Cheeses are inherently microbiologically and biochemically dynamic. Numerous biotic and abiotic drivers govern the establishment and assembly of a core microbiota in cheese, which, for internally-ripened cheeses, having an intermediate to long period of ripening, consists of starter and non-starter lactic acid bacteria (SLAB and NSLAB). The management of this dynamic ecosystem has to consider this core as a super-organism, which results from the sums of microbial metabolisms and interactions among individual microbes. This review focuses on all presumptive drivers, raw and pasteurized milk, farming system and house microbiota, and intrinsic and extrinsic factors during cheese manufacture and ripening, which qualitatively and mainly depending on the farm management system and cheese variety may influence the populations of SLAB and NSLAB. The interactions between these two microbial groups are described also. The cheese ecosystem shows a variable flux of its core microbiota from milking through manufacture to ripening. Many and diverse drivers establish and assembly the lactic acid bacteria biota. If such drivers are efficient to guarantee microbial and cheese diversities, on the other hand, their control is the fundamental pre-requisite to synchronize and balance microbiological events. The methodological approaches (e.g., omics techniques and integrated system biology) have markedly improved to concretize this ambitious goal. Facing and improving the knowledge on the main drivers, the current step should focus on a unique puzzle of coexisting species/biotypes likely a super-organism, whose guide has to consider all casehardened microbial elements. •Cheeses are microbiologically and biochemically dynamic.•Biotic and abiotic drivers govern the establishment/assembly of a core microbiota.•The core microbiota consists of starter and non-starter lactic acid bacteria.•The sums of microbial metabolisms and interactions result in a super-organism to be driven.•All presumptive drivers that influence the core microbiota are described.