A genomics study was performed in a preselected Enterococcus faecium R.A73 strain, which showed probiotic characteristics and an interesting efficacy in its use as food additives.
The complete genome annotation was performed using the online server RAST (Rapid Annotation using Subsystem Technology) [14].
The plasmid was absent in Enterococcus faecium R.A73. It may be due to growing temperature, copies number as well as isolation methods [27].
There are many features of the carbohydrate subsystem in Enterococcus faecium R.A73. The degradation of carbohydrates and their related compounds are mainly responsible for the primary metabolic activity of lactic acid bacteria, resulting in energy and carbon source molecules [28, 29]. Further metabolic activities such as proteins, lipids, and other compounds decomposition are important for normal growth. LABs metabolic activities include carbohydrate metabolism, protein metabolism, lipid metabolism, and other metabolic activities.
LAB needs amino acids and peptides to respond to their nitrogen complex [30]. Amino acids and peptides may be obtained through proteases or proteolysis actions. In such actions, peptides are metabolized to free amino acids and other compounds for further use. Due to the requirements of peptide differences, peptides can either be essential growth promoters or stimulating factors, some strains can grow up independently. LAB amino acid requirements are strain-dependent with a large range of species differences [31, 32]. Interestingly, many amino acids and derivatives characteristic of the subsystem, including lysine, threonine, methionine, and cysteine, exist in Enterococcus faecium R.A73. Bacteriocins and protein-coding for ABC transporters have been detected as well. These latter are known to have an antibacterial activity that may contribute to probiotic potential in such strains [33].
Enterococcus faecium genome identified 22 genes involved in bacteriocin production as well as antimicrobial peptides. There are several genes implicated in colicin V (ColV). Colicin V is an antibiotic, which has a naturally occurring peptide to kill sensitive cells, disrupting potential membrane structures. It is produced by certain members of Enterobacteriaceae to kill bacterial cells and reduce the competition for vital nutrients [34, 35]. Furthermore, the protein-coding enterocin gene was detected in the R.A73 genome. A notable property of enterocins is their activity against pathogenic bacteria, including members of the genera Listeria, Clostridium, and Staphylococcus [36–38]. This and many other enterocins, therefore, have great utility in the food industry [39].
The comparative proteomes analysis showed that E. faecium R.A73 presented 208 specific genes including five bacteriocins (bacteriocin (DTX73_07350, DTX73_09680), ThmB bacteriocin enhancer peptide (DTX73_09690), ThmA bacteriocin (DTX73_09695), ABC-type bacteriocin/lantibiotic exporters, contain a N-terminal double-glycine peptidase domain (DTX73_09710), class IIb bacteriocin, lactobin A/cerein 7B family (DTX73_09720)). Lantibiotics that constitute a group of bacteriocins were shown to have several pharmaceutical applications including Blood pressure treatment, inflammations and allergies treatment, Skin, mastitis, herpes infections treatment, dental caries treatment, and peptic ulcer treatment. ThmA/ThmB known as termophilin 13 produced by S. thermophiles SPi13 possesses natural antimicrobial activities [35, 40, 41]. Furthermore, fifty-one genes out of 208 were assigned to COG functional categories associated with carbohydrate transport and metabolism (6 genes), amino acid transport and metabolism (6 genes) and cell wall/membrane/envelope biogenesis (5 genes).
Comparative proteome analysis using BLASTp best reciprocal hits with an E-value < = 1E-05 between Enterococcus faecium R.A73 and related Enterococcus strains was performed. The comparison showed that R.A73 is more close to E. faecium T110 with 2,318 common orthologs genes (80.37%). Moreover, the probabilities of DDH value > 70% accessed via logistic regression under three formulae indicate that E. faecium R.A73 is different from other species of the genus excepting Enterococcus faecium. The comparison against E. faecium T110 corresponded to the highest probability of DDH value (> 96%) and confirmed the previous result. Similarly, the BRIG platform showed a similarity between Enterococcus faecium R.A73 and Enterococcus faecium T110 genomes (Fig. 4). This latter strain is a commercially probiotic widely prescribed for humans, animals, and aquaculture [8].
The presence of virulence genes in the probiotic strain Enterococcus faecium R. A73 was studied. Some virulent genes were found highly homologs to EbpA (DTX73_01685), EbpB (DTX73_01690), EbpC (DTX73_01695), srtC (DTX73_017000), EcbA (DTX73_00685), EfaA (DTX73_03830).
The ebp locus consists of an operon of three genes, ebpA, ebpB, and ebpC, which encode the pilus subunits, or pilins, and srtC, encoding a class C sortase [42]. Enterococcus pili have been demonstrated to be directly involved in biofilm development. Mutations in these genes showed a strong defect in biofilm formation and the initial adherence to the host tissue [43]. Ebp pili may play a role during colonization of the mammalian host, adherence to abiotic surfaces or bacterial surface components [44] rather than the pathogenesis, although their exact biological functions remain to be determined.