Modulating the gut microbiome to enhance drug efficacy

Project Information

BugDrug

Grant agreement ID: 101001678

DOI

10.3030/101001678

EC signature date 25 June 2021

Start date 1 September 2021

End date 31 August 2026

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost

€ 1 999 676,00

EU contribution

€ 1 999 676,00

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 (36)

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

Author(s): Sergio Andreu-Sánchez, Arno R. Bourgonje, Thomas Vogl, Alexander Kurilshikov, Sigal Leviatan, Angel J. Ruiz-Moreno, Shixian Hu, Trishla Sinha, Arnau Vich Vila, Shelley Klompus, Iris N. Kalka, Karina de Leeuw, Suzanne Arends, Iris Jonkers, Sebo Withoff, Lifelines Cohort Study, Elisabeth Brouwer, Adina Weinberger, Cisca Wijmenga, Eran Segal, Rinse K. Weersma, Jingyuan Fu, Alexandra Zhernakova
Published in: Immunity, 2023, ISSN 1097-4180
Publisher: Cell Press
DOI: 10.1016/j.immuni.2023.04.003

iPSC-derived organ-on-a-chip models for personalized human genetics and pharmacogenomics studies

Author(s): Victoria E.J.M. Palasantzas; Isabel Tamargo-Rubio; Kieu Le; Jelle Slager; Cisca Wijmenga; Iris H. Jonkers; Vinod Kumar; Jingyuan Fu; Sebo Withoff
Published in: Trends in Genetics, Issue 3, 2023, ISSN 1362-4555
Publisher: Elsevier
DOI: 10.1016/j.tig.2023.01.002

Implications of blood type in personalised microbiome therapy

Author(s): Yue Zhang, Ranko Gacesa, Jingyuan Fu
Published in: Clinical and Translational Medicine, Issue VOL 14 (3), 2024, ISSN 2001-1326
Publisher: Wiley
DOI: 10.1002/ctm2.1618

The long-term genetic stability and individual specificity of the human gut microbiome

Author(s): Lianmin Chen, Daoming Wang, Sanzhima Garmaeva, Alexander Kurilshikov, Arnau Vich Vila, Ranko Gacesa, Trishla Sinha, Eran Segal, Rinse K Weersma, Cisca Wijmenga, Alexandra Zhernakova, Jingyuan Fu
Published in: CELL, 2021, ISSN 0092-8674
Publisher: Cell Press

Dual UHPLC-HRMS Metabolomics and Lipidomics and Automated Data Processing Workflow for Comprehensive High-Throughput Gut Phenotyping

Author(s): P Vangeenderhuysen, J Van Arnhem, B Pomian, M De Graeve, L De Commer, G Falony, J Raes, A Zhernakova, J Fu, L Y Hemeryck, L Vanhaecke
Published in: Analytical Chemistry, 2023, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.2c05371

CRISPR dynamics during the interaction between bacteria and phage in the first year of life

Author(s): Jiqiu Wu, Hanyun Zhang, Rui Gan, Yan Xia, Fan Zhang, Daoming Wang, Jingyuan Fu, Timothy G Barraclough
Published in: Microbial Genomics, 2023, ISSN 2057-5858
Publisher: Microbiology Society
DOI: 10.1099/mgen.0.001053

Large HDL particles negatively associate with leukocyte counts independent of cholesterol efflux capacity: A cross sectional study in the population-based LifeLines DEEP cohort

Author(s): Anouk G Groenen, Venetia Bazioti, Isabelle A van Zeventer, Lianmin Chen, Hilde E Groot, Jan-Willem Balder, Alexandra Zhernakova, Pim van der Harst, Antoine Rimbert, Jan Albert Kuivenhoven, Jingyuan Fu, Marit Westerterp
Published in: Atherosclerosis, 2022, ISSN 0021-9150
Publisher: Elsevier BV
DOI: 10.1016/j.atherosclerosis.2022.01.008

Gut microbial DL-endopeptidase alleviates Crohn’s disease via the NOD2 pathway

Author(s): Gao, Jie; Zhao, Xinmei; Hu, Shixian; Huang, Zhenhe; Hu, Mengyao; Jin, Shaoqin; Lu, Bingyun; Sun, Kai; Wang, Zhang; Fu, Jingyuan; Weersma, Rinse K; He, Xiaolong; Zhou, Hongwei
Published in: Cell Host & Microbe, 2022, ISSN 1934-6069
Publisher: Elsevier
DOI: 10.1016/j.chom.2022.08.002

The composition and metabolic potential of the human small intestinal microbiota within the context of inflammatory bowel disease

Author(s): Renate AAA Ruigrok, Valerie Collij, Paula Sureda, Marjolein AY Klaassen, Laura A Bolte, Bernadien H Jansen, Michiel D Voskuil, Jingyuan Fu, Cisca Wijmenga, Alexandra Zhernakova, Rinse K Weersma, Arnau Vich Vila
Published in: Journal of Crohn's and Colitis, 2021, ISSN 1873-9946
Publisher: Elsevier Science
DOI: 10.1093/ecco-jcc/jjab020

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

Author(s): Yue Zhang, Sergio Andreu-Sánchez, Nadira Vadaq, Daoming Wang, Vasiliki Matzaraki, Wouter A. van der Heijden, Ranko Gacesa, Rinse K. Weersma, Alexandra Zhernakova, Linos Vandekerckhove, Quirijn de Mast, Leo A. B. Joosten, Mihai G. Netea, André J. A. M. van der Ven, Jingyuan Fu
Published in: Frontiers in Cellular and Infection Microbiology, 2023, ISSN 2235-2988
Publisher: Frontiers Media S. A.
DOI: 10.3389/fcimb.2023.1202035

Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation

Author(s): J. Casper Swarte, Yanni Li, Shixian Hu, Johannes R. Björk, Ranko Gacesa, Arnau Vich Vila, Rianne M. Douwes, Valerie Collij, Alexander Kurilshikov, Adrian Post, Marjolein A. Y. Klaassen, Michele F. Eisenga, António W. Gomes-Neto, Daan Kremer, Bernadien H. Jansen, Tim J. Knobbe, Stefan P. Berger, Jan-Stephan F. Sanders, M. Rebecca Heiner-Fokkema, Robert J. Porte, Frans J. C. Cuperus, Vincent E. d
Published in: Science Translational Medicine, 2022, ISSN 1946-6234
Publisher: American Association for the Advancement of Science
DOI: 10.1126/scitranslmed.abn7566

Faecal metabolome and its determinants in inflammatory bowel disease

Author(s): Arnau Vich Vila, Shixian Hu, Sergio Andreu-Sánchez, Valerie Collij, Bernadien H Jansen, Hannah E Augustijn, Laura A Bolte, Renate A A A Ruigrok, Galeb Abu-Ali, Cosmas Giallourakis, Jessica Schneider, John Parkinson, Amal Al-Garawi, Alexandra Zhernakova, Ranko Gacesa, Jingyuan Fu, Rinse K Weersma
Published in: GUT, 2023, ISSN 1468-3288
Publisher: BMJ Publishing Group Ltd & British Society of Gastroenterology
DOI: 10.1136/gutjnl-2022-328048

Gut microbiome and bile acids in obesity-related diseases

Author(s): Rumei Li, Sergio Andreu-Sánchez, Folkert Kuipers, Jingyuan Fu
Published in: Best Practice & Research Clinical Endocrinology & Metabolism, 2021, ISSN 1521-690X
Publisher: Bailliere Tindall And Cassell
DOI: 10.1016/j.beem.2021.101493

A benchmark of genetic variant calling pipelines using metagenomic short-read sequencing

Author(s): Sergio Andreu-Sánchez, Lianmin Chen, Daoming Wang, Hannah E Augustijn, Alexandra Zhernakova, Jingyuan Fu
Published in: Frontiers in genetics, 2021, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2021.648229

Microbial vitamin production mediates dietary effects on diabetic risk

Author(s): Daoming Wang, T. van Pham, Robert E. Steinert, Alexandra Zhernakova, Jingyuan Fu
Published in: Gut Microbes, 2022, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2022.2154550

Phage-display immunoprecipitation sequencing of the antibody epitope repertoire in inflammatory bowel disease reveals distinct antibody signatures

Author(s): Arno R. Bourgonje, Sergio Andreu-Sánchez, Thomas Vogl, Shixian Hu, Arnau Vich Vila, Ranko Gacesa, Sigal Leviatan, Alexander Kurilshikov, Shelley Klompus, Iris N. Kalka, Hendrik M. van Dullemen, Adina Weinberger, Marijn C. Visschedijk, Eleonora A.M. Festen, Klaas Nico Faber, Cisca Wijmenga, Gerard Dijkstra, Eran Segal, Jingyuan Fu, Alexandra Zhernakova, Rinse K. Weersma
Published in: Immunity, 2023, ISSN 1097-4180
Publisher: Cell Press
DOI: 10.1016/j.immuni.2023.04.017

Oral Microbiome in Relation to Periodontitis Severity and Systemic Inflammation

Author(s): Adelina S Plachokova, Sergio Andreu-Sánchez, Marlies P Noz, Jingyuan Fu, Niels P Riksen
Published in: International Journal of Molecular Sciences, 2021, ISSN 1422-0067
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/ijms22115876

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 DS 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

Population-wide diversity and stability of serum antibody epitope repertoires against human microbiota

Author(s): Thomas Vogl, Shelley Klompus, Sigal Leviatan, Iris N Kalka, Adina Weinberger, Cisca Wijmenga, Jingyuan Fu, Alexandra Zhernakova, Rinse K Weersma, Eran Segal
Published in: Nature Medicine, 2021, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-021-01409-3

Long non-coding RNAs involved in progression of non-alcoholic fatty liver disease to steatohepatitis

Author(s): Biljana Atanasovska, Sander S Rensen, Glenn Marsman, Ronit Shiri-Sverdlov, Sebo Withoff, Folkert Kuipers, Cisca Wijmenga, Bart van de Sluis, Jingyuan Fu
Published in: Cells, 2021, ISSN 2073-4409
Publisher: MDPI
DOI: 10.3390/cells10081883

Environmental factors shaping the gut microbiome in a Dutch population

Author(s): 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. Ho!ker, R. C. H. Vermeulen, S. Sanna, H. J. M. Harmsen, C. Wijmenga, J. Fu, A. Zhernakova, R. K. Weersma
Published in: NATURE, 2022, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-022-04567-7

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

Author(s): 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
Published in: Nature Medicine, 2022, ISSN 1078-8956
Publisher: Nature Publishing Group
DOI: 10.1038/s41591-022-02014-8

Challenges and future directions for studying effects of host genetics on the gut microbiome

Author(s): Serena Sanna, Alexander Kurilshikov, Adriaan van der Graaf, Jingyuan Fu, Alexandra Zhernakova
Published in: Nature genetics, 2022, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-021-00983-z

Microbiome-Related Indole and Serotonin Metabolites are Linked to Inflammation and Psychiatric Symptoms in People Living with HIV

Author(s): Nadira Vadaq, Yue Zhang, Elise Meeder, Lisa Van De Wijer, Muhammad Hussein Gasem, Leo AB Joosten, Mihai G Netea, Quirijn De Mast, Vasiliki Matzaraki, Arnt Schellekens, Jingyuan Fu, André JAM Van Der Ven
Published in: International Journal of Tryptophan Research, 2022, ISSN 1178-6469
Publisher: Libertas Academica Ltd.
DOI: 10.1177/11786469221126888

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

Author(s): Esteban A Lopera-Maya, Alexander Kurilshikov, Adriaan van der Graaf, Shixian Hu, Sergio Andreu-Sánchez, Lianmin Chen, Arnau Vich Vila, Ranko Gacesa, Trishla Sinha, Valerie Collij, Marjiolein AY Klaassen, Laura A Bolte, Milla F Brandao Gois, Pieter BT Neerincx, Morris A Swertz, Hermie JM Harmsen, Cisca Wijmenga, Jingyuan Fu, Rinse K Weersma, Alexandra Zhernakova, Serena Sanna
Published in: Nature Genetics, 2022, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-021-00992-y

the challenge of the cytochrome P450 family

Author(s): Isabel Tamargo-Rubio; Anna Bella Simpson; Joanne A. Hoogerland; Joanne A. Hoogerland; Jingyuan Fu; Jingyuan Fu
Published in: Frontiers in Pharmacology, Vol 14 (2023), Issue 3, 2023, ISSN 1663-9812
Publisher: Frontiers Media S.A.
DOI: 10.3389/fphar.2023.1223108

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

Author(s): 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, Jingyuan Fu
Published in: BMC Medicine, Issue VOL 20, (485), 2022, ISSN 1741-7015
Publisher: BioMed Central
DOI: 10.1186/s12916-022-02688-4

Transmission and dynamics of mother-infant gut viruses during pregnancy and early life

Author(s): Lifelines NEXT cohort study, Sanzhima Garmaeva, Trishla Sinha, Anastasia Gulyaeva, Nataliia Kuzub, Johanne E Spreckels, Sergio Andreu-Sánchez, Ranko Gacesa, Arnau Vich Vila, Siobhan Brushett, Marloes Kruk, Jackie Dekens, Jan Sikkema, Folkert Kuipers, Andrey N Shkoporov, Colin Hill, Sicco Scherjon, Cisca Wijmenga, Jingyuan Fu, Alexander KurilshikovAlexandra Zhernakova
Published in: Nature Communications, 2024, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-024-45257-4

Long-term dietary patterns are associated with pro-inflammatory and anti-inflammatory features of the gut microbiome

Author(s): Laura A Bolte, Arnau Vich Vila, Floris Imhann, Valerie Collij, Ranko Gacesa, Vera Peters, Cisca Wijmenga, Alexander Kurilshikov, Marjo JE Campmans-Kuijpers, Jingyuan Fu, Gerard Dijkstra, Alexandra Zhernakova, Rinse K Weersma
Published in: GUT, 2021, ISSN 0017-5749
Publisher: BMJ Publishing Group
DOI: 10.1136/gutjnl-2020-322670

Genetic, parental and lifestyle factors influence telomere length

Author(s): Sergio Andreu-Sánchez, Geraldine Aubert, Aida Ripoll-Cladellas, Sandra Henkelman, Daria V. Zhernakova, Trishla Sinha, Alexander Kurilshikov, Maria Carmen Cenit, Marc Jan Bonder, Lude Franke, Cisca Wijmenga, Jingyuan Fu, Monique G. P. van der Wijst, Marta Melé, Peter Lansdorp & Alexandra Zhernakova
Published in: Communications Biology, 2022, ISSN 2399-3642
Publisher: Nature Portfolio
DOI: 10.1038/s42003-022-03521-7

Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline

Author(s): Xiaolei Liu, Jiqiu Wu, Jingyi Tang, Zhigang Xu, Bailing Zhou, Yang Liu, Fengjuan Hu, Gongchang Zhang , Rui Cheng, Xin Xia, Yilong Chen, Hongyu Wu, Daoming Wang, Jirong Yue, Biao Dong, Jingyuan Fu, Haopeng Yu, Birong Dong
Published in: J Cachexia Sarcopenia Muscle, Issue VOL 14 (5), 2023, ISSN 2190-5991
Publisher: Springer Verlag
DOI: 10.1002/jcsm.13313

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

Author(s): Anastasia Gulyaeva, Sanzhima Garmaeva, Renate AAA Ruigrok, Daoming Wang, Niels P Riksen, Mihai G Netea, Cisca Wijmenga, Rinse K Weersma, Jingyuan Fu, Arnau Vich Vila, Alexander Kurilshikov, Alexandra Zhernakova
Published in: Cell Reports, 2022, ISSN 2211-1247
Publisher: Cell Press
DOI: 10.1016/j.celrep.2021.110204

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

Author(s): Anastasia Gulyaeva, Sanzhima Garmaeva, Alexander Kurilshikov, Arnau Vich Vila, Niels P Riksen, Mihai G Netea, Rinse K Weersma, Jingyuan Fu, Alexandra Zhernakova
Published in: Virusus, Issue VOL 14 (10), 2022, ISSN 1999-4915
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/v14102305

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

Author(s): Daoming Wang, Marwah Doestzada, Lianmin Chen, Sergio Andreu-Sánchez, Inge C.L. van den Munckhof, Hannah E. Augustijn, Martijn Koehorst, Angel J. Ruiz-Moreno, Vincent W. Bloks, Niels P. Riksen, Joost H.W. Rutten, Leo A.B. Joosten, Mihai G. Netea, Cisca Wijmenga, Alexandra Zhernakova, Folkert Kuipers, Jingyuan Fu
Published in: Cell Host Microbe, 2021, ISSN 1931-3128
Publisher: Cell Press
DOI: 10.1016/j.chom.2021.11.003

Beyond personal space: Unveiling the transmission pattern of the human gut and oral microbiome

Author(s): Sergio Andreu-Sánchez, Jiafei Wu, Jingyuan Fu
Published in: iMeta, 2023, ISSN 2770-596x
Publisher: John Wiley & Sons
DOI: 10.1002/imt2.98

Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses

Author(s): Asier Fernández-Pato, Trishla Sinha, Ranko Gacesa, Sergio Andreu-Sánchez, Milla F Brandao Gois, Jody Gelderloos-Arends, Dianne B H Jansen, Marloes Kruk, Martin Jaeger, Leo A B Joosten, Mihai G Netea, Rinse K Weersma, Cisca Wijmenga, Hermie J M Harmsen, Jingyuan Fu, Alexandra Zhernakova, Alexander Kurilshikov
Published in: Scientific Reports, 2024, ISSN 2045-2322
Publisher: Nature Publishing Group
DOI: 10.1038/s41598-024-54353-w