## 1 Introduction  
The quality of fermented foods is determined mostly by microbial genera and species colonizing food products. The above applies to all processing stages, from the raw material to the final product [1; 2; 3]. Microorganisms are ubiquitous in the farm environment (soil, water, feed, natural fertilizers, and premises). They are also present on animal skin, in animal digestive tracts, and in animal secretions (such as milk), and they colonize the surface of fodder plants. Microorganisms are found on the surface of processing lines, devices, machines, conveyor belts, pipelines, packaging, and auxiliary raw materials. They are added to products as starter cultures, and they are present on the hands of dairy plant employees [4; 5]. Microorganisms spread from the above sources to raw materials and end products, and they influence the attributes of fermented foods. Therefore, cheese microbiota constitute one of the critical factors during cheese ripening and the formation of the sensory properties of cheese. The formation of sensory attributes is a complex biochemical process where environmental and process conditions, such as the heating temperature of the cheese slurry and the time and temperature of cheese ripening, affect the composition and metabolic activity of microbiota [6]. Microbial communities colonizing fermented foods are highly complex, and they have not been thoroughly investigated to date [1; 2; 3]. Many microbial species cannot be cultured in vitro on standard microbiological media, which prevents their identification. Some microorganisms are weakened or sublethally damaged by processing operations, and they enter the viable but not culturable (VBNC) state [7]. Other microorganisms cannot be identified with the use of culture-dependent methods due to their small population size and the overwhelming effect of predominant species, such as starter culture bacteria. A knowledge of the biodiversity of bacterial communities in fermented foods is highly valuable because every microbial species, including low-abundance species, contribute specific enzymes, metabolites, bacteriocins, and genetic material to the metabolome. A better understanding of the interactions between microorganisms, their metabolites, the effects of process parameters, external factors, and disruptions in the production cycle can expand our knowledge of specific microbial communities. This knowledge can be used to develop new tools for designing the most desirable attributes of fermented foods and to precisely control the production process to achieve the desired effects. Considerable advances have been made in molecular analysis since the late 1980s, and they have led to the development of the PCR technique by [PERSON] in 1983 [8], which supports analyses of the complex ecosystems of fermented foods. Technological progress introduced molecular biology methods to traditional food microbiology. The last decade witnessed the emergence of new methods such as next-generation sequencing (NGS) and new research fields such as metagenomics and metatranscriptomics [9]. Modern NGS techniques support the high-throughput sequencing of genes, metagenomes, and metatranscriptomes, and they deliver new insights into the diversity and metabolic properties of fermented food microbiota, including the microbiota of ripened cheese [10]. The resulting data add to current knowledge about the interactions between microorganisms, the environment, and other microorganisms, and they support the development of strategies for improving the production process and cheese quality. In recent years, metagenomic and/or metatranscriptomic analyses have been conducted on samples of regional cheeses, including water buffalo mozzarella cheese [11], Belgian Herve cheese [12], Italian Plaisentif, Mozzarella, Grana Padano and Parmigiano Reggiano cheese [13; 14], Mexican Cotija cheese [15], and French Tomme d'Orchies Livarot-type cheese [16; 17], as well as industrially produced Dutch-type [18] and Swiss-type cheese [19].