Potential Probiotic Enterococcus faecium OV3-6 and Its Bioactive Peptide as Alternative Bio-Preservation

Genetic diversity and distinction of Enterococcus faecium and Enterococcus lactis in traditional Montenegrin brine cheeses and salamis

Introduction

Enterococcus faecium is a widespread acid-lactic bacterium found in the environment, humans, and animal microbiota, and it also plays a role in the production of traditional food. However, the worldwide emergence of multidrug-resistant E. faecium strains represents a major public health threat and is the primary reason that the genus Enterococcus is not recommended for the Qualified Presumption of Safety (QPS) list of the European Food Safety Authority (EFSA), raising concerns about its presence in food products.

Methods

In this study, 39 E. faecium and 5 E. lactis isolates were obtained from artisanal brine cheeses and dry sausages, sourced from 21 different Montenegrin producers. The isolates were collected following the ISO 15214:1998 international method and processed for whole-genome sequencing (WGS).

Results

Genome analysis based on core genome multilocus sequence type (cgMLST) revealed a high diversity among isolates. Furthermore, the isolates carried antimicrobial resistance genes; the virulence genes acm, sgrA, and ecbA; the bacteriocin genes Enterolysin A, Enterocin A, Enterocin P, Duracin Q, Enterocin B, Bacteriocin 31, Enterocin EJ97, Sactipeptides, and Enterocin SEK4; the secondary metabolite genes T3PKS, cyclic lactone autoinducer, RiPP-like, and NRPS and a maximum of eight plasmids.

Conclusion

This study highlights the need for careful monitoring of E. faecium and E. lactis strains in food to ensure they do not pose any potential risks to consumer safety.

A Review on Bacteriocin Extraction Techniques from Lactic Acid Bacteria

Lactic acid bacteria (LAB) are widely known for the production of secondary metabolites such as organic acids and other bioactive compounds such as bacteriocins. Finding a broad application in food and healthcare, bacteriocins have received increased attention due to their inherent antimicrobial properties. However, the extraction of bacteriocins is often plagued with low yields due to the complexity of the extraction processes and the diversity of bacteriocins themselves. Here, we review the current knowledge related to bacteriocin extraction on the different extraction techniques for isolating bacteriocins from LAB. The advantages and disadvantages of each technique will also be critically appraised, taking into account factors such as extraction efficiency, scalability and cost-effectiveness. This review aims to guide researchers and professionals in selecting the most suitable approach for bacteriocin extraction from LAB by illuminating the respective advantages and limitations of various extraction techniques.

Identification, Safety Assessment, and Antimicrobial Characteristics of Cocci Lactic Acid Bacteria Isolated from Traditional Egyptian Dairy Products

The main objective of this study is to isolate and identify lactic acid bacteria (LAB) from various Egyptian dairy products, examine their antibacterial and hemolysis potential, and ensure their safety when used as starter cultures in different dairy industries. Egyptian dairy products are often made without the use of commercial starter cultures, using raw milk and artisanal methods. The most popular traditional dairy products are Laban Rayeb and Zabady, as well as the cheese varieties of Ras, Domiati, and Karish. The microbial communities used for fermentation and the diversity of lactic acid bacteria are the most important factors that can affect the quality of these products. In order to investigate the diversity of cocci lactic acid bacteria in Egyptian dairy products, 70 samples of raw or fermented milk and cheeses were collected from traditional cheese-making factories, local markets, and farmhouses located in the Delta area of Egypt. Following this, the LAB were isolated from the samples. One hundred fifty-seven isolates of Gram-positive, catalase-negative, and cocci bacterial species were identified via rep-PCR, and some isolates were confirmed using pheS and 16S rRNA gene sequencing, as follows: Streptococcus infantarius subsp. infantarius (three isolates), Enterococcus hirae (three isolates), Enterococcus faecium (ninety-six isolates), Enterococcus faecalis (forty isolates), Enterococcus durans (six isolates), Lactococcus garvieae (one isolate), Pediococcus acidilactici (seven isolates), and Lactococcus lactis subsp. Lactis (one isolate). These findings validate that five strains have strong antibacterial activity against Escherichia coli, Salmonella typhimurium, and Listeria monocytogenes, and one hundred thirty-four strains were safe for hemolysis. The five strains were selected as protective cultures, including Pediococcus acidilactici, Lactococcus lactis subsp. lactis, E. faecalis, and E. faecium.

Antilisterial and antioxidant exopolysaccharide from Enterococcus faecium PCH.25 isolated from cow butter: characterization and probiotic potential

Exopolysaccharides produced by lactic acid bacteria have gained attention for their potential health benefits and applications in functional foods. This study explores the isolation and characterization of a novel exopolysaccharide-producing strain from dairy products. The aim was to evaluate its probiotic potential and investigate the properties of the produced exopolysaccharide. A strain identified as Enterococcus faecium PCH.25, isolated from cow butter, demonstrated exopolysaccharide production. The study's novelty lies in the comprehensive characterization of this strain and its exopolysaccharide, revealing unique properties with potential applications in food, cosmetic, and pharmaceutical industries. The E. faecium PCH.25 strain exhibited strong acid tolerance, with a 92.24% viability rate at pH 2 after 2 h of incubation. It also demonstrated notable auto-aggregation (85.27% after 24 h) and co-aggregation abilities, antibiotic sensitivity, and absence of hemolytic activity, suggesting its probiotic potential. The exopolysaccharide produced by this strain showed bactericidal activity (MIC and MBC = 1.8 mg/ml) against Listeria monocytogenes and antioxidant properties (22.8%). Chemical analysis revealed a heteropolysaccharide composed of glucose and fructose monomers, with various functional groups contributing to its bioactivities. Physical characterization of the exopolysaccharide indicated thermal stability up to 270 °C, a negative zeta-potential (-27 mV), and an average particle size of 235 nm. Scanning electron microscopy and energy dispersive X-ray analysis revealed a smooth, nonporous structure primarily composed of carbon and oxygen, with an amorphous nature. These findings suggest that the exopolysaccharide from E. faecium PCH.25 has potential as a natural antibacterial and antioxidant polymer for use in functional foods, cosmetics, and pharmaceuticals.

Assessment of the Safety and Probiotic Properties of Enterococcus faecium B13 Isolated from Fermented Chili

Enterococcus faecium B13, selected from fermentation chili, has been proven to promote animal growth by previous studies, but it belongs to opportunistic pathogens, so a comprehensive evaluation of its probiotic properties and safety is necessary. In this study, the probiotic properties and safety of B13 were evaluated at the genetic and phenotype levels in vitro and then confirmed in vivo. The genome of B13 contains one chromosome and two plasmids. The average nucleotide identity indicated that B13 was most closely related to the fermentation-plant-derived strain. The strain does not carry the major virulence genes of the clinical E. faecium strains but contains aac(6')-Ii, ant (6)-Ia, msrC genes. The strain had a higher tolerance to acid at pH 3.0, 4.0, and 0.3% bile salt and a 32.83% free radical DPPH clearance rate. It can adhere to Caco-2 cells and reduce the adhesion of E. coli to Caco-2 cells. The safety assessment revealed that the strain showed no hemolysis and did not exhibit gelatinase, ornithine decarboxylase, lysine decarboxylase, or tryptophanase activity. It was sensitive to twelve antibiotics but was resistant to erythromycin, rifampicin, tetracycline, doxycycline, and minocycline. Experiments in vivo have shown that B13 can be located in the ileum and colon and has no adverse effects on experiment animals. After 28 days of feeding, B13 did not remarkable change the α-diversity of the gut flora or increase the virulence genes. Our study demonstrated that E. faecium B13 may be used as a probiotic candidate.

Effects of Synbiotic Lacticaseibacillus paracasei, Bifidobacterium breve, and Prebiotics on the Growth Stimulation of Beneficial Gut Microbiota

The gut microbiota is a complex community of microorganisms that plays a vital role in maintaining overall health, and is comprised of Lactobacillus and Bifidobacterium. The probiotic efficacy and safety of Lacticaseibacillus paracasei and Bifidobacterium breve for consumption were confirmed by in vitro experiments. The survival rate of the probiotics showed a significant decline in in vitro gut tract simulation; however, the survival rate was more than 50%. Also, the probiotics could adhere to Caco-2 cell lines by more than 90%, inhibit the pathogenic growths, deconjugate glycocholic acid and taurodeoxycholic acid through activity of bile salt hydrolase (BSH) proteins, and lower cholesterol levels by over 46%. Regarding safety assessment, L. paracasei and B. breve showed susceptibility to some antibiotics but resistance to vancomycin and were examined as γ-hemolytic strains. Anti-inflammatory properties of B. breve with Caco-2 epithelial cell lines showed the significantly highest value (p < 0.05) for interleukin-10. Furthermore, probiotics and prebiotics (inulin, fructooligosaccharides, and galactooligosaccharides) comprise synbiotics, which have potential effects on the increased abundance of beneficial microbiota, but do not affect the growth of harmful bacteria in feces samples. Moreover, the highest concentration of short chain fatty acid was of acetic acid, followed by propionic and butyric acid.

Bacteriocin-Producing Enterococcus faecium OV3-6 as a Bio-Preservative Agent to Produce Fermented Houttuynia cordata Thunb. Beverages: A Preliminary Study

Microbial contamination affects the quality of the fermented Houttuynia cordata Thunb. (H. cordata) beverage (FHB). The present study aimed to assess the bio-preservative property of Enterococcus faecium OV3-6 (E. faecium OV3-6) during the production of FHB. The antimicrobial activity against Escherichia coli, Salmonella, Bacillus cereus, and Staphylococcus aureus and the survival of E. faecium OV3-6 were studied. Then, FHB fermentation was performed with different preservatives (non-preservative, E. faecium OV3-6, cell-free supernatant of E. faecium OV3-6, and nisin) with and without representative pathogens. The maximum antimicrobial activity against S. aureus and B. cereus was observed after 18 h of cultivation in an MRS medium. E. faecium OV3-6 was used as a starter to produce the FHB, and the strain survived up to 48 h in the fermented beverage. E. faecium OV3-6 and its cell-free supernatant inhibited the growth of E. coli, Salmonella, B. cereus, and S. aureus in the stimulated FHB. The non-preservatives and nisin-containing FHB showed inhibition against Gram-positive pathogens. The FHB treated with E. faecium OV3-6 was rich in lactic acid bacteria, and the product was at an acceptable level of pH (less than 4.3). Certain limitations were identified in the study, such as lack of nutritional, metabolomics analysis, and safety and consumer acceptability of FHB. The results suggested that E. faecium OV3-6 could be used as a bio-preservative to produce fermented plant beverages (FPBs).

Screening of bacteriocin-producing dairy Enterococcus strains using low-cost culture media

This study was carried out to select the bacteriocinogenic strains among Enterococcus strains isolated from Ukrainian traditional dairy products using a low-cost media for screening, that containing molasses and steep corn liquor. A total of 475 Enterococcus spp. strains were screened for antagonistic activity against Pseudomonas aeruginosa, Escherichia coli, Staphylococcus aureus, and Listeria monocytogenes indicator strains. The initial screening revealed that 34 Enterococcus strains during growth in low-cost medium containing corn steep liquor, peptone, yeast extract, and sucrose produced metabolites with inhibition activity against at least of the indicator strains used. Enterocin genes entA, entP, and entB were detected in 5 Enterococcus strains by PCR assay. Genes of enterocins A and P were found in E. faecalis 58 and Enterococcus sp. 226 strains, enterocins B and P - in Enterococcus sp. 423, enterocin A - in E. faecalis 888 and E. durans 248 strains. Bacteriocin-like inhibitory substances (BLIS) produced by these Enterococcus strains were thermostable and sensitive to proteolytic enzymes. To our knowledge, this is the first report on the isolation of enterocin-producing wild Enterococcus strains from traditional Ukrainian dairy products using a low-cost media for screening bacteriocinogenic strains. Strains E. faecalis 58, Enterococcus sp. 423, and Enterococcus sp. 226 are promising candidates for practical use as producers of bacteriocins with inhibitory activity against L. monocytogenes using molasses and steep corn liquor as cheap sources of carbon and nitrogen, that can significantly reduce the cost of industrial bacteriocin production. Further studies will be required to determine the dynamic of bacteriocin production, its structure, and mechanisms of antibacterial action.

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.

Effect of Gastrointestinal Digestion on the Bioaccessibility of Phenolic Compounds and Antioxidant Activity of Fermented Aloe vera Juices

Plant-based beverages are enriched by the fermentation process. However, their biocompounds are transformed during gastrointestinal digestion, improving their bioaccessibility, which is of primary importance when considering the associated health benefits. This study aimed to evaluate the effect of in vitro gastrointestinal digestion on phenolic compound bioaccessibility and antioxidant activity of novel Aloe vera juices fermented by probiotic Enterococcus faecium and Lactococcus lactis. Aloe vera juices were digested using the standardized static INFOGEST protocol. During digestion, phenolic compounds and antioxidant activity (DPPH, ABTS, and FRAP) were accessed. The digestion process was seen to significantly increase the total phenolic content of the fermented Aloe vera juices. The fermentation of Aloe vera increased the bioaccessibility of juice biocompounds, particularly for kaempferol, ellagic acid, resveratrol, hesperidin, ferulic acid, and aloin. The phenolics released during digestion were able to reduce the oxidative radicals assessed by ABTS and FRAP tests, increasing the antioxidant action in the intestine, where they are absorbed. The fermentation of Aloe vera by probiotics is an excellent process to increase the bioavailability of beverages, resulting in natural added-value functional products.

Assessment of the safety and probiotic properties of Roseburia intestinalis: A potential “Next Generation Probiotic”

Roseburia intestinalis is an anaerobic bacterium that produces butyric acid and belongs to the phylum Firmicutes. There is increasing evidence that this bacterium has positive effects on several diseases, including inflammatory bowel disease, atherosclerosis, alcoholic fatty liver, colorectal cancer, and metabolic syndrome, making it a potential “Next Generation Probiotic.” We investigated the genomic characteristics, probiotic properties, cytotoxicity, oral toxicity, colonization characteristics of the bacterium, and its effect on the gut microbiota. The genome contains few genes encoding virulence factors, three clustered regularly interspaced short palindromic repeat (CRISPR) sequences, two Cas genes, no toxic biogenic amine synthesis genes, and several essential amino acid and vitamin synthesis genes. Seven prophages and 41 genomic islands were predicted. In addition to a bacteriocin (Zoocin A), the bacterium encodes four metabolic gene clusters that synthesize short-chain fatty acids and 222 carbohydrate-active enzyme modules. This bacterium is sensitive to antibiotics specified by the European Food Safety Authority, does not exhibit hemolytic or gelatinase activity, and exhibits some acid resistance. R. intestinalis adheres to intestinal epithelial cells and inhibits the invasion of certain pathogens. In vitro experiments showed that the bacterium was not cytotoxic. R. intestinalis did not affect the diversity or abundance of the gut flora. Using the fluorescent labelling method, we discovered that R. intestinalis colonizes the cecum and mucus of the colon. An oral toxicity study did not reveal any obvious adverse effects. The lethal dose (LD)50 of R. intestinalis exceeded 1.9 × 10⁹ colony forming units (CFU)/kg, whereas the no observed adverse effect level (NOAEL) derived from this study was 1.32 × 10⁹ CFU/kg/day for 28 days. The current research shows that, R. intestinalis is a suitable next-generation probiotic considering its probiotic properties and safety.

[E.faecium QH06 alleviates TNBS-induced colonic mucosal injury in rats]

OBJECTIVE

To investigate the effect of Enterococcus faecium QH06 on TNBS-induced ulcerative colitis (UC) in rats and explore the mechanisms in light of intestinal flora and intestinal immunity.

METHODS

Thirty-six male Wistar rats were randomized equally into control group, UC model group, and E.faecium QH06 intervention group. The rats in the latter two groups were subjected to colonic enema with 5% TNBS/ethanol to induce UC, followed by treatment with intragastric administration of distilled water or E.faecium QH06 at the dose of 0.21 g/kg. After 14 days of treatment, the rats were examined for colon pathologies with HE staining. The mRNA and protein expression levels of IL-4, IL-10, IL-12, and IFN-γ in the colon tissues were detected using RT-qPCR and ELISA, and the expression of TLR2 protein was detected with immunohistochemistry and ELISA. Illumina Miseq platform was used for sequencing analysis of the intestinal flora of the rats with bioinformatics analysis. The correlations of the parameters of the intestinal flora with the expression levels of TLR2 and cytokines were analyzed.

RESULTS

The rats with TNBS- induced UC showed obvious weight loss (P < 0.01) and severe colon tissue injury with high pathological scores (P < 0.01). The protein expression levels of IFN-γ, IL-12, and TLR2 (P < 0.01) and the mRNA expression levels of IFN-γ, IL-12 and IL-10 (P < 0.05) were significantly increased in the colon tissues of the rats with UC. Illumina Miseq sequence analysis showed that in UC rats, the Shannon index (P < 0.05) ACE (P < 0.01)and Chao (P < 0.05) index for the diversity of intestinal flora both decreased with a significantly increased abundance of Enterobacteriaceae (P < 0.01) and a lowered abundance of Burkholderiaceae (P < 0.05). Compared with the UC rats, the rats treated with E. faecium QH06 showed obvious body weight gain (P < 0.05), lessened colon injuries, lowered pathological score of the colon tissue (P < 0.05), decreased protein expressions of IFN- γ, IL- 12, and TLR2 and mRNA expressions of IFN- γ and IL-12 (P < 0.01 or 0.05), and increased protein expressions of IL- 4 (P < 0.05). The Shannon index ACE (P < 0.05) and Chao (P < 0.05) index of intestinal microflora were significantly increased, the abundance of Enterobacteriaceae was lowered and that of Burkholderiaceae and Rikenellaceae was increased in E.faecium QH06- treated rats (P < 0.01 or 0.05). Correlation analysis showed that IFN-γ was positively correlated with the abundance of Enterobacteriaceae, and IFN-γ was negatively correlated with the abundance of Prevotellaceae, Desulfovibrionaceae, norank_o_Mollicutes_RF39 and Clostridiales_vadinBB60_group; TLR2 was negatively correlated with Clostridiales_vadinBB60_group, norank_o_Mollicutes_RF39 and Prevotellaceae.

CONCLUSION

E.faecium QH06 can alleviate TNBS-induced colonic mucosal injury in rats, and its effect is mediated possibly by increasing the abundance of SCFA-producing bacteria such as Prevotellaceae and inhibiting abnormal immune responses mediated by TLR2.

Proteomics reveal the protective effects of chlorogenic acid on Enterococcus faecium Q233 in a simulated pro-oxidant colonic environment

Certain phytochemicals have been found to promote the beneficial effects of probiotic bacteria although the molecular mechanisms of such interactions are poorly understood. The objective of the present study was to evaluate the impact of the exposure to 0.5 mM chlorogenic acid (CA) on the redox status and proteome of Enterococcus faecium isolated from cheese and challenged with 2.5 mM hydrogen peroxide (H₂O₂). The bacterium was incubated in anaerobic conditions for 48 h at 37 °C. CA exposure led to a more intense oxidative stress and accretion of bacterial protein carbonyls than those induced by H₂O₂. The oxidative damage to bacterial proteins was even more severe in the bacterium treated with both CA and H₂O₂, yet, such combination led to a strengthening of the antioxidant defenses, namely, a catalase-like activity. The proteomic study indicated that H₂O₂ caused a decrease in energy supply and the bacterium responded by reinforcing the membrane and wall structures and counteracting the redox and pH imbalance. CA stimulated the accretion of proteins related to translation and transcription regulators, and hydrolases. This phytochemical was able to counteract certain proteomic changes induced by H₂O₂ (i.e. increase of ATP binding cassete (ABC) transporter complex) and cause the increase of Rex, a redox-sensitive protein implicated in controlling metabolism and responses to oxidative stress. Although this protection should be confirmed under in vivo conditions, such effects point to benefits in animals or humans affected by disorders in which oxidative stress plays a major role.

Genomic analysis of Enterococcus durans NT21, a putative bacteriocin-producing isolate

Enterococcus species are a long-standing and non-pathogenic commensal bacterium, representing an important part of the normal. Enterococcus durans is a rarely isolated species from animals and humans, and it was a tiny constituent of human oral cavity and animal intestinal flora, as well as animal-derived foods, particularly dairy products. This study evaluated the security of our strain E. durans NT21 by using whole-genome sequencing (WGS), physicochemical features, and antimicrobial activity. The complete genomic of our strain Enterococcus durans NT21was sequenced and analyzed by using several bioinformatics tools to identify bacteriocin genes, virulence genes, antibiotic resistance genes, Crispr-Cas and pathogenicity islands. The results showed that our strain NT21 lacks the presence of virulence genes, pathogenicity islands, plasmids and has only two antibiotic resistance genes. On the other hand, it produces three bacteriocin-like inhibitory substances (Enterolysin A, P and L50a). It has six gene-encoded Crisper-Cas and one cluster Crispr-Cas gene. According to our findings, E. durans NT21 is a possible probiotic strain that is safe for both human and animal use.