The new ITN (MARIE SKŁODOWSKA-CURIE ACTION Innovative Training Network) Project “MICROMETABOLITE”, Microbial Enhancement of Bioactive Secondary Metabolite Production in Plants started in May 2017.


MICROMETABOLITE is an international PhD programme for highly motivated young scientists, offering 11 early-stage researchers the opportunity to improve their research and entrepreneurial skills and enhance their career prospects. This Marie Skłodowska-Curie Innovative Training Network is funded by the European Community’s Framework programme HORIZON 2020.MICROMETABOLITE will bring together multi-disciplinary and multi-sectoral expertise to elaborate the application of microorganisms, aimed at improving the production of natural plant products as the basis for a wide range of pharmaceutical and cosmetics products.

MICROMETABOLITE provides an international and highly interdisciplinary framework of collaborators from academia and industry. MICROMETABOLITE combines 5 academic and 1 SME beneficiaries and is supported by 5 company partners (4 SMEs and a big pharmaceutical/cosmeceutical company) and 2 partner organisations belonging to the broader public sector. MICROMETABOLITE’s approach is:


MICROMETABOLITE combines experts on microbial diversity assessment, plant-microbe interactions, plant and microbial genome and transcriptome analysis, plant-based production systems, natural product chemistry and technology, metabolomics, secondary metabolites identification and metabolite production and application, who will share their know-how within the consortium.


MICROMETABOLITE reinforces the interaction between public and private sectors. The participation of SMEs and a big company active in the production of medicinal plants, application of microorganisms, and discovery/development of novel bioactive compounds enable to follow a novel and innovative concept, and it empowers the partners and ESRs to transfer the concept to additional partners of the industry sector. MICROMETABOLITE will include the active participation of 7 partner organisations providing expertise by offering trainings in analytical procedures needed in different industry sectors, regulatory issues, and complementary skills.

This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 721635

The overall objective of MICROMETABOLITE is to explore interactions between plants and microorganisms involved in the production of secondary metabolites (SM) for introducing novel ingredients in pharmaceutical and cosmeceutical industry. Effects of microorganisms on the plant metabolome and the biosynthesis of bioactive SM will be studied in the Boraginaceae plant family, aimed at optimising plant cultivation and alkannins/shikonins (A/S) production. Microorganisms will be integrated in plant production systems, and protocols needed for efficient implementation in industry will be elaborated. Thereby a platform will be established that will support long-term interactions between academia and industry.

- To identify plant genotypes with high alkannins and shikonins (A/S) production, particularly when inoculated with microorganisms

- To determine the vegetation stage in cultivated Boraginaceous species with peak A/S production

- To investigate relationships between A/S contents, plant metabolome, genotype and microbiome

- To identify and select microorganisms that alter plant metabolite composition in a desirable manner (i.e. enhance the production of desirable compounds and induce synthesis of novel metabolites)

- To understand the mechanisms employed by microorganisms to stimulate plant metabolite production and the interaction with the plant at a molecular level

- To identify novel SM produced in response to the interaction with selected microorganisms

- To select microorganisms that have in addition the potential to promote plant growth

- To develop innovative plant production systems integrating those microorganisms shown to stimulate A/S

- Production and plant growth - to develop eco-friendly down-streaming processes from lab to industrial scale

- To up-scale plant cultivation and establish a pilot SM production system

- To explore other biological activities of A/S and Boraginaceous extracts for potential use in technological applications (e.g. tissue engineering scaffolds impregnated with active A/S)

MICROMETABOLITE is original and innovative because:

- it considers a completely new approach to enhancing the production of therapeutically relevant SM in plants it is unique as it aims at understanding the mechanisms involved in  microbially-enhanced SM production in plants and at integrating them in production

- it considers the diversity of natural plants and microorganisms and opens new avenues for exploring plant-derived SM for medical and food applications

- it trains ESRs in multi-disciplinary fields (e.g. microbiology, metabolomics, production, regulatory…) needed for implementation in European (pharmaceutical and cosmeceutical) industry

- it includes the collaboration between multiple stakeholders including academic and industrial institutions and public bodies and thereby involves multiple sectors in the research, exploration, and development components of MICROMETABOLITE and also allows ESRs to become highly familiar with industry and public needs.

- Enhancing the career perspectives and employability of researchers and contribution to their skills development

- Contribution to structuring doctoral/early-stage research training at the European level and to strengthening European innovation capacity, including the potential for meaningful contribution of the non-academic sector to the doctoral / research training

- Quality of the proposed measures to exploit and disseminate the project results

The Scientific Advisory Board of MICROMETABOLITE are:

  • Prof. Dr. Günter Vollmer
    Molekulare Zellphysiologie & Endokrinologie
    Fachrichtung Biologie
    Technische Universität Dresden, Germany


  • Univ. Prof. Dr. Judith Rollinger
    Head of Phytochemistry & Biodiscovery
    Department of Pharmacognosy
    University of Vienna, Austria


  • Jamal Ouazzani,
    Research Director, CNRS
    Institut de Chimie des Substances Naturelles
    ICSN, CNRS, France