Sequencing of the Cheese Microbiome and Its Relevance to Industry

Abstract

The microbiota of cheese plays a key role in determining its organoleptic and other physico-chemical properties. It is essential to understand the various contributions, positive or negative, of these microbial components in order to promote the growth of desirable taxa and, thus, characteristics. The recent application of high throughput DNA sequencing (HTS) facilitates an even more accurate identification of these microbes, and their functional properties, and has the potential to reveal those microbes, and associated pathways, responsible for favorable or unfavorable characteristics. This technology also facilitates a detailed analysis of the composition and functional potential of the microbiota of milk, curd, whey, mixed starters, processing environments, and how these contribute to the final cheese microbiota, and associated characteristics. Ultimately, this information can be harnessed by producers to optimize the quality, safety, and commercial value of their products. In this review we highlight a number of key studies in which HTS was employed to study the cheese microbiota, and pay particular attention to those of greatest relevance to industry.

Characterizing Halloumi cheese's bacterial communities through metagenomic analysis

“…Halloumi is characterized by unique organoleptic characteristics arising from the specific methods of production, as well as by the contribution of the indigenous microflora that exists in the milk (Papademas & Robinson, 1998). The application of thermal process and the absence of starter culture, indicates that the existing microbiome is affected by several factors, including: a) milk pasteurization and cooking procedures, b) microbial contamination by rennet, as well as salt and Mentha viridis leaves addition, c) microbial contamination from dairy unit environment and d) the preservation in brined whey (CYS 94, 1985;Calasso et al, 2016;De Pasquale et al, 2016;Delcenserie et al, 2014;Stellato et al, 2015;Yeluri Jonnala et al, 2018). Culture-based techniques identified the presence of spore forming bacteria, such as Bacillus, as well as thermophilic species, such as members of the genus Lactobacillus and Enterococcus, in addition to yeasts, in Halloumi samples (Bintsis & Papademas, 2002;Tamime, 2007).…”

“…Additional advantages of applying the current technology for the identification and characterization of the microbial communities in Protected Denomination of Origin (PDO) cheeses has been reviewed recently (Kamilari et al 2019). The microbiome of Halloumi can be expected to be diverse among producers due to variations in the microbial composition of the milk, differences associated with the manufacturing conditions, including geographical area, microbiota of the dairy plant environment and animal breed of the milk (Bokulich and Mills, 2013;Dalmasso et al, 2016;Yeluri Jonnala et al, 2018;Kamilari et al 2019). The main contribution of this paper is to reveal the bacterial communities of Cyprus Halloumi, as sold in the Cypriot market, produced by small or large industries, with or without the addition of cow milk, following the CYS 94 (1985) standard.…”

Deep microbial community profiling along the fermentation process of pulque, a major biocultural resource of Mexico

“…cerevisiae inoculation can also increase the total ester concentration, such as isoamyl acetate, ethyl hexanoate and 3-hydroxybutanoate . While Penicillium roqueforti, known for cheese production, has been reported to generate methyl ketones also can produce alcohol (Kinsella and Hwang, 1976;Frisvad and Samson, 2004;Yeluri-onnala et al, 2018).…”

DAIRYdb: A manually curated gold standard reference database for improved taxonomy annotation of 16S rRNA gene sequences from dairy products

“…Increasing number of whole genome sequences (WGS) will more likely lead to a replacement of incomplete 16S sequences in the DAIRYdb by full-length sequences that cover all HVRs. The cheese microbiome is often dominated by few phylogenetically closely related species, of lactic acid bacteria (LAB) belonging to a few genera (e.g., Lactobacillus, Lactococcus, Leuconostoc and Streptococcus) (9). Therefore, special attention was put into the manual curation of the DAIRYdb sequences at species rank.…”

“…The exploration of microbial communities has experienced a boost during the last decade with the advent of next generation sequencing (NGS) technologies (1). Previously undetectable, since unculturable, micro-organisms in soils (2), water (3,4), airborne (5,6), snow (7), ice (8), food (9), human gut (10)(11)(12) etc. could be unravelled at an unprecedented depth and resolution.…”