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

Total Cost €


EC-Contrib. €






Project "BabyVir" data sheet

The following table provides information about the project.


Organization address
address: HANZEPLEIN 1
postcode: 9713 GZ

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Total cost 1˙499˙881 €
 EC max contribution 1˙499˙881 € (100%)
 Programme 1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
 Code Call ERC-2016-STG
 Funding Scheme ERC-STG
 Starting year 2017
 Duration (year-month-day) from 2017-04-01   to  2022-03-31


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 


 Project objective

The role of intestinal bacteria in human health and disease has been intensively studied; however the viral composition of the microbiome, the virome, remains largely unknown. As many of the viruses are bacteriophages, they are expected to be a major factor shaping the human microbiome. The dynamics of the virome during early life, its interaction with host and environmental factors, is likely to have profound effects on human physiology. Therefore it is extremely timely to study the virome in depth and on a wide scale. This ERC project aims at understanding how the gut virome develops during the first year of life and how that relates to the composition of the bacterial microbiome. In particular, we will determine which intrinsic and environmental factors, including genetics and the mother’s microbiome and diet, interact with the virome in shaping the early gut microbiome ecosystem. In a longitudinal study of 1,000 newborns followed at 7 time points from birth till age 12 months, I will investigate: (1) the composition and evolution of the virome and bacterial microbiome in the first year of life; (2) the role of factors coming from the mother and from the host genome on virome and bacterial microbiome development and their co-evolution; and (3) the role of environmental factors, like infectious diseases, vaccinations and diet habits, on establishing the virome and overall microbiome composition during the first year of life. This project will provide crucial knowledge about composition and maturation of the virome during the first year of life, and its symbiotic relation with the bacterial microbiome. This longitudinal dataset will be instrumental for identification of microbiome markers of diseases and for the follow up analysis of the long-term effect of microbiota maturation later in life. Knowledge of the role of viruses in shaping the microbiota may promote future directions for manipulating the human gut microbiota in health and disease.


year authors and title journal last update
List of publications.
2019 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.
Gut microbiome structure and metabolic activity in inflammatory bowel disease
published pages: 293-305, ISSN: 2058-5276, DOI: 10.1038/s41564-018-0306-4
Nature Microbiology 4/2 2019-12-16
2019 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
SLC39A8 missense variant is associated with Crohn\'s disease but does not have a major impact on gut microbiome composition in healthy subjects
published pages: e0211328, ISSN: 1932-6203, DOI: 10.1371/journal.pone.0211328
PLOS ONE 14/1 2019-12-16
2019 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
Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk
published pages: 1808-1820, ISSN: 0009-7330, DOI: 10.1161/circresaha.118.314642
Circulation Research 124/12 2019-12-16
2019 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
Global phylogeography and ancient evolution of the widespread human gut virus crAssphage
published pages: 1727-1736, ISSN: 2058-5276, DOI: 10.1038/s41564-019-0494-6
Nature Microbiology 4/10 2019-12-16
2019 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
Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases
published pages: 600-605, ISSN: 1061-4036, DOI: 10.1038/s41588-019-0350-x
Nature Genetics 51/4 2019-12-16
2019 Sanzhima Garmaeva, Trishla Sinha, Alexander Kurilshikov, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova
Studying the gut virome in the metagenomic era: challenges and perspectives
published pages: , ISSN: 1741-7007, DOI: 10.1186/s12915-019-0704-y
BMC Biology 17/1 2019-12-16
2019 David Zeevi, Tal Korem, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Segal
Structural variation in the gut microbiome associates with host health
published pages: 43-48, ISSN: 0028-0836, DOI: 10.1038/s41586-019-1065-y
Nature 568/7750 2019-12-16
2019 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
Gut microbiome composition and its relation to joint pain and inflammation
published pages: S26, ISSN: 1063-4584, DOI: 10.1016/j.joca.2019.02.040
Osteoarthritis and Cartilage 27 2019-12-16
2018 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,
Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome
published pages: eaap8914, ISSN: 1946-6234, DOI: 10.1126/scitranslmed.aap8914
Science Translational Medicine 10/472 2019-12-16
2019 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
The neuroactive potential of the human gut microbiota in quality of life and depression
published pages: 623-632, ISSN: 2058-5276, DOI: 10.1038/s41564-018-0337-x
Nature Microbiology 4/4 2019-12-16
2018 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
Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles
published pages: 1-9, ISSN: 1949-0976, DOI: 10.1080/19490976.2018.1528822
Gut Microbes 2019-05-14
2018 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 Kraaij, Alexandra Zhernakova
Meta-analysis of human genome-microbiome association studies: the MiBioGen consortium initiative
published pages: , ISSN: 2049-2618, DOI: 10.1186/s40168-018-0479-3
Microbiome 6/1 2019-05-14
2018 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
Detection of stable community structures within gut microbiota co-occurrence networks from different human populations
published pages: e4303, ISSN: 2167-8359, DOI: 10.7717/peerj.4303
PeerJ 6 2019-05-14
2018 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
Bioinformatics Meets Virology: The European Virus Bioinformatics Center’s Second Annual Meeting
published pages: 256, ISSN: 1999-4915, DOI: 10.3390/v10050256
Viruses 10/5 2019-05-14
2017 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
The influence of proton pump inhibitors and other commonly used medication on the gut microbiota
published pages: 351-358, ISSN: 1949-0976, DOI: 10.1080/19490976.2017.1284732
Gut Microbes 8/4 2019-05-14
2018 Lianmin Chen, Sanzhima Garmaeva, Alexandra Zhernakova, Jingyuan Fu, Cisca Wijmenga
A system biology perspective on environment–host–microbe interactions
published pages: R187-R194, ISSN: 0964-6906, DOI: 10.1093/hmg/ddy137
Human Molecular Genetics 27/R2 2019-05-14
2018 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
Individual variations in cardiovascular-disease-related protein levels are driven by genetics and gut microbiome
published pages: 1524-1532, ISSN: 1061-4036, DOI: 10.1038/s41588-018-0224-7
Nature Genetics 50/11 2019-05-14
2018 Marwah Doestzada, Arnau Vich Vila, Alexandra Zhernakova, Debby P. Y. Koonen, Rinse K. Weersma, Daan J. Touw, Folkert Kuipers, Cisca Wijmenga, Jingyuan Fu
Pharmacomicrobiomics: a novel route towards personalized medicine?
published pages: 432-445, ISSN: 1674-800X, DOI: 10.1007/s13238-018-0547-2
Protein & Cell 9/5 2019-05-14

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