Published May 1, 2020 | Version Preprint
Journal article Open

Characterizing Halloumi cheese's bacterial communities through metagenomic analysis

  • 1. Department of Agricultural Sciences, Biotechnology and Food Science, Cyprus University of Technology, Limassol, Cyprus
  • 2. Faculty of Electrical Engineering, Mathematics and Computer Science (EEMCS) of the University of Twente, the Netherlands


Halloumi is a semi-hard cheese produced in Cyprus for centuries and its popularity has significantly risen over the past years. High-throughput sequencing (HTS) was applied in the present research to characterize traditional Cyprus Halloumi bacterial diversity. Eighteen samples made by different milk mixtures and produced in different areas of the country were analyzed, to reveal that Halloumi’s microbiome was mainly comprised by lactic acid bacteria (LAB), including Lactobacillus, Leuconostoc, and Pediococcus, as well as halophilic bacteria, such as Marinilactibacillus and Halomonas. Additionally, spore forming bacteria and spoilage bacteria, were also detected. Halloumi produced with the “traditional” method, had significantly richer bacterial diversity compared to Halloumi produced with the “industrial” method. Variations detected among the bacterial communities highlight the contribution of the initial microbiome that existed in milk and survived pasteurization, as well as factors associated with Halloumi manufacturing conditions, in the final microbiota composition shaping. Identification and characterization of Halloumi microbiome provides an additional, useful tool to characterize its typicity and probably safeguard it from fraud products that may appear in the market. Also, it may assist producers to further improve its quality and guarantee consumers’ safety.


This work has received funding from the European Union's Horizon 2020 Research and Innovation Programme under Grant Agreement No 739578 and the Government of the Republic of Cyprus through the Directorate General for European Programmes, Coordination and Development.



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RISE – Research Center on Interactive Media, Smart System and Emerging Technologies 739578
European Commission