Downstream Bioprocessing

Downstream Bioprocessing encompasses the design, development and implementation of biomanufacturing schemes, with an emphasis on separation technology and microbial biotechnology. Of current interest is integrated bioprocessing where sustainable-by-design criteria apply. Moreover, the group actively seeks to implement bioprocess digitalization to alleviate process bottlenecks, increase productivity and reduce hardware and operational costs.

The group is particularly involved with the recovery, purification and advanced formulation of bioproducts, including low molecular weight compounds (“Organics”), macromolecular species (proteins, polypeptides, enzymes, others) and supra-macromolecular constructs (“Nanoplexes”). Preferred separation methods are based on the principles of adsorption or partitioning, including continuous chromatography.

The group has an interest in the exploitation of fungal strains to produce secondary metabolites, enzymes, and other products by combining high throughput metabolomic/proteomic screening of compounds with a cutting-edge bioprospecting platform for the heterologous expression of entire fungal biosynthetic gene clusters (BGCs) in genetically tractable hosts. Fungus-based bioproduction deploys both submerged fermentation and solid-state fermentation strategies. Classical mutation-and-screening and synthetic biology approaches are employed to gain process productivity.

The Downstream Bioprocessing group also develops end-to-end solutions for valorizing, characterizing, modifying, and functionalizing industrially relevant hydrocolloids (polysaccharides and proteins) sourced from food industry side-streams or underexploited food biomass resources adopting the circular bioeconomy and clean/green label principles. The group designs new product innovation concepts based on soft matter (structurally and interfacially engineered bio-templates) to enhance the quality, organoleptic, shelf-life and bio-functional aspects of food, nutraceutical, and personal care product formulations.

Main expertise fields

  • Adsorption and Chromatography: Adsorbent screening and ligand design; packed bed and fluidized bed chromatography; continuous chromatography, including periodic counter-current (PCC) and true moving bed (TMB) systems; fibrous adsorbents, including moving belt systems.
  • Non-chromatographic methods e.g. Liquid-liquid extraction and Leaching: Partitioning in aqueous two-phase systems of cells and macromolecules; deep eutectic solvents; pilot extraction of natural compounds.
  • Fungal Biotechnology: Genome sequence-independent methods for the heterologous expression of intact fungal biosynthetic gene clusters (BGCs) in genetically tractable hosts; genome-scale metabolic modelling coupled with multi-omics analyses, classical mutation, and synthetic biology approaches for microbial strain and bioprocess improvement; scale-up of fermentation processes [SSF and SmF] from the bench to the pilot plant (up to 300 L scale).
  • Microbial Metabolomics and Fluxomics: Mass spectrometry-based metabolomics to assess the metabolic state of microbial cells and characterize key extracellular metabolic processes; determination of metabolic flux distributions and metabolic pathway activity of microorganisms using intracellular metabolite profiling, quantitative metabolomics and isotope-labelling data; chemical characterization of fungal secondary metabolites.
  • Advanced bioproduct formulation. The key technologies the group relyies on to provide solutions for the food, nutraceuticals and personal care product sector are as follows: a) Design and optimization of clean label methods for hydrocolloid extraction, isolation and purification, based on soft-processing i.e. physical or enzymatic processes; b) Hydrocolloid modification and functionalization for imparting novel technological (i.e. thickening, gelling, texturizing, air-water and lipid-water interface stabilizing, bulking) and bio-functional (digestibility, prebiotic activity, wall materials for controlled/sustained release of bioactive compounds, muco-adhesion, colon fermentability) characteristics; c) Design and optimization of soft matter (hydrogels, dry particulates, complex emulsion templates, xerogels, aerogels, 3D printed scaffolds, food composites etc.) -based product formulations for the food nutraceutical and personal care product industry.

Research challenges

  • Continuous biomanufacturing
  • Bioprocess development and scale-up
  • Bioprocess efficiency and techno-economic competitivity
  • Sustainable design of bioprocess scenarios
  • Eco-green isolation and modification of bio-macromolecules
  • Soft-matter inspired product development
  • Biodiscovery

Application AREAS

  • Food and nutraceuticals: functional foods, alternative proteins, and clean label food biopolymers
  • Cosmetics and para-pharmaceuticals, particularly when challenging formulation options are needed
  • Green chemical processing, as materialized via bioconversion and biocatalysis
  • Biorefining, with emphasis on product biorefining and biomass conversion
  • Biopesticides and biostimulants
  • Biomaterials and functional molecules [biopolymers].

Main assets

  • PROCEED project (2019 – 2023): Exploitation of plant seed mucilage in the development of protein based xero-scaffolds embedding human gut relevant probiotic cells (FNR- CORE/2018)
  • ALGRPO project (2021 – 2025): Impact of microalgal proteins on the adhesion properties, release profile and biological activity of microporous scaffolds hosting probiotic living cells (FNR-Industrial fellowships/2021)
  • DEEPCELL project (2022 – 2026): Exploration Of The Potential Of Deep Eutectic Solvent – Physical Processing Driven Strategies In The Production Of Functional Nanocellulose Pickering Particles (FNR-CORE/2021)
  • ROUTAKTIV project (2021 – 2022): Characterisation of a water-soluble antifungal compound produced by an endophytic fungus (Initialist)
  • BIOHOLISTICS project (2023 – 2025): Developing integrated bioprocesses for a holistic chemical recycling of plastics (FNR-FORMAS-SNF-WEAVE)
  • SHIELD project (2022 – 2023): Radical optimisation of fluidised bed adsorption systems via polymer shielding (Initialist)
  • JUMPRO project (2023 – 2025): A Fluidized Bed Riser Adsorption System for Selective Protein Recovery (FBRAS) (FNR)


  • Oscillatory rheometer
  • Laser static light scattering and dynamic light particle size analysers
  • Light and confocal laser scattering microscopes
  • In-vitro digestion system based on sequential mini-reactors
  • High pressure and ultra-high-pressure homogenizers
  • 3D bioprinter
  • Microplate reader
  • Turbovap® evaporator
  • Rotary evaporator
  • Bioreactors (0.5 L-300 L, stirred- and wave-tank, with and without illumination)
  • Bioreactor for solid state fermentation
  • Ultrasound devices
  • Freeze dryers
  • Vacuum oven
  • Controlled atmosphere/temperature incubators
  • Gas and liquid chromatographers coupled with high resolution mass spectrometers
  • Preparative and semi-preparative chromatographer
  • ÄKTA avant protein purification system
  • ÄKTA PCC continuous protein purification system

Selected publications









Research domains
  • Environment

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