## 4 Discussion  
Enterococci are largely commensal organisms and several strains have been proven to have probiotic effects for their hosts. Furthermore, they can be used as adjunct cultures in fermenting dairy products, where they modulate the metabolic network created during fermentation and thus affect the organoleptic properties of the end products [8; 9]. The dark side of Enterococci is manifested in several strains, mainly of _E. ficecium_ and _E. ficealis_, which are causative agents of persistent nosocomial infections. For this reason, _Enterococcus_ species have not been granted the QPS status [9] and thus cannot be freely used as starter, adjunct cultures or generally as food-additives. In this context, we aimed to provide a high-resolution genomic characterization of an Enterococci collection retrieved from dairy products, such as raw sheep milk, artisanal Feta cheese, and artisanal Kefalograviera cheese, with _E. ficecium_ being the dominant isolated species and _E. ficealis_, _E. italicus_, and _E. durans_ appearing less frequently. A subsystem is a set of CDSs that together implement a specific biological process or structural complex [53]. Apart from an enriched metabolism repertoire in _E. faecalis_, the subsystem analysis did not reveal major differences in the main cellular processes of this Enterococci collection. Bacterios are peptides synthesized by bacteria that kill other bacteria by creating pores in target membranes. They have been suggested to play a promising role as food preservatives by modulating the food microbiome and suppressing pathogens [54]. Prophages that integrate in bacterial genomes often harbor resistance or virulence determinants [55]. Thus, the existence of CRISPR/Cas systems can help to protect bacterial genomes from prophage integration [8]. The abundance of bacterios and CRISPR/Cas systems suggested the ability of the isolates to suppress pathogens and evade bacteriophages, respectively. Furthermore, analysis for resistance and virulence determinants showed a diverse collection RGs and VGs present in Enterococci, though known hallmark pathogenicity factors were either absent, e.g., vancomycin RGs and the CyIR2, CyIL-1, CyIL-s, and CyIM exotoxins, or occurred rarely, e.g., the _gelE_ VG found in two out of 30 isolates. It is important to note, however, that the absence of hallmark pathogenicity factors cannot guarantee the safety of isolates. With regard to the plasmids and other MGEs, we found the Inc18 replicon type plasmids to be prevalent. These plasmids have been found to carry genes that encode resistance to vancomycin, chloramphenicol, as well as the MLS group of antibiotics. They are also widespread in nosocomial settings, but they have been isolated from food-producing animals, the environment, and wastewater facilities as well [56]. The most prevalent IS element was ISE_nf4_. Although this IS has been associated with the MDR gene _cfr_[57], this gene was not identified in our collection. ISE_fn2/ISL_gar5_, the second most dominant IS, has been linked to the _Tn1546_-like transposon that often harbors the _vanA_ vancomycin RG [57]. However, none of the two genetic elements were detected in our collection. Furthermore, ISE_lpl1_ (14.4%), an IS first described in _Lactobacillus plantarum_, is considered to be linked to bacteriocin production and sugar utilization [58; 59]. Interestingly, all the isolates were predicted as potential human pathogens by the PathogenFinder machine learning algorithm. However, in their publication, [PERSON] et al. [34] report that the performance of their classifier was suboptimal for Enterococci, explained by the few _Enterococcus_ spp. isolates included in their training dataset. We thus focused on the comparative genomic and phylogenetic analysis to juxtapose de facto pathogenic isolates from human infections and isolates from dairy and other sources. The comparative genomic analysis with a large collection of _E. ficecium_ isolates from various origins provided deeper insights.