## 4 Discussion
Although phylogenetically diverse, clusters of closely related isolates were formed according to their origin, with three large dairy, human, and mixed cluster arrangements appearing in the phylogenetic tree (Figure 4). A similar structure was observed in the hierarchical cluster-heatmap created with the resistance, virulence, and CAzyme content of these isolates (Figure 5). Statistical analysis using the presence-absence of related gene suggested that _E. ficecium_ of dairy origin are not associated with particular factors, while those of human origin (both clinical and intestinal)are strongly linked with notorious resistance and virulence determinants. Important RGs enriched in the human sources were the vancomycin RGs (_vun_-like) and regulator genes (_vunR_-like), the tetracycline RGs (_tet_-like), and the _lsaE_ MDR efflux pump. These RGs, especially the vancomycin resistance determinants, are strongly associated with persistent nosocomial infections, which alarmingly show increasing rates and are becoming more difficult to manage [5, 6, 52]. Noteworthy VGs were the _sgrA_ and _ecbA_ adhesins, which were shown to play a role in adhesion to medical-device-related infections by forming biofilms [60], as well as the _scm_ adhesin. Several RGs and VGs, such as the _efmA_ efflux pump and _acm_ adhesin, were ubiquitous across all isolate origins (Figure 4). This finding suggests that certain genetic elements might not be directly linked to pathogenicity and, in the absence of other hallmark pathogenic factors, they might contribute to the attachment and survival of Enterococcus in the GI tract where the bacteria can exert their beneficial probiotic properties [7, 8, 61]. Enzymes responsible for the synthesis and metabolism of carbohydrates are known as carbohydrate-active enzymes (CAZymes). Apart from being interesting in biotechnological applications, the biotransformation of food carbohydrates by bacteria can produce valuable metabolites [62]. Additionally, the combination of pre- and probiotics can lead to significant beneficial effects such as the inhibition of inflammatory processes and the reduction of cholesterol levels [63]. CBMs were significantly enriched in dairy-related isolates. They act as catalytic modules of long CAZymes, such as glycoside hydrolases, with the latter being essential in the degradation of complex carbohydrates, such as lactose and starch [64]. Within the human sources, the CBM61, CE12, and GH154 CAZymes were significantly enriched, which also showed a strong negative association in the dairy origin isolates. Interestingly, the AA10 CAZyme, which was strongly associated only with the human-clinical source, was found to play a key role in the binding of (opportunistic) pathogens [65, 66]. Lastly, analysis with [PERSON] highlighted associations between the isolate source and specific phenotypic traits. Remarkably, dairy origin isolates presented a strong association with the utilization of starch and malonate, suggesting that these strains could be used in both dairy and vegetable fermentation [67]. On the contrary, human origin isolates were found to be significantly related with the catabolism of L-Hamnose, D-sorbitol, and raffinose. The fermentation of the latter two sugars has indeed been found to be associated with nosocomial _E.ecium_ pathogens [68, 69]. Even though our comparative analysis provided some notable insights regarding the genomic composition of Enterococcus in the context of their origin, our approach cannot provide a definitive answer as to which genomic features can distinguish pathogenic from commensal isolates. Although beyond the scope of this study, this goal can be achieved through a systematic genome-wide association study (GWAS) coupled with machine learning methods and involving large numbers (1000-2000) of properly labeled isolates (e.g., pathogenic vs. commensal) to establish sufficient statistical power [70].