Indicators and Monitoring of the Ripening of Cheddars

Project entitled:

Systems Biology Applied to Cheddar Production

Sylvain Moineau


  • One of the challenges in the milk processing industry is producing high quality cheeses on a consistent basis.
  • Many factors influence quality, including the microbiological composition of milk and the effectiveness of starter cultures and bacteriophages.
  • This project investigates these factors using a “systems biology” approach to better understand the impact of the microbiological network on cheddar production.
  • Systems biology integrates different levels of information to develop an operating model for the entire system.
  • Systems biology uses techniques to quantify changes in the genome, transcriptome, proteome and metabolome in response to a given situation (cheddar, in this case).
  • This ambitious project will generate new results that will put dairy processors in a very competitive position internationally.
  • Functional assembly (from the genome to the metabolome) will also provide added-value in order to better understand and intervene in regards to the major variables affecting these products.



This project is divided into five objectives:

  • 1) Determine the microbiome and virome of milk and cheddar.
  • 2) Determine the microbial and viral transcriptome of milk and cheddar.
  • 3) Determine the microbial and viral proteome of milk and cheddar.
  • 4) Determine the metabolome of milk and cheddar.
  • 5) Determine the biology of the cheddar system. This inclusive objective will allow us to pinpoint trends during the ageing process for cheddar. A mathematical algorithm which will use all of the information produced (objectives 1 to 4) will be developed to calculate divergence between the samples.



Results and potential benefits

Results in relation to objectives:

  • 1) Currently, eighteen batches of cheddar are being monitored (after 4 days of production, after 3 months, 6 months and 18 months). To date, the milk and cheese samples that were sampled at 4 days and 3 months have been received, and biochemical and organoleptic analyses have been completed. A protocol has been adapted to separate bacteria and bacteriophages from the dairy matrices. The starter cultures used have been obtained and their genomes are in the process of being sequenced. We have also developed a database containing the DNA sequences of the microbial species recognized as being part of the microbiome of various cheeses.
  • 2) We have not yet begun work on this objective.
  • 3) Currently, our extraction and detection methods by LC/MS-MS detect 80% of viral proteins and 57% of bacterial proteins.
  • 4) We have developed a protocol for the extraction and analysis through LC/MS-MS of the metabolites contained in cheese using an ionic mobility cell. Our preliminary tests showed a high level of metabolic diversity in the samples analyzed. For example, we have detected 8,000 ions as potential metabolites contained in cheddar.
  • 5) We have not yet begun work on this overarching objective. Ultimately, we will propose a mathematical algorithm that will integrate all of the data. It will allow us to pinpoint trends during the cheese ageing process and identify specific indicators of cheddar quality. Ultimately, this approach will create a network which will allow for interpretation of the microbial and viral composition of cheddar. It will also provide new insights on how to modulate the ageing process in order to improve consistency and quality.


Professionals trained

  • Marie-Laurence Lemay, PhD student in microbiology
  • Pier-Luc Plante, PhD student in bioinformatics
  • Alexia Lacelle-Côté, master’s student in microbiology
  • Frédéric Raymond, post-doctoral researcher in bioinformatics
  • Simon Labrie, post-doctoral researcher in microbiology
  • Jessie Bélanger, undergraduate student in microbiology


Financial contributions

Partnership for innovation in dairy production and dairy processing (EPI2011-2017):

  • Fonds de recherche du Québec – Nature et technologies
  • Ministère de l’Agriculture, des Pêcheries et de l’Alimentation du Québec
  • Novalait

The industrial partner has provided cheese and lactic ferments.