Evaluating the Safety of Potential Probiotic Enterococcus durans KLDS6.0930 Using Whole Genome Sequencing and Oral Toxicity Study

Identification and Safety Assessment of Enterococcus casseliflavus KB1733 Isolated from Traditional Japanese Pickle Based on Whole-Genome Sequencing Analysis and Preclinical Toxicity Studies

The present study involves the precise identification and safety evaluation of Enterococcus casseliflavus KB1733, previously identified using 16S rRNA analysis, through whole-genome sequencing, phenotypic analysis, and preclinical toxicity studies. Analyses based on the genome sequencing data confirm the identity of KB1733 as E. casseliflavus and show that the genes related to vancomycin resistance are only present on the chromosome, while no virulence factor genes are present on the chromosome or plasmid. Phenotypic analyses of antibiotic resistance and hemolytic activity also indicated no safety concerns. A bacterial reverse mutation test showed there was no increase in revertant colonies of heat-killed KB1733. An acute toxicity test employing heat-killed KB1733 at a dose of 2000 mg/kg body weight in rats resulted in no deaths and no weight gain or other abnormalities in the general condition of the animals, with renal depression foci and renal cysts only occurring at the same frequency as in the control. Taking the background data into consideration, the effects on the kidneys observed in the current study were not caused by KB1733. Our findings suggest that KB1733 is non-pathogenic to humans/animals, although further studies involving repeated oral toxicity tests and/or clinical tests are required.

Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China

Microbial communities inhabiting sedimentary environments in river source regions serve as pivotal indicators of pristine river ecosystems. While the correlation between antibiotic resistome and pathogenicity with core gut bacteria in humans is well established, there exists a significant knowledge gap concerning the interaction of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) with specific microbes in river source basins, often referred to as "terrestrial gut". Understanding the microbial composition, including bacteria and resident genetic elements such as ARGs, HPB, Mobile Genetic Elements (MGEs), and Virulence Factors (VFs), within natural habitats against the backdrop of global change, is imperative. To address this gap, an enrichment-based culturomics complementary along with metagenomics was conducted in this study to characterize the microbial biobank and provide preliminary ecological insights into profiling the dissemination of ARGs in the Lancang River Source Basin. Based on our findings, in the main stream of the Lancang River Source Basin, 674 strains of bacteria, comprising 540 strains under anaerobic conditions and 124 under aerobic conditions, were successfully isolated. Among these, 98 species were identified as known species, while 4 were potential novel species. Of these 98 species, 30 were HPB relevant to human health. Additionally, bacA and bacitracin emerged as the most abundant ARGs and antibiotics in this river, respectively. Furthermore, the risk assessment of ARGs predominantly indicated the lowest risk rank (Rank Ⅳ) in terms of endangering human health. In summary, enrichment-based culturomics proved effective in isolating rare and unknown bacteria, particularly under anaerobic conditions. The emergence of ARGs showed limited correlation with MGEs, indicating minimal threats to human health within the main stream of the Lancang River Source Basin.

Enterococcus durans 98D alters gut microbial composition and function to improve DSS-induced colitis in mice

Enterococcus durans, is a potential functional strain with the capacity to regulate intestinal health and ameliorate colonic inflammation. However, the strain requires further investigation regarding its safety profile and potential mechanisms of colitis improvement. In this study, the safety of E. durans 98D (Ed) as a potential probiotic was studied using in vitro methods. Additionally, a dextran sulfate sodium (DSS)-induced murine colitis model was employed to investigate its impact on the intestinal microbiota and colitis. In vitro antimicrobial assays revealed Ed sensitivity to common antibiotics and its inhibitory effect on the growth of Escherichia coli O157, Streptococcus pneumoniae CCUG 37328, and Staphylococcus aureus ATCC 25923. To elucidate the functional properties of Ed, 24 weight-matched 6-week-old female C57BL/6J mice were randomly divided into three groups (n = 8): NC group, Con group (DSS), and Ed group (DSS + Ed). Ed administration demonstrated a protective effect on colitis mice, as evidenced by improvements in body weight, colonic length, reduced disease activity index, histological scores, diminished splenomegaly, and decreased goblet cell loss. Furthermore, Ed downregulated the expression of the pro-inflammatory cytokine genes (IL-6, IL-1β, and TNF-α) and upregulated the expression of the anti-inflammatory cytokine gene IL-10. The 16S rRNA gene sequencing revealed significant alterations in microbial α-diversity, with principal coordinate analysis indicating distinct differences in microbial composition among the three groups. At the phylum level, the relative abundance of Actinomycetota significantly increased in the Ed-treated group. At the genus level, Ed treatment markedly elevated the relative abundance of Paraprevotella, Rikenellaceae_RC9, and Odoribacter in DSS-induced colitis mice. In conclusion, Ed exhibits potential as a safe and effective therapeutic agent for DSS-induced colitis by reshaping the colonic microbiota.

Pre-clinical safety and toxicity assessment of Limosilactobacillus fermentum NCDC 400 in murine model

Comprehensive safety assessment of potential probiotic strains is crucial in the selection of risk-free strains for clinical translation. This study aimed to evaluate the biosafety of Limosilactobacillus fermentum NCDC 400, a potential probiotic strain, using oral toxicity tests in a Swiss albino mouse model. Mice were orally gavaged with low (108 CFU/mouse/day) and high (1010 CFU/mouse/day) doses of NCDC 400 for 14 (acute), 28 (subacute), and 90 (subchronic) days to assess behavioral, hematological, biochemical, immunological, and histological effects. The administration of NCDC 400 did not result in any observable adverse effects on general health parameters, including body weight, feed and water intake, and organ indices. Hematological and biochemical parameters, such as glucose, serum enzymes, urea, creatinine, serum minerals, total serum proteins, and lipid profile, remained largely unaffected by the test strain. Notably, NCDC 400 administration led to a significant reduction in harmful intestinal enzymes and improvement in gut health indices, as indicated by fecal pH, lactate, ammonia, and short-chain fatty acids. There were no instances of bacterial translocation of NCDC 400 to blood or extra-intestinal organs. Immune homeostasis was not adversely affected by repeated exposure to NCDC 400 in all three oral toxicity studies. Histopathological examination revealed no strain-related changes in various tissues. Based on these findings, a dose of 1010 CFU/mouse/day was considered as the No Observable Effect Level (NOEL) in healthy mice. In conclusion, this study demonstrates the safe and non-toxic behavior of L. fermentum NCDC 400. The results support and ensure the safety and suitability for clinical trials and eventual translation into clinical practice as potential probiotic.

Genome-based taxonomic identification and safety assessment of an Enterococcus strain isolated from a homemade dairy product

The aim of this study was to explore the taxonomic identification and evaluate the safety of a bacterium, Enterococcus lactis IDCC 2105, isolated from homemade cheese in Korea, using whole genome sequence (WGS) analysis. It sought to identify the species level of this Enterococcus spp., assess its antibiotic resistance, and evaluate its virulence potential. WGS analysis confirmed the bacterial strain IDCC 2105 as E. lactis and identified genes responsible for resistance to erythromycin and clindamycin, specifically msrC, and eatAv, which are chromosomally located, indicating a minimal risk for horizontal gene transfer. The absence of plasmids in E. lactis IDCC 2105 further diminishes the likelihood of resistance gene dissemination. Additionally, our investigation into seven virulence factors, including hemolysis, platelet aggregation, biofilm formation, hyaluronidase, gelatinase, ammonia production, and β-glucuronidase activity, revealed no detectable virulence traits. Although bioinformatic analysis suggested the presence of collagen adhesion genes acm and scm, these were not corroborated by phenotypic virulence assays. Based on these findings, E. lactis IDCC 2105 presents as a safe strain for potential applications, contributing valuable information on its taxonomy, antibiotic resistance profile, and lack of virulence factors, supporting its use in food products.

Complete genome sequence of Enterococcus faecium strain AK_C_05 with potential characteristics applicable in livestock industry

The Enterococcus faecium (E. faecium) strain AK_C_05 was isolated from cheonggukjang, the Korean traditional food, collected from a local market in South Korea. In this report, we presented the complete genome sequence of E. faecium strain AK_C_05. The genome of E. faecium strain AK_C_05 genome consisted of one circular chromosome (2,691,319 bp) with a guanine + cytosine (GC) content of 38.3% and one circular plasmid (177,732 bp) with a GC content of 35.48%. The Annotation results revealed 2,827 protein-coding sequences (CDSs), 18 rRNAs, and 68 tRNA genes. It possesses genes, which encodes enzymes such as alpha-galactosidase (EC 3.2.1.22), beta-glucosidase (EC 3.2.1.21) and alpha-L-arabinofuranosidase (EC 3.2.1.55) enabling efficient utilization of carbohydrates. Based on Clusters of Orthologous Groups analysis, E. faecium strain AK_C_05 showed specialization in carbohydrate transport and metabolism indicating the ability to generate energy using a variety of carbohydrates.

Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages

The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.

Genetic and phenotypic assessments for the safety of probiotic Bacillus clausii 088AE

In this study, we report on whole genome sequence analysis of clinically documented, commercial probiotic Bacillus clausii 088AE and genome features contributing to probiotic properties. The whole genome sequence of B. clausii 088AE generated a single scaffold of 4,598,457 bp with 44.74 mol% G + C. This assembled genome sequence annotated by the RAST resulted in 4371 coding genes, 75 tRNAs, and 22 rRNAs. Gene ontology classification indicated 39.5% proteins with molecular function, 44.24% cellular component, and 16.25% proteins involved in biological processes. In taxonomic analysis, B. clausii 088AE shared 99% identity with B. clausii DSM 8716. The gene sequences related to safety and genome stability such as antibiotic resistance (840), virulence factors (706), biogenic amines (1), enterotoxin (0), emetic toxin (0), lanthipeptides (4), prophage (4) and clustered regularly interspaced short palindromic repeats (CRISPR) sequences (11), were identified and evaluated for safety and functions. The absence of functional prophage sequences and the presence of CRISPR indicated an advantage in genome stability. Moreover, the presence of genome features contributing to probiotic characteristics such as acid, and bile salt tolerance, adhesion to the gut mucosa, and environmental resistance ensure the strains survivability when consumed as a probiotic. In conclusion, the absence of risks associated with sequences/genes in the B. clausii 088AE genome and the presence of essential probiotic traits confirm the strain to be safe for use as a probiotic.

Physicochemical, rheological, and bioactive properties of exopolysaccharide produced by a potential probiotic Enterococcus faecalis 84B

Exopolysaccharides (EPS) have attracted a great interest due to their potential health-promoting properties and industrial applications. This study aimed to investigate the physicochemical, rheological, and biological properties of an EPS produced by a potential probiotic strain Enterococcus faecalis 84B. The results show that the extracted EPS, designated EPS-84B, had an average molecular weight of 604.8 kDa, particles size diameter of 322.0 nm, and mainly composed of arabinose and glucose with a molar ratio of 1:2. Furthermore, EPS-84B exhibited a shear-thinning behavior and had a high melting point. The rheological properties of EPS-84B were strongly influenced by the type of salt than by the pH value. EPS-84B displayed ideal viscoelastic properties, with both viscous and storage moduli increasing with frequency. The antioxidant activity of EPS-84B at a concentration of 5 mg/mL was 81.1 % against DPPH and 35.2 % against ABTS. At 5 mg/mL, the antitumor activity of EPS-84B against Caco-2 and MCF-7 cell lines was 74.6 and 38.6 %, respectively. In addition, the antidiabetic activity of EPS-84B towards α-amylase and α-glucosidase was 89.6 and 90.0 %, respectively at 100 μg/mL. The inhibition of foodborne pathogens by EPS-84B was up to 32.6 %. Overall, EPS-84B has promising properties that could be utilized in food and pharmaceutical industries.

Preparation, characteristic and anti-inflammatory effect of selenium nanoparticle-enriched probiotic strain Enterococcus durans A8-1

BACKGROUND

Elemental selenium, a new type of selenium supplement, can be biosynthesized via microorganisms. This study is to characterize a patent probiotic bacteria Enterococcus durans A8-1, capable of reducing selenite (Se⁶⁺ or Se⁴⁺) to elemental selenium (Se⁰) with the formation of Se nanoparticles (SeNPs).

METHODS

The selenium nanoparticles synthesized from A8-1 were characterized using scanning electron microscopy (SEM), transmission electron microscopy (TEM), energy dispersive spectroscopy (EDS), and X-ray photoelectron energy (XPS). The Caco2 cells were used to investigate the effects of Se-enriched A8-1 on the viability, membrane integrity, and the regulation of cellular inflammation through MTT and ELISA assays. The selenium-enriched metabolic function of A8-1 was analyzed by transcriptome sequencing.

RESULTS

E. durans A8-1 has the ability to synthesize intracellular SeNPs that are incubated with 60 mg/L sodium selenite for 18 h at 37 °C with 7 % inoculum under aerobic conditions. The selenium-enriched transformation rate increased to 43.46 %. After selenium enrichment, there were no significant morphological changes in E. durans A8-1 cells. The cells also exhibited no cytotoxicity when incubated with Caco-2 cells, and increased cellular proliferation. Furthermore, Se-enriched A8-1 cells antagonize the adhesion of S. typhimurium ATCC14028 onto the surface of Caco-2 cells protecting cell membrane integrity and was assessed by measuring LDH and AKP activities (P <0.001, P <0.001). Moreover, Se-enriched A8-1 could protect Caco-2 cells from inflammation induced by lipopolysaccharide and help the cells alleviate the inflammation through the reduced expression of cytokine IL-8 (P = 0.0012, P <0.001) and TNF-α (P <0.001, P <0.001). Based on transcriptome sequencing in Se-enriched E. durans A8-1 cells, there were 485 up-regulated genes and 322 down-regulated genes (P_adj < 0.05). There were 19 predicted up-regulated genes that are highly related to the potential selenium metabolism pathway, which focuses on the transportation of Na₂SeO₃ by membrane proteins, and gradually reduces Na₂SeO₃ to elemental selenium aggregates that are deposited onto the membrane surface via the intracellular redox response.

CONCLUSION

E. durans A8-1 could convert extracellular selenite into intracellular biological SeNPs via redox pathway with strong selenium-rich metabolism, and its biological SeNPs have anti-inflammatory properties, which have the potential for the development of composite selenium nanomaterials and can be further studied for the function of SeNPs with potential applications.

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.

Isolation and Characterization of Human Intestinal Bacteria Cytobacillus oceanisediminis NB2 for Probiotic Potential

Systemic characterization of the human gut microbiota highlighted its vast therapeutic potential. Despite having enormous potential, the non-availability of their culture representatives created a bottleneck to understand the concept of microbiome-based therapeutics. The present study is aimed to isolate and evaluate the probiotic potential of a human gut isolate. Physiochemical, morphological, and phylogenetic characterization of a human gut isolate identifies it as a rod-shaped gram-negative microbe taxonomically affiliated with the Cytobacillus genus, having an optimal growth at 37°C in a partially alkaline environment (pH 8.0). This human gut isolate showed continuous growth in the presence of salts (up to 7% NaCl and 10% KCl), antibiotics, metals and metalloids [silver nitrate (up to 2 mM); lead acetate (up to 2 mM); sodium arsenate (up to 10 mM); potassium dichromate (up to 2 mM)], gastric and intestinal conditions, diverse temperature (25–50°C), and pH (5–9) conditions making it fit to survive in the highly variable gut environment. Genomic characterization identified the presence of gene clusters for diverse bio-catalytic activity, stress response, and antimicrobial activity, as well as it indicated the absence of pathogenic gene islands. A combination of functional features like anti-amylase, anti-lipase, glutenase, prolyl endopeptidase, lactase, bile salt hydrolase, cholesterol oxidase, and anti-pathogenic activity is indicative of its probiotic potential in various disorders. This was further substantiated by the CaCo-2 cell line assay confirming its cellular adherence and biosafety. Conclusively, human gut isolate possessed significant probiotic potential that can be used to promote animal and human health.

Revealing Probiotic Potential of Enterococcus Strains Isolated From Traditionally Fermented Chhurpi and Healthy Human Gut

In this study, the two lactic acid bacterial strains Enterococcus durans and Enterococcus lactis previously isolated from soft chhurpi, a traditionally fermented milk product prepared by the indigenous community of Sikkim Himalayas and healthy human gut were used. In this study, we attempted to investigate the probiotic attributes, safety, and health beneficial role, and hypercholesterolemia of Enterococcus durans and Enterococcus lactis. Both probiotic potential strains showed good hypocholesterolemic activity in vitro along with tolerance to acid pH (2 and 2.5), tolerance to three bile salts, oxbile, cholic acid, and taurocholic acid (0.5 and 1%), presence of BSH enzyme and its activity, and cell surface adherence. On assessing for safety, both LAB strains were sensitive to antibiotics and exhibited no hemolytic activity. The probiotic strains were tested in vivo in the Sprague–Dawley rats which were divided into five experimental groups: Normal Control (ND), probiotic strain Enterococcus durans HS03 (BSH-negative) and high-cholesterol diet (HCD1), probiotic strain Enterococcus lactis YY1 (BSH-positive) and high-cholesterol diet (HCD2), and a combination of both strains and high-cholesterol diet (HCD3) and Negative Control (HCD). The probiotic-treated groups HCD1, HCD2, and HCD3 showed a decrease in serum cholesterol levels up to 22.55, 6.67, and 31.06%; the TG and VLDL concentrations were 25.39, 26.3, and 33.21%; reduction in LDL-cholesterol was 33.66, 28.50, and 35.87%; and increase of HDL was 38.32, 47.9, and 41.92%. Similarly, the effects of total cholesterol and TG in the liver, kidney and liver histopathology, liver and body lipid index, and oxidative stress in rat liver were also studied. The fecal lactobacilli were more in the samples of the probiotic-treated groups and their fecal coliform and E. coli counts decreased relatively as compared to the control groups in 0, 7, 14, and 21 days. This is the first report on the probiotic potential of Enterococcus durans HS03 and Enterococcus lactis YY1 strains that gives a new insight into the cholesterol-lowering and probiotic product development with wide health attributes.

Electrostatically self-assembled filamentous sodium alginate/ε-polylysine fiber with antibacterial, bioadhesion and biocompatible in suturing wound

In the work, a novel filamentou sodium alginate (SA) /ε-polylysine (PL) fiber with excellent mechanical properties and controllable sizes is prepared in an efficient and environmentally friendly manner via continuous pulling of an electrostatically assembled SA/PL composites at the contact interface of aqueous solutions of cationic polyelectrolyte ε-PL and anionic natural polysaccharide SA. The SA/PL fiber exhibits good antibacterial activity, low cytotoxicity, anti-hemolysis, bioadhesion, and environmental friendliness due to its natural raw materials and green preparation process. In vivo experiments have shown that the SA/PL fiber can promote the healing and repair of skin wounds on the backs of mice via resistance to pathogen infection, reduction of inflammation, and anti-allogeneic allergy of the wound. In summary, these results demonstrate that the SA/PL fiber is a green and biosafe multifunctional natural polymer material, with potential applications in suturing wound.

A potentially probiotic strain of Enterococcus faecalis from human milk that is avirulent, antibiotic sensitive, and nonbreaching of the gut barrier

Human milk is a key source of promising probiotic lactic acid bacteria. The Enterococcus species, because of their dual commensal and pathogenic nature, demand critical safety analysis to establish them as probiotic candidates. In this study, eighteen E. faecalis strains from human milk of mothers living in Pakistan were typed at the strain level by riboprinting. The typed strains were then evaluated in vitro for physiological safety and the presence of transmissible antibiotic resistance genes, adhesion genes, biogenic amines, and virulence factors. Selected strains were then checked for tolerance to gastrointestinal acid and bile as criteria for probiotic efficacy. Molecular typing revealed that the strains fell into five distinct clusters or ribotypes. Testing revealed that they were non-hemolytic; however, all strains had gelatinase activity except NPL-493. The isolates were susceptible to most clinically important antibiotics except streptomycin. Molecular screening for antibiotic resistance genes, adhesion genes, biogenic amines, and virulence factors indicated that none of the strains possessed resistance genes for aminoglycosides, vancomycin, bacitracin, tetracycline, or clindamycin. Most virulence factors were absent except for the genes gelE and efaAs associated with gut adhesion and translocation, which were present in all except NPL-493. Strain NPL-493 was the most promising probiotic candidate demonstrating significant tolerance to the acid, bile, and digestive enzymes in the human GIT and antibacterial activity against multiple pathogens. The study concluded that E. faecalis NPL-493 from human milk was safe among all the strains and could be considered a potential probiotic.

Enterococci as Dominant Xylose Utilizing Lactic Acid Bacteria in Eri Silkworm Midgut and the Potential Use of Enterococcus hirae as Probiotic for Eri Culture

Simple Summary

This study focused on isolation and identification of xylose utilizing lactic acid bacteria from the midgut of Eri silkworm to understand their characteristics such as tannin tolerance, production of cellulolytic enzymes, and antimicrobial activity against insect pathogenic bacteria. The Enterococcus was found as the dominant genus among xylose utilizing lactic acid bacteria. Within this genus, Enterococcus hirae SX2 showed the potential to be used as a probiotic in Eri silkworm culture due to its tannin tolerance and antimicrobial activity against insect pathogenic bacteria. The trial experiment for applying live E. hirae SX2 supplemented to castor leaves in Eri silkworm rearing showed a positive effect for improving larval weight and survival. These findings led to the development of a new probiotic for Eri culture and also could be the experimental model for screening of the potential probiotic from mulberry silkworm (Bombyx mori).

Abstract

A total of 51 pentose utilizing lactic acid bacteria (LAB) were isolated from acid-forming bacteria in the midgut of healthy mature Eri silkworm using de Man, Rogosa and Sharpe (MRS) agar containing 10 g/L xylose (MRS-xylose) as the carbon source supplemented with 0.04% (w/v) bromocresol purple. Further analysis of 16S rRNA gene sequences revealed the highest prevalence of up to 35 enterococci isolates, which included 20 isolates of Enterococcus mundtii, followed by Entercoccus faecalis (eight isolates), Weissella cibaria (four isolates), Enterococcus hirae (two isolates), Enterococcus lactis (one isolate), and Enterococcus faecium (one isolate). All 51 LAB isolates showed positive growth on MRS containing a range of polysaccharides as the sole carbon source. All isolates were able to grow and form clear zones on MRS supplemented with 1 g/L xylose, while E. faecalis SC1, E. faecalis SCT2, and E. hirae SX2 showed tannin tolerance ability up to 5 g/L. Moreover, five isolates showed antimicrobial activity against Eri silkworm pathogens, including Bacillus cereus, Staphylococcus aureus, and Proteus vulgaris, with E. hirae SX2 having the highest inhibitory effect. Supplementation of live E. hirae SX2 on castor leaves significantly improved the weight and reduced the silkworm mortality when compared with the control group (p < 0.05). This cocci LAB can be considered as the new probiotic for Eri culture. Additionally, this finding presented the perspective of non-mulberry silkworm that could also be used as the model for further applying to new trends of the sericulture industry.

Probiotic Potential Analysis and Safety Evaluation of Enterococcus durans A8-1 Isolated From a Healthy Chinese Infant

To evaluate the probiotic characteristics and safety of Enterococcus durans isolate A8-1 from a fecal sample of a healthy Chinese infant, we determined the tolerance to low pH, survival in bile salts and NaCl, adhesion ability, biofilm formation, antimicrobial activity, toxin gene distribution, hemolysis, gelatinase activity, antibiotic resistance, and virulence to Galleria mellonella and interpreted the characters by genome resequencing. Phenotypically, E. durans A8-1 survived at pH 5.0 in 7.0% NaCl and 3% bile salt under aerobic and anaerobic condition. The bacterium had higher adhesion ability toward mucin, collagen, and Bovine Serum Albumin (BSA) in vitro and showed high hydrophobicity (79.2% in chloroform, 49.2% in xylene), auto-aggregation activity (51.7%), and could co-aggregate (66.2%) with Salmonella typhimurium. It had adhesion capability to intestinal epithelial Caco-2 cells (38.74%) with moderate biofilm production and antimicrobial activity against several Gram-positive pathogenic bacteria. A8-1 can antagonize the adhesion of S. typhimurium ATCC14028 on Caco-2 cells to protect the integrity of the cell membrane by detection of lactate dehydrogenase (LDH) and AKP activities. A8-1 also helps the cell relieve the inflammation induced by lipopolysaccharide by reducing the expression of cytokine IL-8 (P = 0.002) and TNF-α (P > 0.05), and increasing the IL-10 (P < 0.001). For the safety evaluation, A8-1 showed no hemolytic activity, no gelatinase activity, and had only asa1 positive in the seven detected virulence genes in polymerase chain reaction (PCR), whereas it was not predicted in the genome sequence. It was susceptible to benzylpenicillin, ampicillin, ciprofloxacin, levofloxacin, moxifloxacin, tigecycline, nitrofurantoin, linezolid, vancomycin, erythromycin, and quinupristin/dalofopine except clindamycin, which was verified by the predicted lasA, lmrB, lmrC, and lmrD genes contributing to the clindamycin resistance. The virulence test of G. mellonella showed that it had toxicity lower than 10% at 1 × 10⁷ CFU. According to the results of these evaluated attributes, E. durans strain A8-1 could be a promising probiotic candidate for applications.

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.

Safety Evaluation of Lactobacillus delbrueckii subsp. lactis CIDCA 133: a Health-Promoting Bacteria

Lactobacillus delbrueckii subsp. lactis CIDCA is a new potential probiotic strain whose molecular basis attributed to the host's benefit has been reported. This study investigated the safety aspects of Lactobacillus delbrueckii subsp. lactis CIDCA 133 based on whole-genome sequence and phenotypic analysis to avoid future questions about the harmful effects of this strain consumption. Genomic analysis showed that L. delbrueckii subsp. lactis CIDCA 133 harbors virulence, harmful metabolites, and antimicrobial resistance-associated genes. However, none of these genetic elements is flanked or located within prophage regions and plasmid sequence. At a phenotypic level, it was observed L. delbrueckii subsp. lactis CIDCA 133 antimicrobial resistance to aminoglycosides streptomycin and gentamicin antibiotics, but no hemolytic and mucin degradation activity was exhibited by strain. Furthermore, no adverse effects were observed regarding mice clinical and histopathological analysis after the strain consumption (5 × 10⁷ CFU/mL). Overall, these findings reveal the safety of Lactobacillus delbrueckii subsp. lactis CIDCA 133 for consumption and future probiotic applications.

Bifidobacterium dentium N8 with potential probiotic characteristics prevents LPS-induced intestinal barrier injury by alleviating the inflammatory response and regulating the tight junction in Caco-2 cell monolayers

The intestinal barrier is vital for preventing inflammatory bowel disease (IBD). This study aimed to investigate the potential mechanism behind the protective effects of B. dentium N8 on the intestinal barrier using the lipopolysaccharide (LPS)-induced Caco-2 cells model. Our probiotic validation results showed that B. dentium N8 had a higher adhesion ability and a more substantial inhibition effect on Escherichia coli ATCC 25922 adhesion to HT-29 cells. Regarding the epithelial integrity, B. dentium N8 significantly increased the trans-epithelial electrical resistance (TEER) value and decreased the paracellular permeability of Caco-2 cells stimulated by lipopolysaccharide (LPS). In addition, B. dentium N8 significantly increased ZO-1, occludin, and claudin-1 mRNA expression. B. dentium N8 downregulated the mRNA expression level of TLR4 and pro-inflammatory cytokines (TNF-α, IL-1β, IL-6). Furthermore, B. dentium N8 had a better protective effect on the intestinal barrier than that of E7. Comparative genomics of B. dentium N8 and E7 showed B. dentium N8 had the specific genes encoding for adhesion ability and immune system regulation. The findings provide the theoretical basis for B. dentium N8 possessing a protective effect on the intestinal barrier, which indicate that it could be used as a novel therapy for IBD.

Probiotic and Safety Properties Screening of Enterococcus faecalis from Healthy Chinese Infants

The aim of this study was to evaluate the probiotic characteristics and safety of seven Enterococcus faecalis isolates from fecal samples of healthy Chinese infants. We evaluated the isolates' tolerance to low pH, survival in bile salts and NaCl, adhesion ability, biofilm formation, antimicrobial activity, toxin gene distribution, hemolysis, gelatinase activity, antibiotic resistance, and virulence to Galleria mellonella. All strains survived at pH 5.0, in 7.0% NaCl, and in 3% bile salt. Adhesion to Caco-2 cells was above 10%. Strain A3-1 had higher adhesion ability toward mucin, collagen, and BSA in vitro, better antibacterial activity, and the strongest biofilm production. We detected seven virulence genes with a distribution of asa1 (100%), cylA (71.4%), esp (85.7%), hyl (14.3%), gelE (85.7%), ace (42.9%), and agg (71.4%). Although all strains were γ-hemolytic, none showed gelatinase activity based on physiological activity detection. All isolates were susceptible to benzylpenicillin, ampicillin, ciprofloxacin, levofloxacin, moxifloxacin, tigecycline, nitrofurantoin, linezolid, and vancomycin; they were not susceptible to erythromycin, quinupristin/dalofopine, and clindamycin. The virulence test of G. mellonella showed that, except for strains 106-1 and 113-1, the other strains had toxicity lower than 10%. Strain A3-1 may have the greatest potential to be developed as a probiotic.

Next Generation Probiotics for Neutralizing Obesogenic Effects: Taxa Culturing Searching Strategies

The combination of diet, lifestyle, and the exposure to food obesogens categorized into "microbiota disrupting chemicals" (MDC) could determine obesogenic-related dysbiosis and modify the microbiota diversity that impacts on individual health-disease balances, inducing altered pathogenesis phenotypes. Specific, complementary, and combined treatments are needed to face these altered microbial patterns and the specific misbalances triggered. In this sense, searching for next-generation beneficial microbes or next-generation probiotics (NGP) by microbiota culturing, and focusing on their demonstrated, extensive scope and well-defined functions could contribute to counteracting and repairing the effects of obesogens. Therefore, this review presents a perspective through compiling information and key strategies for directed searching and culturing of NGP that could be administered for obesity and endocrine-related dysbiosis by (i) observing the differential abundance of specific microbiota taxa in obesity-related patients and analyzing their functional roles, (ii) developing microbiota-directed strategies for culturing these taxa groups, and (iii) applying the successful compiled criteria from recent NGP clinical studies. New isolated or cultivable microorganisms from healthy gut microbiota specifically related to obesogens' neutralization effects might be used as an NGP single strain or in consortia, both presenting functions and the ability to palliate metabolic-related disorders. Identification of holistic approaches for searching and using potential NGP, key aspects, the bias, gaps, and proposals of solutions are also considered in this review.

Assessment of Safety and Probiotic Traits of Enterococcus durans OSY-EGY, Isolated From Egyptian Artisanal Cheese, Using Comparative Genomics and Phenotypic Analyses

An Enterococcus durans strain, designated OSY-EGY, was previously isolated from artisanal cheese. In this work, comparative genomic and phenotypic analyses were utilized to assess the safety characteristics and probiotic traits of the bacterium. The comparative genomic analysis revealed that the strain is distantly related to potentially pathogenic Enterococcus spp. The genome was devoid of genes encoding acquired antibiotic resistance or marker virulence factors associated with Enterococcus spp. Phenotypically, the bacterium is susceptible to vancomycin, ampicillin, tetracycline, chloramphenicol, and aminoglycosides and does not have any hemolytic or gelatinase activity, or cytotoxic effect on Caco-2 cells. Altogether, these findings confirm the lack of hazardous traits in E. durans OSY-EGY. Mining E. durans OSY-EGY genome, for probiotic-related sequences, revealed genes associated with acid and bile salts tolerance, adhesion, competitiveness, antioxidant activitiy, antimicrobial activity, essential amino acids production, and vitamins biosynthesis. Phenotypically, E. durans OSY-EGY was tolerant to acidic pH (3.0), and presence of 0.3% bile salts. The bacterium showed adhesion capability to Caco-2 cells, cholesterol-lowering effect, DPPH scavenging activity, and antimicrobial activity against several Gram-positive pathogenic bacteria. Based on the current work, we propose that E. durans OSY-EGY is a potentially safe strain with desirable probiotic and antimicrobial traits. Thus, the investigated strain could be a promising candidate for several industrial applications.

Molecular detection, phylogenetic analysis, and antibacterial performance of lactic acid bacteria isolated from traditional cheeses, North-West Iran

Lactic acid bacteria (LAB) are candidate probiotic bacteria that can provide health benefits when delivered via functional foods. The purpose of this study was to isolate and characterize LAB from traditional cheeses consumed in north-west regions of Iran. A number of sixty traditional cheeses samples were collected and initially screened as LAB using biochemical and molecular methods. A fragment of 1,540 bp in size of 16s rRNA gene was amplified from 70 bacterial isolates. Restriction fragment length polymorphism (RFLP) was employed to differentiate LAB isolates. LAB isolates generated three different RFLP patterns using HinfI restriction enzyme. Phylogenetic analysis revealed that LAB isolates belonged to three genera including Enterococcus, Lactobacillus, and Lactococcus. Most of the isolated LAB strains belonged to Enterococcus spp. The antimicrobial performance of eight LAB isolates with different RFLP patterns ranged from 6.72 to 14.00 mm. It was concluded that molecular characterization of LAB strains in traditional cheeses will enhance our understanding of traditional food microbiota and will help to find bacterial strains with probiotic potential with great benefit both in health and industry.

High-quality genome sequence assembly of R.A73 Enterococcus faecium isolated from freshwater fish mucus

BACKGROUND

Whole-genome sequencing using high throughput technologies has revolutionized and speeded up the scientific investigation of bacterial genetics, biochemistry, and molecular biology. Lactic acid bacteria (LABs) have been extensively used in fermentation and more recently as probiotics in food products that promote health. Genome sequencing and functional genomics investigations of LABs varieties provide rapid and important information about their diversity and their evolution, revealing a significant molecular basis. This study investigated the whole genome sequences of the Enterococcus faecium strain (HG937697), isolated from the mucus of freshwater fish in Tunisian dams. Genomic DNA was extracted using the Quick-GDNA kit and sequenced using the Illumina HiSeq2500 system. Sequences quality assessment was performed using FastQC software. The complete genome annotation was carried out with the Rapid Annotation using Subsystem Technology (RAST) web server then NCBI PGAAP.

RESULTS

The Enterococcus faecium R.A73 assembled in 28 contigs consisting of 2,935,283 bps. The genome annotation revealed 2884 genes in total including 2834 coding sequences and 50 RNAs containing 3 rRNAs (one rRNA 16 s, one rRNA 23 s and one rRNA 5 s) and 47 tRNAs. Twenty-two genes implicated in bacteriocin production are identified within the Enterococcus faecium R.A73 strain.

CONCLUSION

Data obtained provide insights to further investigate the effective strategy for testing this Enterococcus faecium R.A73 strain in the industrial manufacturing process. Studying their metabolism with bioinformatics tools represents the future challenge and contribution to improving the utilization of the multi-purpose bacteria in food.

Development of Selenized Lactic Acid Bacteria and their Selenium Bioaccummulation Capacity

Selenized lactic acid bacteria (LAB) represent potentially safe and effective sources of selenium (Se), essential for human health, as lactic acid fermentation improves Se bioavailability and reduces its toxicity. LAB are generally recognized as safe (GRAS) and widely used in fermented dairy products. To facilitate selenized LAB implementation as a functional food, we developed and characterized new Se-enriched strains based on the food industry commercial strains Streptococcus thermophilus CCDM 144 and Enterococcus faecium CCDM 922A as representatives of two LAB genera. We evaluated Se bioaccumulation capacity, Se biotransformation and growth ability in the presence of different sodium selenite concentrations (0–50 mg/L), and antioxidant properties (2, 2-diphenyl-1-picrylhydrazyl (DPPH) method) and cell surface hydrophobicity between Se-enriched and parental strains in vitro. Sodium selenite addition did not negatively influence growth of either strain; thus, 50 mg/L was chosen as the optimal concentration based on strain accumulation capacity. Selenization improved the antioxidant properties of both strains and significantly increased their cell surface hydrophobicity (p < 0.05). To our knowledge, this represents the first report of Se-enriched strain hydrophobicity as well as the first on Se speciation in families Enterococcaceae and Streptococcaceae. Moreover, both tested strains demonstrated good potential for Se-enrichment, providing a foundation for further in vitro and in vivo studies to confirm the suitability of these Se-enriched strains for industrial applications.

Complete genome sequence and comparative analysis of two potential probiotics Bacillus subtilis isolated from honey and honeybee microbiomes

BACKGROUND

We have previously isolated Bacillus subtilis HMNig-2 and MENO2 strains, from honey and the honeybee gut microbiome respectively, and demonstrated these strains to produce levansucrase with potential probiotics characteristics. Here we report their complete genome sequence and comparative analysis with other and other B. subtilis strains.

RESULTS

The complete genome sequences of Bacillus subtilis HMNig-2 and MENO2 were de novo assembled from MiSeq paired-end sequence reads and annotated using the RAST tool. Whole-genome alignments were performed to identify functional differences associated with their potential use as probiotics.

CONCLUSIONS

The comparative analysis and the availability of the genome sequence of these two strains will provide comprehensive analysis about the diversity of these valuable Bacillus strains and the possible impact of the environment on bacterial evolution.

SIGNIFICANCE AND IMPACT OF STUDY

We introduce complete genome sequence of two new B. subtilis strains HMNig-2 and MENO2 with probiotic potential and as cell factories for the production of levan and other valuable components for pharmaceutical and industrial applications.

Safety, beneficial and technological properties of enterococci for use in functional food applications - a review

Enterococci are ubiquitous lactic acid bacteria (LAB) that predominantly reside in the gastrointestinal tract of humans and animals but are also widespread in food and the environment due to their robust nature. Enterococci have the paradoxical position of providing several benefits of technological interest in food fermentations but are also considered as opportunistic pathogens capable of causing infection in immunocompromised patients. Several species of the genus have been correlated with disease development in humans such as bacteremia, urinary tract infections, and endocarditis. The pathogenesis of enterococci has been attributed to the increasing incidence of antibiotic resistance and the possession of virulence determinants. On the contrary, enterococci have led to improvements in the aroma, texture, and flavor of fermented dairy products, while their beneficial use as probiotic and protective cultures has also been documented. Furthermore, they have emerged as important candidates for the generation of bioactive peptides, particularly from milk, which provide new opportunities for the development of functional foods and nutraceuticals for human nutrition and health. The detection of pathogenic traits among some species is compromising their use in food applications and subsequently, the genus neither has Generally Regarded as Safe (GRAS) status nor has it been included in the Qualified Presumption of Safety (QPS) list. Nevertheless, the use of certain enterococcal strains in food has been permitted on the basis of a case-by-case assessment. Promisingly, enterococcal virulence factors appear strain specific and food isolates harbor fewer determinants than clinical isolates, while they also remain largely susceptible to clinically relevant antibiotics and thus, have a lower potential for pathogenicity. Ideally, strains considered for use in foods should not possess any virulence determinants and should be susceptible to clinically relevant antibiotics. Implementation of an appropriate risk/benefit analysis, establishment of a strain's innocuity, and consideration for relevant guidelines, legislation, and regulatory aspects surrounding functional food development, may help industry, health-staff and consumers accept enterococci, like other LAB, as important candidates for useful and beneficial applications in food biotechnology.

Risks associated with enterococci as probiotics

Probiotics are naturally occurring microorganisms that confer health benefits by altering host commensal microbiota, modulating immunity, enhancing intestinal barrier function, or altering pain perception. Enterococci are human and animal intestinal commensals that are used as probiotics and in food production. These microorganisms, however, express many virulence traits including cytolysin, proteases, aggregation substance, capsular polysaccharide, enterococcal surface protein, biofilm formation, extracellular superoxide, intestinal translocation, and resistance to innate immunity that can lead to serious hospital-acquired infections. In addition, enterococci are facile in acquiring antibiotic resistance genes to many clinically important antibiotics encoded on a wide variety of conjugative plasmids, transposons, and bacteriophages. The pathogenicity and disease burden caused by enterococci render them poor choices as probiotics. No large, randomized, placebo-controlled clinical trials have demonstrated the safety and efficacy of any enterococcal probiotic. As a result, no enterococcal probiotic has been approved by the United States Food and Drug Administration for the treatment, cure, or amelioration of human disease. In 2007, the European Food Safety Authority concluded that enterococci do not meet the standard for "Qualified Presumption of Safety". Enterococcal strains used or proposed for use as probiotics should be carefully screened for efficacy and safety.

Probiotic Potential and Safety Evaluation of Enterococcus faecalis OB14 and OB15, Isolated From Traditional Tunisian Testouri Cheese and Rigouta, Using Physiological and Genomic Analysis

Lactic acid bacteria (LAB) strains OB14 and OB15 were isolated from traditional Tunisian fermented dairy products, Testouri cheese and Rigouta, respectively. They were identified as Enterococcus faecalis by the MALDI TOF-MS (matrix assisted laser desorption-ionization time of flight mass spectrometry) biotyper system and molecular assays (species-specific PCR). These new isolates were evaluated for probiotic properties, compared to E. faecalis Symbioflor 1 clone DSM 16431, as reference. The bacteria were found to be tolerant to the harsh conditions of the gastrointestinal tract (acidity and bile salt). They were low to moderate biofilm producers, can adhere to Caco-2/TC7 intestinal cells and strengthen the intestinal barrier through the increase of the transepithelial electrical resistance (TER). Susceptibility to ampicillin, vancomycin, gentamicin and erythromycin has been tested using the broth microdilutions method. The results demonstrated that E. faecalis OB14 and OB15 were sensitive to the clinically important ampicillin (MIC = 1 μg/mL) and vancomycin (MIC = 2 μg/mL) antibiotics. However, Whole Genome Sequencing (WGS) showed the presence of tetracycline resistance and cytolysin genes in E. faecalis OB14, and this led to high mortality of Galleria Mellonella larvae in the virulence test. Hierarchical cluster analysis by MALDI TOF-MS biotyper showed that E. faecalis OB15 was closely related to the E. faecalis Symbioflor 1 probiotic strain than to OB14, and this has been confirmed by WGS using the average nucleotide identity (ANI) and Genome-to-Genome Hybridization similarity methods. According to these results, E. faecalis OB15 seems to be reliable for future development as probiotic, in food or feed industry.

Probiotic Properties of Enterococcus Isolated From Artisanal Dairy Products

The present study focused on probiotic characterization and safety evaluation of Enterococcus isolates from different artisanal dairy products. All the isolates exhibited inhibitory activity against several food spoilage bacteria and food-borne pathogens, including Shigella flexneri, Staphylococcus aureus, Listeria monocytogenes, Yersinia enterocolitica, Klebsiella pneumoniae, Escherichia coli, and Bacillus subtilis. The PCR results indicated the presence of at least one enterocin structural gene in all the tested strains. The Enterococcus isolates were further evaluated regarding their safety properties and functional features. The isolates were susceptible to vancomycin, gentamycin, and chloramphenicol. The results of PCR amplification revealed that all the tested isolates harbored none of the tested virulence genes except E. faecalis (ES9), which showed the presence of esp gene. The Enterococcus isolates showed cholesterol lowering properties. The selected isolates showed a high tolerance to low pH, and toward bile salts. They also demonstrated hydrophobicity activity, auto-aggregation, and adhesion ability to the human intestinal Caco-2 cell line. These properties may contribute the bacteria colonizing the gut. This study revealed that the Enterococcus isolates, especially E. durans ES11, ES20 and ES32, might be excellent candidates for production of functional foods to promote health benefits.