved from OpenAIRE .

Publications

Peer reviewed articles (28)

Environmental factors shaping the gut microbiome in a Dutch population.

Author(s): Gacesa R, Kurilshikov A, Vich Vila A, Sinha T, Klaassen MAY, Bolte LA, Andreu-Sánchez S, Chen L, Collij V, Hu S, Dekens JAM, Lenters VC, Björk JR, Swarte JC, Swertz MA, Jansen BH, Gelderloos-Arends J, Jankipersadsing S, Hofker M, Vermeulen RCH, Sanna S, Harmsen HJM, Wijmenga C, Fu J, Zhernakova A, Weersma RK.
Published in: Nature, 2022, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-04567-7

Role of the gut microbiome in mediating lactose intolerance symptoms.

Author(s): Brandao Gois MF, Sinha T, Spreckels JE, Vich Vila A, Bolte LA, Weersma RK, Wijmenga C, Fu J, Zhernakova A, Kurilshikov A.
Published in: Gut, 2021, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2020-323911

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

Author(s): Gulyaeva A, Garmaeva S, Kurilshikov A, Vich Vila A, Riksen NP, Netea MG, Weersma RK, Fu J, Zhernakova A.
Published in: Viruses, 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14102305

Milk and bugs educate infant immune systems.

Author(s): Spreckels JE, Zhernakova A.
Published in: Immunity, 2021, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2021.07.013

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

Author(s): 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.
Published in: Immunity, 2023, ISSN 1074-7613
Publisher: Cell Press
DOI: 10.1016/j.immuni.2023.04.003

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

Author(s): Chen L, Zhernakova DV, Kurilshikov A, Andreu-Sánchez S, Wang D, Augustijn HE, Vich Vila A; Lifelines Cohort Study; Weersma RK, Medema MH, Netea MG, Kuipers F, Wijmenga C, Zhernakova A, Fu J
Published in: Nature Medicine, 2022, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-022-02014-8

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles

Author(s): Trishla Sinha, Arnau Vich Vila, Sanzhima Garmaeva, Soesma A. Jankipersadsing, Floris Imhann, Valerie Collij, Marc Jan Bonder, Xiaofang Jiang, Thomas Gurry, Eric J. Alm, Mauro D’Amato, Rinse K. Weersma, Sicco Scherjon, Cisca Wijmenga, Jingyuan Fu, Alexander Kurilshikov, Alexandra Zhernakova
Published in: Gut Microbes, 2018, Page(s) 1-9, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2018.1528822

Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome

Author(s): Daria V. Zhernakova, Trang H. Le, Alexander Kurilshikov, Biljana Atanasovska, Marc Jan Bonder, Serena Sanna, Annique Claringbould, Urmo Võsa, Patrick Deelen, Lude Franke, Rudolf A. de Boer, Folkert Kuipers, Mihai G. Netea, Marten H. Hofker, Cisca Wijmenga, Alexandra Zhernakova, Jingyuan Fu
Published in: Nature Genetics, Issue 50/11, 2018, Page(s) 1524-1532, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-018-0224-7

Pharmacomicrobiomics: a novel route towards personalized medicine?

Author(s): Marwah Doestzada, Arnau Vich Vila, Alexandra Zhernakova, Debby P. Y. Koonen, Rinse K. Weersma, Daan J. Touw, Folkert Kuipers, Cisca Wijmenga, Jingyuan Fu
Published in: Protein & Cell, Issue 9/5, 2018, Page(s) 432-445, ISSN 1674-800X
Publisher: Springer Verlag
DOI: 10.1007/s13238-018-0547-2

Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative

Author(s): Jun Wang, Alexander Kurilshikov, Djawad Radjabzadeh, Williams Turpin, Kenneth Croitoru, Marc Jan Bonder, Matthew A. Jackson, Carolina Medina-Gomez, Fabian Frost, Georg Homuth, Malte Rühlemann, David Hughes, Han-na Kim, Tim D. Spector, Jordana T. Bell, Claire J. Steves, Nicolas Timpson, Andre Franke, Cisca Wijmenga, Katie Meyer, Tim Kacprowski, Lude Franke, Andrew D. Paterson, Jeroen Raes, Robert
Published in: Microbiome, Issue 6/1, 2018, ISSN 2049-2618
Publisher: Springer Nature
DOI: 10.1186/s40168-018-0479-3

A system biology perspective on environment–host–microbe interactions

Author(s): Lianmin Chen, Sanzhima Garmaeva, Alexandra Zhernakova, Jingyuan Fu, Cisca Wijmenga
Published in: Human Molecular Genetics, Issue 27/R2, 2018, Page(s) R187-R194, ISSN 0964-6906
Publisher: Oxford University Press
DOI: 10.1093/hmg/ddy137

Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting

Author(s): Bashar Ibrahim, Ksenia Arkhipova, Arno Andeweg, Susana Posada-Céspedes, François Enault, Arthur Gruber, Eugene Koonin, Anne Kupczok, Philippe Lemey, Alice McHardy, Dino McMahon, Brett Pickett, David Robertson, Richard Scheuermann, Alexandra Zhernakova, Mark Zwart, Alexander Schönhuth, Bas Dutilh, Manja Marz
Published in: Viruses, Issue 10/5, 2018, Page(s) 256, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10050256

Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

Author(s): Matthew A. Jackson, Marc Jan Bonder, Zhana Kuncheva, Jonas Zierer, Jingyuan Fu, Alexander Kurilshikov, Cisca Wijmenga, Alexandra Zhernakova, Jordana T. Bell, Tim D. Spector, Claire J. Steves
Published in: PeerJ, Issue 6, 2018, Page(s) e4303, ISSN 2167-8359
Publisher: PeerJ
DOI: 10.7717/peerj.4303

The influence of proton pump inhibitors and other commonly used medication on the gut microbiota

Author(s): Floris Imhann, Arnau Vich Vila, Marc Jan Bonder, Ailine G. Lopez Manosalva, Debby P.Y. Koonen, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Rinse K. Weersma
Published in: Gut Microbes, Issue 8/4, 2017, Page(s) 351-358, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2017.1284732

Gut microbiome structure and metabolic activity in inflammatory bowel disease

Author(s): Eric A. Franzosa, Alexandra Sirota-Madi, Julian Avila-Pacheco, Nadine Fornelos, Henry J. Haiser, Stefan Reinker, Tommi Vatanen, A. Brantley Hall, Himel Mallick, Lauren J. McIver, Jenny S. Sauk, Robin G. Wilson, Betsy W. Stevens, Justin M. Scott, Kerry Pierce, Amy A. Deik, Kevin Bullock, Floris Imhann, Jeffrey A. Porter, Alexandra Zhernakova, Jingyuan Fu, Rinse K. Weersma, Cisca Wijmenga, Clary B.
Published in: Nature Microbiology, Issue 4/2, 2019, Page(s) 293-305, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-018-0306-4

Studying the gut virome in the metagenomic era: challenges and perspectives

Author(s): Sanzhima Garmaeva, Trishla Sinha, Alexander Kurilshikov, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova
Published in: BMC Biology, Issue 17/1, 2019, ISSN 1741-7007
Publisher: BioMed Central
DOI: 10.1186/s12915-019-0704-y

Structural variation in the gut microbiome associates with host health

Author(s): David Zeevi, Tal Korem, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Segal
Published in: Nature, Issue 568/7750, 2019, Page(s) 43-48, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-019-1065-y

Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases

Author(s): Serena Sanna, Natalie R. van Zuydam, Anubha Mahajan, Alexander Kurilshikov, Arnau Vich Vila, Urmo Võsa, Zlatan Mujagic, Ad A. M. Masclee, Daisy M. A. E. Jonkers, Marije Oosting, Leo A. B. Joosten, Mihai G. Netea, Lude Franke, Alexandra Zhernakova, Jingyuan Fu, Cisca Wijmenga, Mark I. McCarthy
Published in: Nature Genetics, Issue 51/4, 2019, Page(s) 600-605, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-019-0350-x

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk

Author(s): Alexander Kurilshikov, Inge C.L. van den Munckhof, Lianmin Chen, Marc J. Bonder, Kiki Schraa, Joost H.W. Rutten, Niels P. Riksen, Jacqueline de Graaf, Marije Oosting, Serena Sanna, Leo A.B. Joosten, Marinette van der Graaf, Tessa Brand, Debby P.Y. Koonen, Martijn van Faassen, P. Eline Slagboom, Ramnik J. Xavier, Folkert Kuipers, Marten H. Hofker, Cisca Wijmenga, Mihai G. Netea, Alexandra Zhernakov
Published in: Circulation Research, Issue 124/12, 2019, Page(s) 1808-1820, ISSN 0009-7330
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circresaha.118.314642

Global phylogeography and ancient evolution of the widespread human gut virus crAssphage

Author(s): Robert A. Edwards, Alejandro A. Vega, Holly M. Norman, Maria Ohaeri, Kyle Levi, Elizabeth A. Dinsdale, Ondrej Cinek, Ramy K. Aziz, Katelyn McNair, Jeremy J. Barr, Kyle Bibby, Stan J. J. Brouns, Adrian Cazares, Patrick A. de Jonge, Christelle Desnues, Samuel L. Díaz Muñoz, Peter C. Fineran, Alexander Kurilshikov, Rob Lavigne, Karla Mazankova, David T. McCarthy, Franklin L. Nobrega, Alejandro Reye
Published in: Nature Microbiology, Issue 4/10, 2019, Page(s) 1727-1736, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-019-0494-6

The neuroactive potential of the human gut microbiota in quality of life and depression

Author(s): Mireia Valles-Colomer, Gwen Falony, Youssef Darzi, Ettje F. Tigchelaar, Jun Wang, Raul Y. Tito, Carmen Schiweck, Alexander Kurilshikov, Marie Joossens, Cisca Wijmenga, Stephan Claes, Lukas Van Oudenhove, Alexandra Zhernakova, Sara Vieira-Silva, Jeroen Raes
Published in: Nature Microbiology, Issue 4/4, 2019, Page(s) 623-632, ISSN 2058-5276
Publisher: Nature Publishing Group
DOI: 10.1038/s41564-018-0337-x

SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects

Author(s): Valerie Collij, Floris Imhann, Arnau Vich Vila, Jingyuan Fu, Gerard Dijkstra, Eleonora A. M. Festen, Michiel D. Voskuil, Mark J. Daly, Ramnik J. Xavier, Cisca Wijmenga, Alexandra Zhernakova, Rinse K. Weersma
Published in: PLOS ONE, Issue 14/1, 2019, Page(s) e0211328, ISSN 1932-6203
Publisher: Public Library of Science
DOI: 10.1371/journal.pone.0211328

Gut microbiome composition and its relation to joint pain and inflammation

Author(s): C.G. Boer, D. Radjabzadeh, C. Medina-Gomez, S. Garmaeva, D. Schiphof, P. Arp, T. Koet, A. Kurilshikov, J. Fu, A.M. Ikram, S. Bierma-Zeinstra, A.G. Uitterlinden, R. Kraaij, A. Zhernakova, J.B. van Meurs
Published in: Osteoarthritis and Cartilage, Issue 27, 2019, Page(s) S26, ISSN 1063-4584
Publisher: W. B. Saunders Co., Ltd.
DOI: 10.1016/j.joca.2019.02.040

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome

Author(s): Arnau Vich Vila, Floris Imhann, Valerie Collij, Soesma A. Jankipersadsing, Thomas Gurry, Zlatan Mujagic, Alexander Kurilshikov, Marc Jan Bonder, Xiaofang Jiang, Ettje F. Tigchelaar, Jackie Dekens, Vera Peters, Michiel D. Voskuil, Marijn C. Visschedijk, Hendrik M. van Dullemen, Daniel Keszthelyi, Morris A. Swertz, Lude Franke, Rudi Alberts, Eleonora A. M. Festen, Gerard Dijkstra, Ad A. M. Masclee,
Published in: Science Translational Medicine, Issue 10/472, 2018, Page(s) eaap8914, ISSN 1946-6234
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scitranslmed.aap8914

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

Author(s): 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.
Published in: Nature Genetics, 2022, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-021-00992-y

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

Author(s): Sinha T, Brushett S, Prins J, Zhernakova A.
Published in: Current Opinion in Microbiology, 2023, ISSN 1369-5274
Publisher: Elsevier BV
DOI: 10.1016/j.mib.2023.102309

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

Author(s): Gulyaeva A, Garmaeva S, Ruigrok RAAA, Wang D, Riksen NP, Netea MG, Wijmenga C, Weersma RK, Fu J, Vila AV, Kurilshikov A, Zhernakova A.
Published in: Cell Reports, 2022, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2021.110204

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

Author(s): Sanzhima Garmaeva, Anastasia Gulyaeva, Trishla Sinha, Andrey N. Shkoporov, Adam G. Clooney, Stephen R. Stockdale, Johanne E. Spreckels, Thomas D.S. Sutton, Lorraine A. Draper, Bas E. Dutilh, Cisca Wijmenga, Alexander Kurilshikov, Jingyuan Fu, Colin Hill, Alexandra Zhernakova
Published in: Cell Reports, 2021, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2021.109132

Other (1)

Mother-Infant Gut Viruses and their Bacterial Hosts: Transmission Patterns and Dynamics during Pregnancy and Early Life

Author(s): Sanzhima Garmaeva, Trishla Sinha, Anastasia Gulyaeva, Nataliia Kuzub, Johanne E Spreckels, Sergio Andreu-Sánchez, Ranko Gacesa, Arnau Vich Vila, Siobhan Brushett, Marloes Kruk, Lifelines NEXT cohort study, Jackie Dekens, Jan Sikkema, Folkert Kuipers, Andrey Shkoporov, Colin Hill, Sicco Scherjon, Cisca Wijmenga, Jingyuan Fu, Alexander Kurilshikov, Alexandra Zhernakova
Published in: 2023
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.21.554108