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

Informazioni relative al progetto

BabyVir

ID dell’accordo di sovvenzione: 715772

DOI

10.3030/715772

Progetto chiuso

Data della firma CE 20 Febbraio 2017

Data di avvio 1 Aprile 2017

Data di completamento 30 Giugno 2023

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale

€ 1 499 881,00

Contributo UE

€ 1 499 881,00

Coordinato da

ACADEMISCH ZIEKENHUIS GRONINGEN
Netherlands

CORDIS fornisce collegamenti ai risultati finali pubblici e alle pubblicazioni dei progetti ORIZZONTE.

I link ai risultati e alle pubblicazioni dei progetti del 7° PQ, così come i link ad alcuni tipi di risultati specifici come dataset e software, sono recuperati dinamicamente da .OpenAIRE .

Pubblicazioni

Peer reviewed articles (28)

Environmental factors shaping the gut microbiome in a Dutch population.

Autori: 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.
Pubblicato in: Nature, 2022, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-022-04567-7

Role of the gut microbiome in mediating lactose intolerance symptoms.

Autori: Brandao Gois MF, Sinha T, Spreckels JE, Vich Vila A, Bolte LA, Weersma RK, Wijmenga C, Fu J, Zhernakova A, Kurilshikov A.
Pubblicato in: Gut, 2021, ISSN 0017-5749
Editore: 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.

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

Milk and bugs educate infant immune systems.

Autori: Spreckels JE, Zhernakova A.
Pubblicato in: Immunity, 2021, ISSN 1074-7613
Editore: 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.

Autori: 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.
Pubblicato in: Immunity, 2023, ISSN 1074-7613
Editore: 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.

Autori: 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
Pubblicato in: Nature Medicine, 2022, ISSN 1078-8956
Editore: Nature Publishing Group
DOI: 10.1038/s41591-022-02014-8

Analysis of 1135 gut metagenomes identifies sex-specific resistome profiles

Autori: 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
Pubblicato in: Gut Microbes, 2018, Pagina/e 1-9, ISSN 1949-0976
Editore: Landes Bioscience
DOI: 10.1080/19490976.2018.1528822

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

Autori: 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
Pubblicato in: Nature Genetics, Numero 50/11, 2018, Pagina/e 1524-1532, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-018-0224-7

Pharmacomicrobiomics: a novel route towards personalized medicine?

Autori: Marwah Doestzada, Arnau Vich Vila, Alexandra Zhernakova, Debby P. Y. Koonen, Rinse K. Weersma, Daan J. Touw, Folkert Kuipers, Cisca Wijmenga, Jingyuan Fu
Pubblicato in: Protein & Cell, Numero 9/5, 2018, Pagina/e 432-445, ISSN 1674-800X
Editore: Springer Verlag
DOI: 10.1007/s13238-018-0547-2

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

Autori: 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
Pubblicato in: Microbiome, Numero 6/1, 2018, ISSN 2049-2618
Editore: Springer Nature
DOI: 10.1186/s40168-018-0479-3

A system biology perspective on environment–host–microbe interactions

Autori: Lianmin Chen, Sanzhima Garmaeva, Alexandra Zhernakova, Jingyuan Fu, Cisca Wijmenga
Pubblicato in: Human Molecular Genetics, Numero 27/R2, 2018, Pagina/e R187-R194, ISSN 0964-6906
Editore: Oxford University Press
DOI: 10.1093/hmg/ddy137

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

Autori: 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
Pubblicato in: Viruses, Numero 10/5, 2018, Pagina/e 256, ISSN 1999-4915
Editore: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v10050256

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

Autori: 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
Pubblicato in: PeerJ, Numero 6, 2018, Pagina/e e4303, ISSN 2167-8359
Editore: PeerJ
DOI: 10.7717/peerj.4303

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

Autori: 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
Pubblicato in: Gut Microbes, Numero 8/4, 2017, Pagina/e 351-358, ISSN 1949-0976
Editore: Landes Bioscience
DOI: 10.1080/19490976.2017.1284732

Gut microbiome structure and metabolic activity in inflammatory bowel disease

Autori: 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.
Pubblicato in: Nature Microbiology, Numero 4/2, 2019, Pagina/e 293-305, ISSN 2058-5276
Editore: Nature Publishing Group
DOI: 10.1038/s41564-018-0306-4

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

Autori: Sanzhima Garmaeva, Trishla Sinha, Alexander Kurilshikov, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova
Pubblicato in: BMC Biology, Numero 17/1, 2019, ISSN 1741-7007
Editore: BioMed Central
DOI: 10.1186/s12915-019-0704-y

Structural variation in the gut microbiome associates with host health

Autori: David Zeevi, Tal Korem, Anastasia Godneva, Noam Bar, Alexander Kurilshikov, Maya Lotan-Pompan, Adina Weinberger, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Eran Segal
Pubblicato in: Nature, Numero 568/7750, 2019, Pagina/e 43-48, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-019-1065-y

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

Autori: 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
Pubblicato in: Nature Genetics, Numero 51/4, 2019, Pagina/e 600-605, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-019-0350-x

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

Autori: 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
Pubblicato in: Circulation Research, Numero 124/12, 2019, Pagina/e 1808-1820, ISSN 0009-7330
Editore: Lippincott Williams & Wilkins Ltd.
DOI: 10.1161/circresaha.118.314642

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

Autori: 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
Pubblicato in: Nature Microbiology, Numero 4/10, 2019, Pagina/e 1727-1736, ISSN 2058-5276
Editore: Nature Publishing Group
DOI: 10.1038/s41564-019-0494-6

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

Autori: 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
Pubblicato in: Nature Microbiology, Numero 4/4, 2019, Pagina/e 623-632, ISSN 2058-5276
Editore: 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

Autori: 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
Pubblicato in: PLOS ONE, Numero 14/1, 2019, Pagina/e e0211328, ISSN 1932-6203
Editore: Public Library of Science
DOI: 10.1371/journal.pone.0211328

Gut microbiome composition and its relation to joint pain and inflammation

Autori: 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
Pubblicato in: Osteoarthritis and Cartilage, Numero 27, 2019, Pagina/e S26, ISSN 1063-4584
Editore: 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

Autori: 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,
Pubblicato in: Science Translational Medicine, Numero 10/472, 2018, Pagina/e eaap8914, ISSN 1946-6234
Editore: 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

Autori: 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.
Pubblicato in: Nature Genetics, 2022, ISSN 1061-4036
Editore: Nature Publishing Group
DOI: 10.1038/s41588-021-00992-y

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

Autori: Sinha T, Brushett S, Prins J, Zhernakova A.
Pubblicato in: Current Opinion in Microbiology, 2023, ISSN 1369-5274
Editore: 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.

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

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

Autori: 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
Pubblicato in: Cell Reports, 2021, ISSN 2211-1247
Editore: 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

Autori: 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
Pubblicato in: 2023
Editore: Cold Spring Harbor Laboratory
DOI: 10.1101/2023.08.21.554108