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Developing novel phage-based techniques for removing spoilage bacteria from meat products

Primary Supervisor: Professor Martha Clokie, Department of Genetics and Genome Biology

Secondary supervisor: Prof. Paul Monks, Department of Chemistry

PhD project title: Developing novel phage-based techniques for removing spoilage bacteria from meat products

University of Registration: University of Leicester

Project outline:

When vacuum-packed meat is first opened it is common for consumers to smell a bad odour. This smell can discourage consumers as they may presume the meat has gone off, but after a few minutes of the packaging having been opened, the smell disappears. The meat is harmless and the smell arises as a result of the activity of spoilage bacteria that thrive on the surface of the meat in the vacuum-packed environment. These bacteria are not pathogenic and do not cause disease in humans if the meat is cooked properly then consumed. However, because many consumers are unaware of the problem of these odour producing bacteria, this phenomena leads to food waste, economic loss to the producers, and it can negatively impact the commercial product brand.

As such, the suitability of bacteriophages for removing odour producing species has been assessed and phages have been identified to several of these genera. Encouragingly, in terms of developing phage products for food, the FDA (USA Food and Drug Administration) has classified phages as being safe and commercial phage products for food processing and several are already available on the market, such as a phage cocktail to prevent Listeria in ready meals, meat, and fruit [1]. Consequently, due to their ‘safe status’, phages could be used on meat products directly on products or embedded into packaging to prevent growth of odour producing bacteria and thus, reduce the production of bad odours.

The odour producing spoilage organisms associated with UK meat spoilage have previously been identified in our laboratory as species of Leuconostoc, Latilactobacillus, Lactococcus, and Aeromonas. These bacteria are standard commensals of the surface of the meat and with restrictions on meat processing procedures, chemical cleaning of the meat before packaging is not a viable option. Previous work, again largely in our laboratory, has shown that successful killing of bacteria by bacteriophages alters the host metabolism [2,3] which, in turn successfully reduces the abundance of volatile compounds that are associated with off odours. We have also shown that phage interact differently with bacteria under different Oxygen concentrations [4]. We are now perfectly poised to extend our collection of suitable phages and to optimise the delivery and formulation parameters for the phage product. 

The student will gain valuable industrial experience by working alongside a major UK meat producer in order to undertake the following objectives:

  1. To build a library of phages that infect a variety of odour producing bacteria
  2. To assess the efficacy of phages under conditions representing that of Vacuum Packed meat in cold storage
  3. To combine the phages to design a phage cocktail that efficiently kills target bacteria
  4. To use transcriptomic and metabolomic approaches to identify phage metabolomes
  5. To demonstrate that the application of the phage cocktail reduces the production of volatile compounds associated with off odours

References:

  1. Moye, Z.D., Woolston, J. and Sulakvelidze, A. Bacteriophage Applications for Food Production and Processing. 2018. Viruses. 10(4). doi: 3390/v10040205.
  2. De Smet, J., Zimmerman, M., Kogadeeva, M. et al. High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection. ISME J. 10, pp. 1823-1835. doi: 10.1038/ismej.2016.3.
  3. Howard-Varona, C., Lindback, M.M., Bastien, G.E. et al. Phage-specific metabolic reprogramming of virocells. 2020. ISME J. 14, pp. 881–895. doi: 1038/s41396-019-0580-z.
  4. Hodges, F.E., Sicheritz-Pontén, T. and Clokie, M.R.J. The Effect of Oxygen Availability on Bacteriophage Infection: A Review. Bacteriophage: Therapy, Applications and Research. 2(1). 16-25. http://doi.org/10.1089/phage.2020.0041.
  5. Storms, Z.J., Teel, M.R., Mercurio, K. and Sauvageau, D. The Virulence Index: a metric for quantitative analysis of phage virulence. 2020. Bacteriophage: Therapy, Applications and Research. 1(1), pp. 27-36. doi: 10.1089/phage.2019.0001.
  6. Haines, M.K., Hodges, F.E., Nale, J.Y., et al. Analysis of selection methods to develop novel phage therapy cocktails against antimicrobial resistant clinical isolated of bacteria. 2021. Frontiers Microbiology. 12(613529).doi: 10.3389/fmicb.2021.613529.

BBSRC Strategic Research Priority: Sustainable Agriculture and Food: Microbial Food Safety & Understanding the Rules of Life: Microbiology  

Techniques that will be undertaken during the project:

  • Routine maintenance and handling of a variety of microbial species
  • Bacteriophage isolation, enumeration, and imaging
  • DNA extraction, genome sequencing, and bioinformatic analysis of bacterial and phage genomes
  • Routine maintenance and running of mass-spec equipment
  • Metabolomic analysis of phage-infected bacterial cultures and phage-treated meat products using mass-spectrometry
  • Large scale metabolomic data processing and statistical analysis

Contact: Professor Martha Clokie, University of Leicester