Cluster 6: MIBIREM

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HORIZON-CL6-2021-CIRCBIO-01-07: Microbiomes for bio-based innovation and environmental applications (MIBIREM)

The MIBIREM consortium consists of 12 partners from 6 European countries including 5 companies and with the Austrian Institute of Technology as coordinator.


Microbiomes are the sum of microbes in any defined location, like our gut, our skin, surface of a plant leave, a rock, etc. They play innumerable, still underappreciated roles not only for living organisms but also the environment. While some microbiomes like that of the human gut get high scientific attention, others are much less explored, despite potentially high economic and ecologic significance. In environmental applications, microbiomes degrading chemicals in soil and groundwater have a high potential to provide eco-friendly and cost-effective solutions to clean up (remediate) contaminated sites. In Europe approx. 324,000 severely contaminated sites exist and many more with less severe but still substantial contaminations that require clean-up like fuel stations. Bioremediation by use of microorganisms is cost-effective and eco-friendly to remediate sites polluted with organic contaminants: no net water extraction (no water footprint), no extensive on-site treatment plant, no waste and no transport to and treatment by an off-site soil cleaner. Key for a successful application of bioremediation is the understanding and control of the microbial networks that lead to degradation of contaminants. This requires a detailed knowledge of the interplay between the degrading microbiome and chemical and physical site characteristics, and tools to identify and monitor bacteria within microbiomes that actively clean up polluted sites. These tools, together with the isolation and evolutionary improvement of microbiomes with high degradation potential, will boost the number of sites that are bioremediated in the future.

The overall objective is that:

MIBIREM will adapt and streamline microbiome science to the needs of applications, to exploit microbiomes for bioremediation, creating and applying a TOOLBOX to identify, analyse, cultivate and up-scale microbiomes, while ensuring safety and policy alignment.

Project description

Many technologies and tools exist to analyse and work with single bacterial strains and some also to analyse microbiomes (e.g. -omics and sequencing). However, there are no workflows, guidelines or services to bring this all together, integrating the new –omics and sequencing data with existing physical and chemical environmental data. But only this will truly enable microbiomes for bio-based innovation and make bioremediation of contaminated sites an attractive alternative. MIBIREM is ground-breaking by taking tools and technologies to the next level: Single-strain technology will be adapted for microbiomes, and everything combined in the unique ‘MIBIREM approach’, leading to a microbiome TOOLBOX. This MIBIREM TOOLBOX will be used to offer services post-project to analyse and up-scale microbiomes for bioremediation, all the way to field application. The ambition lies both in advancing several single methods and technologies, but most importantly in integrating tools and services in the TOOLBOX. This is not only a technical challenge (e.g. defining parameters and sensitivities, standards, data sharing, etc.) but also a business development challenge as several partners combine their services in the TOOLBOX. The ambition for the TOOLBOX is to reach technology readiness level (TRL) 7: to be demonstrated via the use-cases in an operational environment. Shortly post-project, the MIBIREM TOOLBOX will be first available to environmental engineering and bioremediation companies for their bioremediation projects on PHC, HCH and cyanide contaminated sites. Second, the TOOLBOX is design so that it can easily be adapted to be applied for sites contaminated with other pollutants and later on for other bio-based innovations.


These are the objectives of MIBIREM:

  • Objective 1: Make sample taking & treatment, site selection & access, and data management easy and comparable through harmonised methods and protocols.
  • Objective 2: Get access to highly active degraders in the microbiome by identifying, analysing, isolating and cultivating them.
  • Objective 3: Facilitate public access to bioremediation bacteria and microbiomes, and their genomic information and metadata by sequencing and publicly depositing them.
  • Objective 4: Support decisions, if and how to apply bioremediation through an IT modelling tool that integrates microbiological, chemical, hydrological and physical data and processes.
  • Objective 5: Bring microbiomes into application by analysing at large scale their degradation potential and safety, scale-up production and processes, and finally perform field tests.
  • Objective 6: Ensure that the MIBIREM TOOLBOX – the microbiome and bioremediation tools developed and applied in MIBIREM - fulfils regulatory requirements and addresses market needs.

Role of Ghent University

The main roles of Ghent University are:

  • To perform high-throughput isolation of bioremediation consortia and provide axenic cultures to other partners;
  • To set quality standards for the long-term preservation of bioremediation consortia;
  • To organize public deposits of bioremediation bacteria and their annotated genome sequences;
  • To organize public deposits of bioremediation consortia.




Prof. Peter Vandamme
Department of Biochemistry and microbiology
Phone number: +32 9 264 51 13

Funding info

vlag plat funded by the eu.JPG

Funded by the European Union. Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Executive Agency (REA). Neither the European Union nor the authority can be held responsible for them.