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

Microbiological quality and native lactic acid bacteria diversity of artisanal Mexican cheeses: A review

This review aims to provide an overview of artisanal Mexican cheeses microbiota focused on microbiological quality and safety, as well as native Lactic acid Bacteria (LAB) diversity. For the search, key words of artisanal Mexican cheeses varieties was carried out through several online databases and original articles were screened and data about populations of indicator microorganisms, presence of pathogens, and native LAB identified were extracted. Several artisanal Mexican cheeses exceeded the permissible limit established in Mexican regulation (NOM-243-SSA1-2010) for indicator microorganisms, as well as in some types of cheese, the presence of pathogens was confirmed. However, other varieties of artisanal Mexican cheeses possess unique physicochemical characteristics, and during their manufacturing particular steps are used that contribute to ensuring their quality and safety. Additionally, strains able to control the growth of pathogenic and spoilage bacteria are part of the microbiota of some artisanal Mexican cheeses. About native LAB diversity, it is composed by species of Lactobacillus, Enterococcus, Streptococcus, Leuconostoc, Weisella, Lactococcus, Pediococus, Aerococus, Carnobacterium, Tetragenococus, among others genera. Otherwise, artisanal Mexican cheeses represent an important source of specific LAB with several approaches within human health because they showed potential for the development of functional foods, nutraceutical, and bioprotective cultures.

Microbiome-based precision nutrition: Prebiotics, probiotics and postbiotics

Microorganisms have been used in nutrition and medicine for thousands of years worldwide, long before humanity knew of their existence. It is now known that the gut microbiota plays a key role in regulating inflammatory, metabolic, immune and neurobiological processes. This text discusses the importance of microbiota-based precision nutrition in gut permeability, as well as the main advances and current limitations of traditional probiotics, new-generation probiotics, psychobiotic probiotics with an effect on emotional health, probiotic foods, prebiotics, and postbiotics such as short-chain fatty acids, neurotransmitters and vitamins. The aim is to provide a theoretical context built on current scientific evidence for the practical application of microbiota-based precision nutrition in specific health fields and in improving health, quality of life and physiological performance.

Genomic Insights Into Enterococcus mundtii 203: A Promising Probiotic Candidate Isolated From Camel Feces

Enterococcus, a common commensal organism in the human gut, exhibits a dual nature with certain strains offering probiotic benefits, while others are associated with nosocomial infections. In this study, we conducted a comprehensive examination of the genome of Enterococcus mundtii strain 203 to assess its probiotic potential and safety profile. The complete genome sequencing, assembly, and annotation were performed, followed by bioinformatics analysis. Our investigation reveals a detailed characterization of the Enterococcus mundtii 203 genome, originally isolated from camel feces, with a size of 3,053,234 bases and a GC content of 38.4%. Importantly, our analysis suggests that this strain poses no risk as a human pathogen due to the absence of antibiotic resistance determinants and virulence factors. The genome harbors a multitude of genes responsible for lactic acid production, bioactive peptide synthesis, adhesion molecule expression, resistance to harsh gut conditions, and enhancement of host metabolism. These findings underline the potential probiotic functionality of Enterococcus mundtii 203, positioning it as a promising candidate. Notably, our study did not identify any sequences related to insertion elements or CRISPR-Cas fragments.

Study of an Enterococcus faecium strain isolated from an artisanal Mexican cheese, whole-genome sequencing, comparative genomics, and bacteriocin expression

Enterococci are ubiquitous microorganisms in almost all environments, from the soil we step on to the food we eat. They are frequently found in naturally fermented foods, contributing to ripening through protein, lipid, and sugar metabolism. On the other hand, these organisms are also leading the current antibiotic resistance crisis. In this study, we performed whole-genome sequencing and comparative genomics of an Enterococcus faecium strain isolated from an artisanal Mexican Cotija cheese, namely QD-2. We found clear genomic differences between commensal and pathogenic strains, particularly in their carbohydrate metabolic pathways, resistance to vancomycin and other antibiotics, bacteriocin production, and bacteriophage and CRISPR content. Furthermore, a bacteriocin transcription analysis performed by RT-qPCR revealed that, at the end of the log phase, besides enterocins A and X, two putative bacteriocins not reported previously are also transcribed as a bicistronic operon in E. faecium QD-2, and are expressed 1.5 times higher than enterocin A when cultured in MRS broth.

Genome sequencing of Enterococcus faecium NT04, an oral microbiota revealed the production of enterocin A/B active against oral pathogens

Objective

This study aimed to isolate and investigate a bacterium from an Egyptian adult's healthy oral cavity, focusing on its probiotic properties, especially its antagonistic activity against oral pathogens.

Methods

The isolated bacterium NT04 using 16S rRNA gene sequencing, was identified as Enterococcus faecium. In this study, the whole genome of Enterococcus faecium NT04 was sequenced and annotated by bioinformatics analysis tools.

Results

Numerous genes encoding the production of diverse metabolic and probiotic properties, such as bacteriocin-like inhibitory substances (Enterocin A and B), cofactors, antioxidants, and vitamins, were confirmed by genomic analysis. There were no pathogenicity islands or plasmid insertions found. This strain is virulent for host colonization rather than invasion.

Conclusion

Genomic characteristics of strain NT04 support its potentiality as an anti-oral pathogen probiotic candidate.

A Lactic Acid Bacteria Consortium Impacted the Content of Casein-Derived Biopeptides in Dried Fresh Cheese

This study aimed to define a consortium of lactic acid bacteria (LAB) that will bring added value to dried fresh cheese through specific probiotic properties and the synthesis of bioactive peptides (biopeptides). The designed LAB consortium consisted of three Lactobacillus strains: S-layer carrying Levilactobacillus brevis D6, exopolysaccharides producing Limosilactobacillus fermentum D12 and plantaricin expressing Lactiplantibacillus plantarum D13, and one Enterococcus strain, Enterococcus faecium ZGZA7-10. Chosen autochthonous LAB strains exhibited efficient adherence to the Caco-2 cell line and impacted faecal microbiota biodiversity. The cheese produced by the LAB consortium showed better physicochemical, textural and sensory properties than the cheese produced by a commercial starter culture. Liquid chromatography coupled with matrix-assisted laser desorption/ionization-time of flight tandem mass spectrometry (LC-MALDI-TOF/TOF) showed the presence of 18 specific biopeptides in dried fresh cheeses. Their identification and relative quantification was confirmed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) using multiple reaction monitoring (MRM). The results also showed that their synthesis resulted mainly from β-casein and also α-S1 casein degradation by proteolytic activities of the LAB consortium. The designed LAB consortium enhanced the functional value of the final product through impact on biopeptide concentrations and specific probiotic properties.

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

Since antiquity, the ubiquitous lactic acid bacteria (LAB) Enterococci, which are just as predominant in both human and animal intestinal commensal flora, have been used (and still are) as probiotics in food and feed production. Their qualities encounter several hurdles, particularly in terms of the array of virulence determinants, reflecting a notorious reputation that nearly prevents their use as probiotics. Additionally, representatives of the Enterococcus spp. genus showed intrinsic resistance to several antimicrobial agents, and flexibility to acquire resistance determinants encoded on a broad array of conjugative plasmids, transposons, and bacteriophages. The presence of such pathogenic aspects among some species represents a critical barrier compromising their use as probiotics in food. Thus, the genus neither has Generally Recognized as Safe (GRAS) status nor has it been included in the Qualified Presumption of Safety (QPS) list implying drastic legislation towards these microorganisms. To date, the knowledge of the virulence factors and the genetic structure of foodborne enterococcal strains is rather limited. Although enterococcal infections originating from food have never been reported, the consumption of food carrying virulence enterococci seems to be a risky path of transfer, and hence, it renders them poor choices as probiotics. Auspiciously, enterococcal virulence factors seem to be strain specific suggesting that clinical isolates carry much more determinants that food isolates. The latter remain widely susceptible to clinically relevant antibiotics and subsequently, have a lower potential for pathogenicity. In terms of the ideal enterococcal candidate, selected strains deemed for use in foods should not possess any virulence genes and should be susceptible to clinically relevant antibiotics. Overall, implementation of an appropriate risk/benefit analysis, in addition to the case-by-case assessment, the establishment of a strain's innocuity, and consideration for relevant guidelines, legislation, and regulatory aspects surrounding functional food development seem to be the crucial elements for industries, health-staff and consumers to accept enterococci, like other LAB, as important candidates for useful and beneficial applications in food industry and food biotechnology. The present review aims at shedding light on the world of hurdles and limitations that hampers the Enterococcus spp. genus and its representatives from being used or proposed for use as probiotics. The future of enterococci use as probiotics and legislation in this field are also discussed.

Selection of lactic acid bacteria with promising probiotic aptitudes from fruit and ability to survive in different food matrices

Lactic acid bacteria (LAB) are among the most prevalent microorganisms forming the autochthonous microbiota of fruit. This study aimed to select LAB isolates with probiotic aptitudes from apple, banana, grape, and orange through evaluation of in vitro safety, technological, and functional-related properties. The ability of most promising selected isolates to survive in commercial apple and orange juice, meat stew, vegetable puree, and UHT milk during 28 days of refrigeration storage was evaluated. Ninety-three isolates identified preliminarily as LAB were recovered from fruit and 66 of these isolates passed safety tests. Most of these isolates were pre-identified as belonging to Lactobacillus or Enterococcus genus based on MALDI-ToF MS profiling. These 66 isolates were categorized into three homogeneous groups based on a preliminary cluster analysis run with data from experiments to measure technological characteristics. Nine LAB isolates were selected as the most promising for probiotic use based on a principal component analysis run with data from experiments to measure probiotic-related properties. Four of these isolates were sensitive to different antibiotics and identified (16S-rRNA gene sequencing) as Lactobacillus brevis (recently reclassified as L. brevis) or Lactobacillus spp. These 4 selected isolates had high viable counts and high percentages of physiologically active cells in apple and orange juice, beef stew, vegetable puree, and UHT milk during refrigeration storage. The results showed that apple, banana, orange, and grape are potential sources of LAB with aptitudes to be exploited for a possible probiotic use and distinguished abilities to survive in different food matrices.

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

As a genus that has evolved for resistance against adverse environmental factors and that readily exchanges genetic elements, enterococci are well adapted to the cheese environment and may reach high numbers in artisanal cheeses. Their metabolites impact cheese flavor, texture, and rheological properties, thus contributing to the development of its typical sensorial properties. Due to their antimicrobial activity, enterococci modulate the cheese microbiota, stimulate autolysis of other lactic acid bacteria (LAB), control pathogens and deterioration microorganisms, and may offer beneficial effects to the health of their hosts. They could in principle be employed as adjunct/protective/probiotic cultures; however, due to their propensity to acquire genetic determinants of virulence and antibiotic resistance, together with the opportunistic character of some of its members, this genus does not possess Qualified Presumption of Safety (QPS) status. It is, however, noteworthy that some putative virulence factors described in foodborne enterococci may simply reflect adaptation to the food environment and to the human host as commensal. Further research is needed to help distinguish friend from foe among enterococci, eventually enabling exploitation of the beneficial aspects of specific cheese-associated strains. This review aims at discussing both beneficial and deleterious roles played by enterococci in artisanal cheeses, while highlighting the need for further research on such a remarkably hardy genus.

Anti-Proliferative and Anti-Biofilm Potentials of Bacteriocins Produced by Non-Pathogenic Enterococcus sp

The incidence of cancer is increasing worldwide; likewise, the emergence of antibiotic-resistant biofilm-forming pathogens has led to a tremendous increase in morbidity and mortality. This study aimed to evaluate the probiotic properties of bacteriocin-producing Enterococcus sp. with a focus on their anti-biofilm and anticancer activities. Three of 79 Enterococcus isolates (FM43, FM65, FM50) were identified as producers of broad-spectrum bioactive molecules and were molecularly characterized as Enterococcus faecium by 16S rRNA sequencing. Phenotypic and genotypic screening for potential virulence factors revealed no factors known to promote pathogenicity. Treatment with proteinase K resulted in diminished antimicrobial activity; PCR-based screening for bacteriocin genes suggested the presence of both entA and entB genes that encode enterocins A and B, respectively. Maximum antimicrobial activity was detected during the early stationary phase, while activity disappeared after 24 h in culture. Bacteriocins from these isolates were stable at high temperatures and over a wide range of pH. Interestingly, crude supernatants of Ent. faecium FM43 and Ent. faecium FM50 resulted in significant destruction (80% and 48%, respectively; P < 0.05) of Streptococcus mutans ATCC 25175-associated preformed biofilms. Moreover, in vitro cytotoxicity assays revealed that extracts from Ent. faecium isolates FM43, FM65, and FM50 inhibited Caco-2 cell proliferation by 76.9%, 70%, and 85.3%, respectively. Taken together, the multifunctional capabilities of the microbial-derived proteins identified in our study suggest potentially important roles as alternative treatments for biofilm-associated infections and cancer.

Enterococci: Between Emerging Pathogens and Potential Probiotics

Enterococci are ubiquitous microorganisms that could be found everywhere; in water, plant, soil, foods, and gastrointestinal tract of humans and animals. They were previously used as starters in food fermentation due to their biotechnological traits (enzymatic and proteolytic activities) or protective cultures in food biopreservation due to their produced antimicrobial bacteriocins called enterocins or as probiotics, live cells with different beneficial characteristics such as stimulation of immunity, anti-inflammatory activity, hypocholesterolemic effect, and prevention/treatment of some diseases. However, in the last years, the use of enterococci in foods or as probiotics caused an important debate because of their opportunistic pathogenicity implicated in several nosocomial infections due to virulence factors and antibiotic resistance, particularly the emergence of vancomycin-resistant enterococci. These virulence traits of some enterococci are associated with genetic transfer mechanisms. Therefore, the development of new enterococcal probiotics needs a strict assessment with regard to safety aspects for selecting the truly harmless enterococcal strains for safe applications. This review tries to give some data of the different points of view about this question.

Enhancement of the antibacterial activity of an E. faecalis strain by the heterologous expression of enterocin A

The genus Enterococcus occurs as native microbiota of fermented products due to its broad environmental distribution and its resistance to salt concentrations. Enterococcus faecalis F, a non-pathogenic strain isolated from a ripened cheese, has demonstrated useful enzymatic capabilities, a probiotic behavior and antibacterial activity against some food-borne pathogens, mainly due to peptidoglycan hydrolase activity. Its use as a natural pathogen-control agent could be further enhanced through the production of a bacteriocin, e.g. Enterocin A, because of its remarkable antilisterial activity. In this work, a markerless allelic insertion method was used to obtain an enterococcal strain capable of producing a functional enterocin. Agar diffusion tests showed that the recombinant strain was active against Staphylococcus aureus, Listeria monocytogenes and the pathogenic strain E. faecalis V583. When grown in liquid culture together with L. monocytogenes, it attained a two-log reduction of the pathogen counts in lesser time relative to the native strain. Because the DNA construction is integrated into the chromosome, the improved strain avoids the use of antibiotics as selective pressure; besides, it does not require an inductor because of the inclusion of a constitutive promoter in the construction. Its technological and antibacterial capabilities make the improved E. faecalis strain a potential culture for use in the food industry.