FOODBIOMES Project Overview

FOODBIOMES is a research infrastructure in Greece focusing on microbiome applications in food systems. The infrastructure is at its preparatory stage and is being developed within the framework for research, education, and innovation excellence. FOODBIOMES is co-funded for three years by the Greek government and the European Regional Development Fund and has been awarded the amount of 3.943.705€ for the preparatory stage that spans from December 2020 till May 2023.

The main focus areas of FOODBIOMES are:


The infrastructure aspires to be the link for innovation, education, and research, to implement breakthrough research on food microbiomes and develop educational activities that disseminate knowledge.

  • FOODBIOMES will design and offer services to researchers and professionals in the academic and business sectors that will enhance the know-how and development of the Agri-food sector.
  • To ensure success, FOODBIOMES is building laboratory infrastructure with state-of-the-art equipment, new hires and specialised staff.
  • FOODBIOMES aims to connect, cooperate, and network with companies, researchers, national and European research infrastructures in order to efficiently utilise the emerging technologies. FB will seize and create opportunities for new collaborations of excellence with local businesses and international organisations in an exchange of knowledge and in the effort to gain international recognisability.
  • To do so, FOODBIOMES is working towards strengthening the organisational structure and operating framework of the infrastructure to achieve levels of excellence and standardisation.

All actions of FOODBIOMES project during the preparatory phase are organized in 6 work packages. For more information on these actions please browse the work packages descriptions below.


Work Packages

Organisation & Coordination
of the Infrastructure


This work package includes the necessary actions for the formation of the governance structure and the management, coordination and monitoring of all tasks that are necessary for the effective implementation of the project. The success of the project depends on the smooth collaboration and the timely and efficient coordination of the tasks undertaken by the four collaborating partners. The governance of the infrastructure has four distinct areas of organisation and is under the guidance of four committees:


  • Τhe Infrastructure Coordination Committee, which is made up of members from each partnering university and is the key committee that regulates the works and tasks that the infrastructure aims to complete both short and long term.
  • Τhe Scientific Committee dedicated to organising and benchmarking the progress of the research within FOODBIOMES, making decisions and forging new research paths.
  • Τhe Administration Committee devoting time in administrative duties, financial management and hiring new staff as per the needs and means of the infrastructure.
  • The Advisory Committee with the participation of professionals from the industry or other consulting organisations with main duties to assess and advice on the quality of research, the services for the Agri-food sector, and the procedures employed for attracting external users and providing access.

Equipment and Facilities Upgrade


The aim of this work package is to upgrade the lab facilities with equipment that allows:


  • pilot production of probiotic cultures for the production of foods
  • large scale production of plant extracts using green technologies
  • semi-pilot production and green recovery of biotechnologically produced ingredients
  • the development of technologies for the bioprocessing of bioactive ingredients
  • the study of bioavailability and bioactivity of biofunctional ingredients via in vitro processes and clinical trials

 The new equipment will also allow the partners to:


  • offer better services to third parties both in sequencing and in characterisation of the beneficial functions of microorganisms and bioactive ingredients
  • offer services of small-scale production of probiotic cultures and food starter cultures
  • cover a gap in providing services to the food industry and the primary production actors
  • the development of technologies for the bioprocessing of bioactive ingredients
  • highlight and promote the benefits of the microflora of traditional foods

Valorisation of Mature Technologies


In this work package, each partner uses results of previously implemented research projects that are under the scope of FOODBIOMES in order to deliver innovations for the Agri-food sector. Some examples are:


  • isolated probiotic strains are used as primary cultures for dairy products such as feta cheese.
  • isolated probiotic strains are subjected to in vitro gastrointestinal digestion pre-clinical tests in order to predict the viability tolerance of the strains during digestion
  • bacterial cellulose that is produced using whey are tested as an encapsulation agent for probiotic strains
  • plant extracts from existing libraries are used to determine potential pre-biotic and bio-preservative properties
  • sequencing protocols that have been developed are further used in sequencing of dairy food genomes
  • isolated native yeast strains are studied to determine their winemaking capacity and the quality characteristics of
    the end products

Collaborative Research


This work package involves collaborative research tasks between the participating laboratories with main objectives:

  • to isolate beneficial microorganisms from traditional fermented foods, dry fruits and other sources and the in vitro study of their probiotic properties
  • production and isolation of bioactive ingredients from microbial fermentations of wastes and by-products the agri-food sector
  • immobilization of probiotic strains on food substrates in order to develop functional food ingredients
  • study of the biological actions of the functional food ingredients and how they impact the gut biome using experiment-based guinea-pig models
  • production of bioactive and functional food ingredients at a semi-pilot scale
  • development of biofunctional foods
  • study of the bioavailability of functional food ingredients and investigative nutritious interventions of bioactivity focus on the microbiome
  • nutritious interventions and analysis of the gut biome of samples from volunteers
  • microbiome and chemical screening as authenticity markers for foods

Networking and Promotion
of the Infrastructure


FOODBIOMES aims to become the national node of know-how on food microbiome and its impact to the human microbiome and an international link for research infrastructures, research centres, consumer groups and the food and pharma industry to exchange and disseminate innovation and knowledge. To this end, in this work package FOODBIOMES develops and implements a strategic plan of networking and promotion that aims to:


  • disseminate research results, through academic conferences, papers publications and participation to exhibitions.
  • share innovation in line with the commitment towards an open science infrastructure
  • establish two-way interactions with infrastructures and centres in similar or complementary areas for furthering research and education and fostering innovation
  • sequencing protocols that have been developed are further used in sequencing of dairy food genomes
  • create strong collaborations with the food and pharma industry to best utilise innovative research and develop the capacities of researchers and professionals of the Agri-food sector

Organisation and Support
towards Accessibility and Viability


In order to adapt to its future needs, in work package 6 FOODBIOMES studies the existing frame of research infrastructures at a national and European level and the needs of the Agri-food sector and:

  • redefines its position in the national and European map of research infrastructures
  • develops procedures, policies and guidelines that will support its organisational structure, operational frame and accessibility of its users
  • defines the services offered
  • creates a Sustainability Plan in order to develop a strategy of consolidation and development in the Agri-food sector