Characterizing Halloumi cheese's bacterial communities through metagenomic analysis

Abstract

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.

Evolution of Bacterial Communities, Physicochemical Changes and Sensorial Attributes of Natural Whole and Cracked Picual Table Olives During Spontaneous and Inoculated Fermentation

“…Therefore, this set of techniques has been recommended as an auspicious tool for the evaluation of the microbial diversity during fermentation of several products (Zinno et al, 2017). However, up to now, the monitoring of several dairies fermentations are by far the most explored products studied by such analyses (Fuka et al, 2013;Pasquale, 2014;O'Sullivan et al, 2015;Alessandria et al, 2016;De Filippis et al, 2016;Kamilari et al, 2020), while the investigation of other fermented products is more limited (Bokulich et al, 2014), including the monitoring of "microbial map" of olives fermentation (Randazzo et al, 2017).…”

Cyprus Sausages’ Bacterial Community Identification Through Metataxonomic Sequencing: Evaluation of the Impact of Different DNA Extraction Protocols on the Sausages’ Microbial Diversity Representation

“…For instance, Pseudomonas and Acinetobacter were found to be among the predominant genera in "llama" sausages that originated from a plant in Northwest Argentina and dry-cured "Lachang" sausage that originated from China (Fontana et al, 2016;Wang et al, 2018). These genera were also identified using 16S rDNA metagenomic analysis in several other Cyprus products (Anagnostopoulos et al, 2020;Kamilari et al, 2020aKamilari et al, , 2019Papademas et al, 2020). Pseudomonas spp.…”

“…Using the paired-end approach, 16S rRNA bacterial gene amplification was performed based on the protocol provided by Illumina 2 , as described by Kamilari et al (2020a). The sequencing run was performed with a MiSeq 600-cycle Reagent Kit v3 (Illumina, United States) (5% PhiX) on a MiSeq Illumina sequencing platform.…”

Occurrence of Yeasts in White-Brined Cheeses: Methodologies for Identification, Spoilage Potential and Good Manufacturing Practices

“…Halloumi is a traditional white-brined cheese, produced mainly in Cyprus and Greece as a PDO product in accordance with the EU Regulation No 1151/2012 (European Commission, 2015) ( Table 1). It is commonly made from pasteurized ovine or caprine milk (or a mixture of them), though cow milk can be added as well (Kamilari et al, 2020). Cheese blocks can be wrapped in dry leaves of Mentha viridis, giving the characteristic minty flavor to the cheese.…”

“…This step ensures the prevention of contamination, and it is essential for the characteristic flavor and elastic texture of Halloumi cheese (Kaminarides et al, 2009). There are two kinds of Halloumi cheese, the fresh and the mature (Kaminarides et al, 2009;European Commission, 2015;Kamilari et al, 2020). The latter type is immersed into the brine (14-16% w/v NaCl) for at least 40 days at 25 • C before storage (Kaminarides et al, 2009;Kamleh et al, 2012).…”