Projects per year
Organisation profile
Organisation profile
The research group Industrial Microbiology and Food Biotechnology (formerly Industrial Microbiology, Fermentation Technology and Downstream Processing; IMDO) has been created in October 1994. It originates from the subunit of Biochemical Engineering of the Department of Chemical Engineering and Industrial Chemistry. The research theme deals with 'Research and Development for a Healthy Diet'. The establishment of IMDO meant the actual start of research in food biotechnology at the Vrije Universiteit Brussel, which is nowadays one of the keystones of the university's research in applied biological sciences/bioengineering sciences. IMDO conquered a very specific niche in the field of industrial food biotechnology, i.e. the qualitative and quantitative (mathematical modelling) study of starter cultures (lactic acid bacteria, acetic acid bacteria, coagulase-negative staphylococci, bifidobacteria, and yeasts) with particular functionalities, within the area of food fermentation, food safety, and human health. IMDO specialised in (spontaneous) food fermentations, process control, and predictive microbiology. Research of IMDO focuses on the microbial ecology of spontaneous food fermentation processes, production of fine chemicals (organic acids, bacteriocins, exopolysaccharides, aromas) and enzyme activities for application in the food industry, both fermentative production processes and their downstream processing, and in situ production processes using functional, multiple starter cultures (bacteriocin-producing starters for cheese, sausage and sourdough manufacture, exopolysaccharide-producing strains for the production of yoghurt and other fermented milk drinks, aroma-producing starter cultures in cheese, sourdough, cocoa, and coffee fermentation). Human health-related topics encompass probiotics and prebiotics as functional foods (antimicrobial potential, underlying mechanisms, microbiological and technological aspects of commerical preparations). In general, the current research topics are: - Exploration of the species diversity and functional analysis (metabolite target analysis, transcriptome analysis) of traditional, artisan fermented foods (dairy products, meat products, sourdoughs, cocoa, vegetables, sour beers): food ecosystem biodiversity, taxonomy, new taxa, new molecules (metabolites); - polyphasic analysis of the population dynamics (culture-dependent and culture-independent) and metabolite kinetics of microbial food ecosystems; - selection of interesting starter cultures or bioprotective cultures, based on physiological and technological characterization of new, natural food isolates; - analysis of the interactions between fucntional starter cultures or bioprotective cultures and the food matrix, including elements from the background microbiota; - mathematical description of the behaviour (growth and product formation), functionality, interactions, and competitiveness of functional starter cultures (lactic acid bacteria, acetic acid bacteria, coagulase-negative staphylococci, bifidobacteria, and yeasts) and bioprotective cultures of lactic acid bacteria and coagulase-negative staphylococci (positive predictive modelling) in simulated food fermentations (milk, meat, cereals, cocoa, coffee) and/or modified-atmosphere-packaged meat products; - linking the species diversity of fermented foods, the microbial fermentation process, and the quality of the food product (food qualitomics); - relationship between milk quality and udder health concerning coagulase-negative staphylococci; antimicrobial potential of probiotic bifidobacteria and lactobacilli (molecular identification); - mechanistic elucidation of the bifidogenic and butyrogenic effects of inulin-type fructans as prebiotic substrates: (non)selective degradation, butyrate production, gas formation; - development and valorisation of new, functioal starter cultures, bioprotective cultures, and efficacious pro- and prebiotics; - development of industrial food fermentation processes (yoghurt, cheese, fermented sausage, sourdough, cocoa, coffee, water kefir) incorporating superior artisan quality and health-promoting characteristics.
Keywords
- outer membrane proteins
- new materials
- yoghurt
- fungal growth
- Fermentation
- Modellisation
- functional foods
- Sourdough
- Yoghurt
- Yeast morphology
- Cheese
- enzymes
- Fungal morphology
- Nanotechnology
- tartaric acid
- sausage
- Rhodococcus
- downstream processing
- Lactobacillus
- starter cultures
- bioconversion
- biosynthesis
- yeast immobilisation
- Microbial Processes
- Yeast immobilization
- Fermented meat products
- predictive modelling
- Beer
- Streptococcus
- chromatography
- Biosynthesis
- Tartaric acid
- Chromatography
- Continuous beer fermentation
- fungal morphology
- continuous beer fermentation
- Probiotics and prebiotics
- Bioprocess Engineering
- Industrial Microbiology
- perfusion
- Exopolysaccharides
- membrane reactors
- Lactic Acid Bacteria
- heavy metal resistance
- Predictive modelling
- Bacteriocins
- cheese
- Functional foods
- fermentations
- Bifidobacterium
- sourdough
- Yoghurt cheese
- New materials
- Food Microbiology
- Saccharomyces
- Fermentation Technology
- Heavy metal resistance
- Downstream Processing
- Aromas
- Membrane reactors
- Starter cultures
- Perfusion
- Downstream processing
- Enzymes
- Lactic acid bacteria
- Fungal growth
- Bioconversion
- Sausage
- Biochemical Technology
- Trichoderma
- Enterococcus
- Microbial Biotechnology
- Food Industry
- Biochemical Processes
- yeast morphology
- nanotechnology
- Environmental Microbiology
- Outer membrane proteins
Fingerprint
Collaborations and top research areas from the last five years
Profiles
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Francesco Bonaldo
- Vrije Universiteit Brussel
- Faculty of Sciences and Bioengineering Sciences
- Department of Bio-engineering Sciences - Doctoral scholarship
- Industrial Microbiology
Person: Researcher, PhD, Doctoral student
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Dries Bongaerts
- Vrije Universiteit Brussel
- Department of Bio-engineering Sciences - Scientific employee
- Faculty of Sciences and Bioengineering Sciences
- Industrial Microbiology
Person: Researcher, PhD, Doctoral student
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Arne Bouchez
- Vrije Universiteit Brussel
- Department of Bio-engineering Sciences - Scientific employee
- Industrial Microbiology
- Faculty of Sciences and Bioengineering Sciences
Person: Researcher, PhD, Doctoral student
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FWOAL1200: Rationally designed sourdoughs with an anticipated pre- and postbiotic profile
Weckx, S. (Administrative Promotor)
1/01/26 → 31/12/29
Project: Fundamental
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FWOAL1198: Agricultural Modelling and Agrarian Resilience in Renaissance and Early Modern Italy: Linking Climate, Environment, and Society
Erdkamp, P. (Administrative Promotor) & Heinrich, F. (CoI (Co-Promotor))
1/01/26 → 31/12/28
Project: Fundamental
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OZR4342: Food From Farm to Fork in the Ancient World: Exploring new methods to assess diet, nutrition, and resilience through ancient and traditional crops and foodstuffs.
Heinrich, F. (Administrative Promotor)
1/10/24 → 30/09/28
Project: Fundamental
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VLAFF3: Use of traditional landraces of cereals and traditional hop varieties to deliver novel sour beers and sourdough breads with authentic flavor (TRADICER)
De Vuyst, L. (Administrative Promotor) & Heinrich, F. (CoI (Co-Promotor))
1/09/24 → 31/08/28
Project: Applied
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OZR4211: Bilateral cooperation within the framework of a joint doctoral project: benchfee for joint PhD VUB - ULiège, ALI Amira
Heinrich, F. (Administrative Promotor)
24/11/23 → 23/11/27
Project: Fundamental
Research output
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Cereal Arabinoxylans—Their Enzymatic Degradation and Relevance for Breadmaking and Human Health
Gonzalez Alonso, V., Verce, M., De Vuyst, L. & Leroy, F., 13 Jan 2026, In: Comprehensive Reviews in Food Science and Food Safety. 25, 1, 28 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile -
163 2024 International Summit: The societal role of meat and livestock.
Belk, K. E., Ederer, P. & Leroy, F., 4 Oct 2025, In: Journal of Animal Science. 103, Supll S3, p. 171-172 2 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile7 Downloads (Pure) -
AEROBICITY SHAPES VITAMIN K2 PRODUCTION BY Staphylococcus shinii IMDO-S216
Bonaldo, F., Pradal-Álvarez-Prida, I., Debrus, V., Duverger, C., Mangelings, D., Weckx, S. & Leroy, F., 2025. 1 p.Research output: Unpublished contribution to conference › Poster
Open AccessFile -
A framework for adequate nourishment: balancing nutrient density and food processing levels within the context of culturally and regionally appropriate diets
Leroy, F., Beal, T., de Mûelenaere, N., De Smet, S., Heinrich, F., Iannotti, L., Johnston, B., Mann, N., Mente, A. & Stanton, A., 1 Feb 2025, In: Animal Frontiers. 15, 1, p. 10-23 14 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile2 Citations (Scopus)77 Downloads (Pure) -
A tale of two agricultural revolutions: crop introductions in the long 1st millennium ce southern Levant
Hansen, A., Heinrich, F., Langgut, D., Weiss, E. & Fuks, D., 2025, In: Vegetation History and Archaeobotany. p. 1-24 24 p.Research output: Contribution to journal › Article › peer-review
Open AccessFile1 Downloads (Pure)
Activities
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Exploration of the microbial and metabolite diversity of household and artisan bakery sourdoughs through a citizen science approach
Gettemans, T. (Speaker), Pradal-Álvarez-Prida, I. (Contributor), Uyttendaele, M. (Contributor), Snijders, A. (Contributor), De Vuyst, L. (Contributor) & Weckx, S. (Contributor)
28 Oct 2025Activity: Talk or presentation › Talk or presentation at a conference
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Genomics-driven approaches for selecting optimal starter cultures for cocoa fermentation
Weckx, S. (Invited speaker)
6 Oct 2025 → 9 Oct 2025Activity: Talk or presentation › Talk or presentation at a conference
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How Genomics can improve food fermentation
Weckx, S. (Invited speaker)
13 Feb 2025Activity: Talk or presentation › Talk or presentation at a workshop/seminar
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High-end computing in Flanders
Weckx, S. (Invited speaker)
15 Apr 2025Activity: Talk or presentation › Talk or presentation at a workshop/seminar
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Improving fermented foods with (meta)genomics-based knowledge
Weckx, S. (Invited speaker)
9 May 2025Activity: Talk or presentation › Talk or presentation at a workshop/seminar
Equipment
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Flemish Supercomputer Center VSC
Weckx, S. (Consortium partner)
Department of Bio-engineering SciencesFacility/equipment: Equipment › no e-resource/single sited
Datasets
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Argentinian fruit surface microbial ecosystems
Weckx, S. (Creator), Vermote, L. (Creator) & De Vuyst, L. (Creator), European Nucleotide Archive, 31 Aug 2022
https://www.ebi.ac.uk/ena/browser/view/PRJEB50285
Dataset
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Wooden barrels help to steer the lambic beer fermentation and maturation process
Weckx, S. (Creator), Vermote, L. (Creator) & De Vuyst, L. (Creator), European Nucleotide Archive, 1 Mar 2023
https://www.ebi.ac.uk/ena/browser/view/PRJEB53155
Dataset
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batch-to-batch variations during Gouda cheese production
Weckx, S. (Creator), Decadt, H. (Creator) & De Vuyst, L. (Creator), European Nucleotide Archive, 20 Jan 2023
https://www.ebi.ac.uk/ena/browser/view/PRJEB58546
Dataset
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Microbial composition of Gouda cheese processing chain (2019 batch)
Weckx, S. (Creator), Decadt, H. (Creator) & De Vuyst, L. (Creator), European Nucleotide Archive, 1 Aug 2023
https://www.ebi.ac.uk/ena/browser/view/PRJEB64168
Dataset
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Decarboxylase activity of Loigolactobacillus rennini gives crack defects in Gouda cheese
Weckx, S. (Creator), Decadt, H. (Creator) & De Vuyst, L. (Creator), European Nucleotide Archive, 1 Aug 2023
https://www.ebi.ac.uk/ena/browser/view/PRJEB64331
Dataset