Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening

Abstract

Enterococcus spp. are present in the native microbiota of many traditional fermented foods. Their ability to produce antibacterial compounds, mainly against Listeria monocytogenes, has raised interest recently. However, there is scarce information about their proteolytic and lipolytic potential, and their biotechnological application is currently limited because enterococcal strains have been related to nosocomial infections. In this work, next-generation sequencing and optimised bioinformatic pipelines were used to annotate the genomes of two Enterococcus strains-one E. faecium and one E. faecalis-isolated from the Mexican artisanal ripened Cotija cheese. A battery of genes involved in their proteolytic system was annotated. Genes coding for lipases, esterases and other enzymes whose final products contribute to cheese aroma and flavour were identified as well. As for the production of antibacterial compounds, several peptidoglycan hydrolase- and bacteriocin-coding genes were identified in both genomes experimentally and by bioinformatic analyses. E. faecalis showed resistance to aminoglycosides and E. faecium to aminoglycosides and macrolides, as predicted by the genome functional annotation. No pathogenicity islands were found in any of the strains, although traits such as the ability of biofilm formation and cell aggregation were observed. Finally, a comparative genomic analysis was able to discriminate between the food strains isolated and nosocomial strains. In summary, pathogenic strains are resistant to a wide range of antibiotics and contain virulence factors that cause host damage; in contrast, food strains display less antibiotic resistance, include genes that encode class II bacteriocins and express virulence factors associated with host colonisation rather than invasion.

Enterococci: Between Emerging Pathogens and Potential Probiotics

“…In fact, some enterococcal strains such as E. faecium M74 and E. faecium SF-68 are included as food supplements in several probiotic preparations that have been proved to be effective and safe, such as FortiFlora® and Cernivet® (containing E. faecium SF68®, Cerbios-Pharma SA, Switzerland), and Symbioflor® 1 with E. faecalis (Symbiopharm, Herborn, Germany) [142, 161, 162].…”

Current Trends of Enterococci in Dairy Products: A Comprehensive Review of Their Multiple Roles

“…Casein degradation by enterococci is first accomplished by the extracellular Clp proteolytic complex. The resulting oligopeptides are then brought into the cell by several transport systems (Opp, Dpp, and DptT), where they are further degraded by aminopeptidases (Pep A, Pep B, Pep C, Pep F, Pep O, Pep Q, Pep S, Pep T and Pep V); they will eventually serve as a source of nitrogen for enterococcal growth, and function as precursors for flavor compounds [186]. Moreover, free amino acids can be converted to biogenic amines by enterococcal decarboxylase systems.…”

“…Amino acid decarboxylation is activated in acidic environments, and may help the enterococcal cell maintain its pH homeostasis under such conditions. It may also support primary metabolism under nutrient depletion conditions [186]. Enterococci have often been identified as one of the main biogenic amine producers in cheese; synthesis of histidine decarboxylase, tyrosine decarboxylase, lysine decarboxylase, ornithine decarboxylase, and agmatine deiminase, as well as production of the corresponding biogenic amines (histidine, tyramine, 2-phenylethylamine, cadaverine, and putrescine) have been described for several species of this genus [187].…”

“…The production of diacetyl and, to a lesser extent, of acetoin have been described in enterococci from cheese [142,153,175,197,198]. Additionally, annotation of enterococcal genomes has revealed genes that encode for enzymes involved in acetaldehyde, diacetyl, and acetoin [186,199]. Some LAB can accumulate extracellular heteropolysaccharides; besides their protective functions, they take part in adhesion to surfaces and in biofilm formation, thus assisting EPS-producing strains in colonizing their environments, including their hosts' gastrointestinal tract (GIT) [200].…”

Enterococcus spp.: Is It a Bad Choice for a Good Use—A Conundrum to Solve?

“…For instance, different probiotic formulas, containing E. faecium M74 and E. faecium SF-68, have been reported to be effective and safe. Amongst these preparations, Cernivet ® and FortiFlora ® (containing E. faecium SF68 ® , Cerbios-Pharma SA, Barbengo, Switzerland), and Symbioflor ® 1 with E. faecalis (Symbiopharm, Herborn, Germany) are the most relevant and commercialized [45,46]. Moreover, numerous enterococcal strains have been described as useful for many health features or technological applications in food systems or in human and/or animal health, including E. durans M4-5 (production of butyrate as short chain fatty acids (SCFAs), induction of significant anti-inflammatory effects and contribution to the intestinal epithelium integrity), E. durans LAB18s (source of dietary selenium supplementation), E. durans KLDS 6.0930 and E. faecium M74 ® (reduction in serum cholesterol levels), E. mundtii ST4SA (production of bacteriocins), E. faecium LCW 44 and E. durans 6HL (production of antimicrobial compounds against Gram-positive and Gram-negative bacteria) [25].…”