Bioconversion and Protective Cultures

We use microorganisms for specific purposes and optimise the quality and safety of food products – for foods that are produced naturally and in environmentally sustainable ways.

In our group we work on a variety of applied research projects that explore the targeted use of microorganisms to optimise the quality and safety of plant- and animal-based foods. These projects involve spontaneous fermentation, the development and use of starter cultures and protective cultures and the maintenance of a robust microbiome for biopreservation. Through our activities we highlight the great potential of the use of microorganisms for the production of natural and environmentally sustainable foods from field to fork.

We use modern microbiological and molecular biological methods to characterise the microorganisms, as well as physicochemical and sensory analysis to identify the effects achieved in the foods. Our projects are conducted in collaboration with various research partners, including Agroscope Liebefeld/Poisieux, which has a unique culture collection as well as advanced molecular biological expertise and know-how.

Expertise and infrastructure

Microbiological and molecular biological methods

  • Traditional microbiological methods for the detection of different microorganism groups

  • Various assays to determine the inhibitory effect of selected microorganisms (e.g. on mycelial growth, which results from the germination of mould spores)

  • Identification using modern molecular biology methods (in-house and externally, qPCR, etc.)

  • MALDI-TOF mass spectrometry (in collaboration with Agroscope)

  • Biolog characterisation of substrate use in lactic acid bacteria (in collaboration with Agroscope)

  • Clarification of QPS status (e.g. antibiotic resistance, virulence or production of biogenic amines)

Physicochemical methods

  • HPLC UV/RID to identify sugars and organic acids, vitamins formed, etc.
  • Verification and quantification of composition (proteins, fats, carbohydrates, micronutrients) and structure (consistency, elasticity, viscosity)
  • Rheometry
  • Selective photometric determination


These research activities centre on the use of microorganisms for specific purposes. Such organisms have a long history of use in the food sector – traditionally in products such as sauerkraut, whey and cheese, but also in products from new resources, such as those made from moringa leaves or by-products of the food processing industry. Bacteria, yeasts and moulds can enhance food quality. They improve the organoleptic properties, shelf life and techno-functional and nutritional properties of the fermented raw materials.

Current projects

  • Innosuisse “FermPlant” project: controlled fermentation of sauerkraut for improved sensory properties and enhanced nutritional value (collaboration with Agroscope and Schöni Finefood)
  • Gebert Rüf (First Ventures) “Fermeat” project: assistance with the development of fermentation strategies (based on the use of moulds) for the production of plant-based alternatives to meat
  • Innosuisse and internal HAFL “Molein” project: extraction and functionalisation of leaf protein from the horseradish tree (Moringa oleifera) for food applications
  • “Wood&Field”: whey fermentation

Completed projects

  • “FermPlant”: fermentation schemes for high-quality plant-based foods (internal HAFL project, HAFL call 2017-2020)
  • Fermentation schemes for natural, in-situ enrichment of vitamin B12 in non-alcoholic, fermented, vegan beverages (internal HAFL project, food systems call 2018-2019)
  • Sustainable, healthy and palatable alternatives to meat (internal HAFL project, food systems call 2018-2019)
  • Swiss Food Research Project (2015): capturing the value of okara – a fibre-rich by-product of tofu processing
  • “Rebels”: recycling of molasses (by-product of sugar manufacture)

Protective cultures

These projects deal with the use of microorganisms to maintain plant health and support a robust microbiome. They involve harnessing the great potential of the use of microorganisms for biopreservation in the production of natural and environmentally sustainable foods from field to fork.

Current projects


The fungus Thielaviopsis (T.) basicola (syn. Chalara elegans) causes black root rot disease, which leads to huge losses of some crops in the field and in storage. The present project seeks to develop an alternative biopreservation method based on a protective culture consisting of lactic acid bacteria. The aim is to establish a resilient microbial system that prevents the development of black rot on carrots (as a model organism). The project involves close collaboration between BFH HAFL, Agroscope and the University of Fribourg; it is supported by the Swiss vegetable sector (Swisscofel, VSGP) and the Sur-la-Croix foundation.

ProBerry (Innosuisse project)

The main aim of this project is to investigate the potential use of lactic acid bacteria (LAB) in the development of protective cultures as an alternative strategy for preventing food spoilage. The project uses strawberries and their main spoilage agent Botrytis cinerea (a mould) as an example. The model serves as proof of concept for the further development of protective cultures for use with fresh or minimally processed fruit and vegetables. The results are expected to include an extended shelf life, a reduction in residues and environmental risks from pesticide use, and a reduction in food losses, thereby improving profitability throughout the food value chain. The ecological potential of useful microorganisms to protect strawberries is being tested in the laboratory, in greenhouses and in the field (pre- and post-harvest).


Only in relation to the metabolism of lactic acid bacteria:



Are you interested in working with us, or would you like to know more about our research activities in the field of bioconversion and protective cultures? Please get in touch.