Colonization resistance: training and research towards microbiome derived solutions to foodborne disease

Project Information

COL_RES

Grant agreement ID: 956279

DOI

10.3030/956279

Project closed

EC signature date 27 July 2020

Start date 1 March 2021

End date 28 February 2025

Funded under

• EXCELLENT SCIENCE - Marie Skłodowska-Curie Actions

Total cost

€ 2 186 997,48

EU contribution

€ 2 186 997,48

Coordinated by

UNIVERSITY COLLEGE CORK - NATIONAL UNIVERSITY OF IRELAND, CORK
Ireland

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 .

Deliverables

Demonstrators, pilots, prototypes (2)

A metabolomics protocol for metabolite annotation

A metabolomics protocol for large-scale and high-throughput metabolite annotation

A computational tool to unravel metabolic interactions among microbiota

A computational tool to unravel metabolic interactions among microbiota combining metaproteomics and metabolomics

Documents, reports (7)

Final report on probiotics in infectious disease

A final report outlining the success or otherwise of using probiotics to impede infectious disease in the models outlined above

Paper on use of phage to prevent infection

Scientific paper outlining potential for phage therapies and preventative measures

Paper on role of diet in Colonization Resistance

Scientific paper outlining the specific effects of dietary factors on individual pathogens

Report describing a meta-analytical workflow

Report outlining a reliable meta-analytic workflow for integration of ‘omics’ datasets

Paper on phage dynamics during infection

Scientific paper outlining the dynamics of phage communities in an infection model

Scientific Paper on Colonization Resistance

Scientific paper outlining the role of specific commensals in colonisation resistance

Report outlining integration of COL_RES data

Report outlining integration and comparison of datasets from infectious disease models in COL_RES

Publications

Peer reviewed articles (15)

Metabolomic signatures of intestinal colonization resistance against Campylobacter jejuni in mice

Author(s): Nizar W. Shayya, Rasmus Bandick, Lia V. Busmann, Soraya Mousavi, Stefan Bereswill, Markus M. Heimesaat
Published in: Frontiers in Microbiology, Issue 14, 2023, ISSN 1664-302X
Publisher: Frontiers Media
DOI: 10.3389/fmicb.2023.1331114

From microbiome composition to functional engineering, one step at a time

Author(s): Burz, Sebastian Dan; Causevic, Senka; Dal Co, Alma; id_orcid0000-0001-8816-7670; Dmitrijeva, Marija; Engel, Philipp; Garrido-Sanz, Daniel; Greub, Gilbert; Hapfelmeier, Siegfried; Hardt, Wolf-Dietrich; id_orcid0000-0002-9892-6420; Hatzimanikatis, Vassily; Heiman, Clara Margot; Herzog, Mathias Klaus-Maria; id_orcid0000-0002-0097-2526; Hockenberry, Alyson; id_orcid0000-0003-0828-1428; Keel, Christoph
Published in: Microbiology and Molecular Biology Reviews, 87 (4), Issue 1, 2023, ISSN 1092-2172
Publisher: American Society for Microbiology
DOI: 10.1128/mmbr.00063-23

Predicting the Predicted: A Comparison of Machine Learning-Based Collision Cross-Section Prediction Models for Small Molecules

Author(s): Sara M. de Cripan, Trisha Arora, Adrià Olomí, Núria Canela, Gary Siuzdak, Xavier Domingo-Almenara
Published in: Analytical Chemistry, Issue 96, 2024, Page(s) 9088-9096, ISSN 0003-2700
Publisher: American Chemical Society
DOI: 10.1021/acs.analchem.4c00630

<i>Akkermansia muciniphila</i> in infectious disease: A new target for this next-generation probiotic?

Author(s): Jonathan M. Keane, Monica Cazzaniga, Cormac G.M. Gahan
Published in: Science Progress, Issue 107, 2025, ISSN 0036-8504
Publisher: Science Reviews Ltd.
DOI: 10.1177/00368504241231159

Non-canonical start codons confer context-dependent advantages in carbohydrate utilization for commensal E. coli in the murine gut

Author(s): Yassine Cherrak, Miguel Angel Salazar, Nicolas Näpflin, Lukas Malfertheiner, Mathias K.-M. Herzog, Christopher Schubert, Christian von Mering, Wolf-Dietrich Hardt
Published in: Nature Microbiology, 2024, ISSN 2058-5276
Publisher: Springer Nature
DOI: 10.1038/s41564-024-01775-x

Sublethal systemic LPS in mice enables gut-luminal pathogens to bloom through oxygen species-mediated microbiota inhibition

Author(s): Sanne Kroon, Dejan Malcic, Lena Weidert, Lea Bircher, Leonardo Boldt, Philipp Christen, Patrick Kiefer, Anna Sintsova, Bidong D. Nguyen, Manja Barthel, Yves Steiger, Melanie Clerc, Mathias K.-M. Herzog, Carmen Chen, Ersin Gül, Benoit Guery, Emma Slack, Shinichi Sunagawa, Julia A. Vorholt, Lisa Maier, Christophe Lacroix, Annika Hausmann, Wolf-Dietrich Hardt
Published in: Nature Communications, Issue 16, 2025, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-025-57979-0

Charting the metabolic biogeography of the colorectum in cancer: challenging the right sided versus left sided classification

Author(s): Abhishek Jain, Montana T. Morris, Domenica Berardi, Trisha Arora, Xavier Domingo-Almenara, Philip B. Paty, Nicholas J. W. Rattray, Daniel Kerekes, Lingeng Lu, Sajid A. Khan, Caroline H. Johnson
Published in: Molecular Cancer, Issue 23, 2024, ISSN 1476-4598
Publisher: BioMed Central
DOI: 10.1186/s12943-024-02133-5

Comparing <i>Campylobacter jejuni</i> to three other enteric pathogens in OligoMM ¹² mice reveals pathogen-specific host and microbiota responses

Author(s): Mathias K.-M. Herzog, Audrey Peters, Nizar Shayya, Monica Cazzaniga, Kardokh Kaka Bra, Trisha Arora, Manja Barthel, Ersin Gül, Luca Maurer, Patrick Kiefer, Philipp Christen, Katharina Endhardt, Julia A. Vorholt, Gad Frankel, Markus M. Heimesaat, Stefan Bereswill, Cormac G. M. Gahan, Marcus J. Claesson, Xavier Domingo-Almenara, Wolf-Dietrich Hardt
Published in: Gut Microbes, Issue 17, 2025, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2024.2447832

Differential antibiosis predisposes mice to Campylobacter jejuni infection: Deeper insights into the impact of the gut microbiota composition in colonization resistance

Author(s): Nizar W. Shayya, Soraya Mousavi, Kerstin Stingl, Stefan Bereswill, Markus M. Heimesaat
Published in: European Journal of Microbiology and Immunology, 2025, ISSN 2062-509X
Publisher: AKjournals
DOI: 10.1556/1886.2024.00140

Mouse models for bacterial enteropathogen infections: insights into the role of colonization resistance.

Author(s): Herzog, Mathias K-M; Cazzaniga, Monica; Peters, Audrey; Shayya, Nizar; Beldi, Luca; Hapfelmeier, Siegfried Hektor; Heimesaat, Markus M; Bereswill, Stefan; Frankel, Gad; Gahan, Cormac G M; Hardt, Wolf-Dietrich
Published in: Gut Microbes, 15 (1), Issue 2, 2023, ISSN 1949-0976
Publisher: Landes Bioscience
DOI: 10.1080/19490976.2023.2172667

Impact of Western Diet on Enterohemorrhagic Escherichia coli Colonization in the Human In Vitro Mucosal Artificial Colon as Mediated by Gut Microbiota

Author(s): Deborah O’Sullivan, Trisha Arora, Claude Durif, Ophélie Uriot, Morgane Brun, Marc Riu, Elisabet Foguet-Romero, Iris Samarra, Xavier Domingo-Almenara, Cormac G. M. Gahan, Lucie Etienne-Mesmin, Stéphanie Blanquet-Diot
Published in: Nutrients, Issue 16, 2024, Page(s) 2046, ISSN 2072-6643
Publisher: Multidisciplinary Digital Publishing Institute (MDPI)
DOI: 10.3390/nu16132046

The gut virome in health and disease: new insights and associations

Author(s): Hiba Shareefdeen, Colin Hill
Published in: Current Opinion in Gastroenterology, 2024, ISSN 0267-1379
Publisher: Lippincott Williams & Wilkins Ltd.
DOI: 10.1097/mog.0000000000000885

The Mobilizable Plasmid P3 of Salmonella enterica Serovar Typhimurium SL1344 Depends on the P2 Plasmid for Conjugative Transfer into a Broad Range of Bacteria In Vitro and In Vivo

Author(s): Gaissmaier, Marla Sofie; Laganenka, Leanid; Herzog, Mathias Klaus-Maria; Bakkeren, Erik; Hardt, Wolf-Dietrich
Published in: Journal of Bacteriology, 204 (12), Issue 1, 2022, ISSN 0021-9193
Publisher: American Society for Microbiology
DOI: 10.1128/jb.00347-22

Nano in Micro: Novel Concepts in Foodborne Pathogen Transmission and Pathogenesis

Author(s): Yue Liu, Xuchuan Ma, Monica Cazzaniga, Cormac G.M. Gahan, Heidy M.W. den Besten, Tjakko Abee
Published in: Annual Review of Food Science and Technology, 2024, ISSN 1941-1413
Publisher: Annual Reviews Inc.
DOI: 10.1146/annurev-food-111523-121811

Microbiota and metabolome dynamics induced by Shiga toxin-producing E. coli in an in vitro model of an infant’s colon

Author(s): Mariana Izquierdo, Deborah O’Sullivan, Ophélie Uriot, Morgane Brun, Claude Durif, Sylvain Denis, Pablo Gallardo, Cormac G M Gahan, Lucie Etienne-Mesmin, Stéphanie Blanquet-Diot, Mauricio J. Farfan
Published in: Microbial Cell, Issue 12, 2025, Page(s) 76-92, ISSN 2311-2638
Publisher: Shared Science Publishers OG
DOI: 10.15698/mic2025.04.847