Project description
Mechanisms enabling phage-bacterial coexistence in the gut
Phages play an important role in intestinal microbial diversity and human health. However, their interaction mechanisms with bacteria are still poorly understood, affecting studies of microbiomes and phage-based therapies. Supported by the Marie Skłodowska-Curie Actions programme, the COEXIGUT project will examine the mechanisms that make it possible for phages and bacteria to coexist in the gut environment. Working with Escherichia coli, Enterococcus faecalis and their phages as model systems, the project will develop in vitro systems to explore the effects of nutrient chemical composition and/or populations diversity on coexistence. In addition, the project will analyse the proteomic and genomic signatures associated with resistance and phage-bacterial persistence.
Objective
Bacteriophages (phages) are major drivers of microbial diversity and ecosystem function in many habitats. In the human gut, they play a crucial role in shaping bacterial populations, influencing host health and microbiome stability. While several studies have revealed that phages and their bacterial hosts can coexist for extended periods, the mechanisms underlying this long-term coexistence remain largely unknown. Understanding how such stability is maintained is essential for both fundamental microbiome research and the development of phage-based therapies.
This project aims to dissect some of the molecular and ecological mechanisms that sustain stable phage-bacterial coexistence in the gut. Using Escherichia coli and Enterococcus faecalis (two commensal species commonly found in the intestinal microbiota) and their corresponding phages, I will establish controlled in vitro systems to study how factors such as nutrient composition, community complexity, and culture conditions influence coexistence dynamics. Combining these assays with deep sequencing, metabolomics and proteomics, genomic changes and molecular pathways involved in resistance and phage persistence will be decoded. The functional role will be validated through the knockdown of the identified pathways and, ultimately, tested in gnotobiotic mice colonized with the OMM12 synthetic microbial community.
The expected outcome is a detailed mechanistic understanding of how phages and their hosts coexist over time in the gut environment. By uncovering the key genetic and ecological factors involved, this project will provide fundamental insights into microbiome resilience and control. This knowledge will also help inform the rational design of microbiome-targeted interventions and improve the predictability and safety of phage therapy in clinical settings.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences biological sciences biochemistry biomolecules proteins proteomics
- natural sciences biological sciences ecology ecosystems
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Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Project’s keywords as indicated by the project coordinator. Not to be confused with the EuroSciVoc taxonomy (Fields of science)
Programme(s)
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
Multi-annual funding programmes that define the EU’s priorities for research and innovation.
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HORIZON.1.2 - Marie Skłodowska-Curie Actions (MSCA)
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Topic(s)
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Calls for proposals are divided into topics. A topic defines a specific subject or area for which applicants can submit proposals. The description of a topic comprises its specific scope and the expected impact of the funded project.
Funding Scheme
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
Funding scheme (or “Type of Action”) inside a programme with common features. It specifies: the scope of what is funded; the reimbursement rate; specific evaluation criteria to qualify for funding; and the use of simplified forms of costs like lump sums.
HORIZON-TMA-MSCA-PF-EF - HORIZON TMA MSCA Postdoctoral Fellowships - European Fellowships
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Call for proposal
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Procedure for inviting applicants to submit project proposals, with the aim of receiving EU funding.
(opens in new window) HORIZON-MSCA-2025-PF
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80333 Muenchen
Germany
The total costs incurred by this organisation to participate in the project, including direct and indirect costs. This amount is a subset of the overall project budget.