Inhibition of Clostridium difficile in Mice Using a Mixture of Potential Probiotic Strains Enterococcus faecalis NM815, E. faecalis NM915, and E. faecium NM1015: Novel Candidates to Control C. difficile Infection (CDI)

Metagenomic nanopore sequencing for exploring the nature of antimicrobial metabolites of Bacillus haynesii

Multidrug-resistant (MDR) pathogens are a rising global health worry that imposes an urgent need for the discovery of novel antibiotics particularly those of natural origin. In this context, we aimed to use the metagenomic nanopore sequence analysis of soil microbiota coupled with the conventional phenotypic screening and genomic analysis for identifying the antimicrobial metabolites produced by promising soil isolate(s). In this study, whole metagenome analysis of the soil sample(s) was performed using MinION™ (Oxford Nanopore Technologies). Aligning and analysis of sequences for probable secondary metabolite gene clusters were extracted and analyzed using the antiSMASH version 2 and DeepBGC. Results of the metagenomic analysis showed the most abundant taxa were Bifidobacterium, Burkholderia, and Nocardiaceae (99.21%, followed by Sphingomonadaceae (82.03%) and B. haynesii (34%). Phenotypic screening of the respective soil samples has resulted in a promising Bacillus isolate that exhibited broad-spectrum antibacterial activities against various MDR pathogens. It was identified using microscopical, cultural, and molecular methods as Bacillus (B.) haynesii isolate MZ922052. The secondary metabolite gene analysis revealed the conservation of seven biosynthetic gene clusters of antibacterial metabolites namely, siderophore lichenicidin VK21-A1/A2 (95% identity), lichenysin (100%), fengycin (53%), terpenes (100%), bacteriocin (100%), Lasso peptide (95%) and bacillibactin (53%). In conclusion, metagenomic nanopore sequence analysis of soil samples coupled with conventional screening helped identify B. haynesii isolate MZ922052 harboring seven biosynthetic gene clusters of promising antimicrobial metabolites. This is the first report for identifying the bacteriocin, lichenysin, and fengycin biosynthetic gene clusters in B. haynesii MZ922052.

Probiotics for Prevention and Treatment of Clostridium difficile Infection

Probiotics have been claimed as a valuable tool to restore the balance in the intestinal microbiota following a dysbiosis caused by, among other factors, antibiotic therapy. This perturbed environment could favor the overgrowth of Clostridium difficile, and in fact, the occurrence of C. difficile-associated infections (CDI) is increasing in recent years. In spite of the high number of probiotics able to in vitro inhibit the growth and/or toxicity of this pathogen, its application for treatment or prevention of CDI is still scarce since there are not enough well-defined clinical studies supporting efficacy. Only a few strains, such as Lactobacillus rhamnosus GG and Saccharomyces boulardii, have been studied in more extent. The increasing knowledge about the probiotic mechanisms of action against C. difficile, some of them reviewed here, makes promising the application of these live biotherapeutic agents against CDI. Nevertheless, more effort must be paid to standardize the clinical studies conducted to evaluate probiotic products, in combination with antibiotics, in order to select the best candidate for C. difficile infections.

Performance responses of lactating Rahmani ewes fed diet supplemented with Enterococcus faecium NRC-3 or Lactobacillus rhamnosus

Production of new types of probiotics for animal nutrition mainly depends on the appropriate bacterial strain and efficient substrate. Therefore, this study aimed to evaluate the impact of two probiotic strains containing 1.2 × 108 (CFU/g), produced on permeate media on performance responses of Rahmani ewes. Thirty early lactating ewes (about 2-3 years old and weighting on average 43.2 ± 0.3 kg) were randomly divided into three groups of 10 animals each using a completely randomized design. The 1st group was fed the basal diet (60% concentrate feed mixture (CFM) + 30% Egyptian clover + 10% bean straw). While the ewes in 2nd and 3rd groups were fed the basal diet + 2 g of Enterococcus faecium NRC-3(EF) and Lactobacillus rhamnosus (LR), respectively for 9 weeks. Ewes' diet supplementation with EF or LR increased (p < 0.05) dry matter, organic matter, crude protein, neutral detergent fiber, acid detergent fiber, and non-structural carbohydrates digestibility compared to ewes of the control group. Glucose, total protein, and albumin concentrations significantly increased in the blood of EF ewes than those of LR and control. Probiotics increased ewes' milk yield as well as milk protein, fat, and lactose yields, but no differences were observed between treatments when milk components were expressed as percentage. Milk fatty acids profile not changed due to EF or LR supplementation. Probiotics (E. faecium and L. rhamnosus) produced on cheese industry waste (permeate) have proven their ability to improve the productive performance of the lactating Rahmani ewes.

Identification, Characterization, and Production Optimization of 6-Methoxy-1H-Indole-2-Carboxylic Acid Antifungal Metabolite Produced by Bacillus toyonensis Isolate OQ071612

Fungal infections currently pose a real threat to human lives. In the current study, soil bacterial isolates were screened for the production of antifungal compounds to combat human fungal pathogens. Notably, the bacterial F1 isolate exhibited antimycotic action towards the Candida albicans ATCC 10231 and Aspergillus niger clinical isolates. By employing phenotypic and molecular techniques, we identified the F1 isolate as the Bacillus toyonensis isolate OQ071612. The purified extract showed stability within a pH range of 6-7 and at temperatures of up to 50 °C. It demonstrated potential antifungal activity in the presence of various surfactants, detergents, and enzymes. The purified extract was identified as 6-methoxy-1H-Indole-2-carboxylic acid using advanced spectroscopic techniques. To optimize the antifungal metabolite production, we utilized response surface methodology (RSM) with a face-centered central composite design, considering nutritional and environmental variables. The optimal conditions were as follows: starch (5 g/L), peptone (5 g/L), agitation rate of 150 rpm, pH 6, and 40 °C temperature. A confirmatory experiment validated the accuracy of the optimization process, resulting in an approximately 3.49-fold increase in production. This is the first documented report on the production and characterization of 6-methoxy-1H-Indole-2-carboxylic acid (MICA) antifungal metabolite from Bacillus toyonensis.

Strategies for applying probiotics in the antibiotic management of Clostridioides difficile infection

The vital role of probiotics in the food field has been widely recognized, and at the same time, probiotics are gradually exhibiting surprising effects in the field of nutraceuticals, especially in regulating gut inflammation and the nutritional environment. As a dietary supplement in clinical nutrition, the coadministration of probiotics with antibiotics model has been applied to prevent intestinal infections caused by Clostridioides difficile. However, the mechanism behind this "bacteria-drug combination" model remains unclear. In particular, the selection of specific probiotic strains, the order of probiotics or antibiotics, and the time interval of coadministration are key issues that need to be further explored and clarified. Here, we focus on the issues mentioned above and give reasonable opinions, mainly including: (1) probiotics are safer and more effective when they intervene after antibiotics have been used; (2) the choice of the time interval between coadministration should be based on the metabolism of antibiotics in the host, differences in probiotic strains, the baseline ecological environment of the host's intestine, and the host immune level; in addition, the selection of the coadministration regime should also take into account factors such as the antibiotic sensitivity of probiotics and dosage of probiotics; and (3) by encapsulating probiotics, combining probiotics with prebiotics, and developing next-generation probiotics (NGPs) and postbiotic formulations, we can provide a more reasonable reference for this type of "bacteria-drug combination" model, and also provide targeted guidance for the application of probiotic dietary supplements in the antibiotic management of C. difficile infection.

In-vitro determination of inhibitory effects of probiotic strains on Clostridioides difficile

Commercial probiotic strains inhibited C. difficile, and other Clostridium cultures with zones 14.2-78.9 mm. The highest inhibition was observed with commercial culture on C. difficile ATCC 700057. Organic acids were the leading cause of inhibition. Probiotic cultures may be used as a support culture or through fermented foods for treatment.

Probiotics: insights and new opportunities for Clostridioides difficile intervention

Clostridioides difficile infection (CDI) is a life-threatening disease caused by the Gram-positive, opportunistic intestinal pathogen C. difficile. Despite the availability of antimicrobial drugs to treat CDI, such as vancomycin, metronidazole, and fidaxomicin, recurrence of infection remains a significant clinical challenge. The use of live commensal microorganisms, or probiotics, is one of the most investigated non-antibiotic therapeutic options to balance gastrointestinal (GI) microbiota and subsequently tackle dysbiosis. In this review, we will discuss major commensal probiotic strains that have the potential to prevent and/or treat CDI and its recurrence, reassess the efficacy of probiotics supplementation as a CDI intervention, delve into lessons learned from probiotic modulation of the immune system, explore avenues like genome-scale metabolic network reconstructions, genome sequencing, and multi-omics to identify novel strains and understand their functionality, and discuss the current regulatory framework, challenges, and future directions.

Evaluation of Safety and Probiotic Potential of Enterococcus faecalis MG5206 and Enterococcus faecium MG5232 Isolated from Kimchi, a Korean Fermented Cabbage

The purpose of this study was to evaluate the genotypic and phenotypic toxicity of Enterococcus faecalis MG5206 and Enterococcus faecium MG5232 isolated from kimchi (fermented vegetable cabbage). In this study, the genotypic toxicity of the strains MG5206 and MG5232 was identified through whole-genome sequencing analysis, and phenotypic virulence, such as susceptibility to antibiotics, hemolytic activity, and gelatinase and hyaluronidase activities, was also evaluated. In addition, the in vivo toxicity of both strains was evaluated using an acute oral administration test in Sprague–Dawley rats. In all the tests, both the strains were determined to be safety by confirming that they did not show antibiotic resistance or virulence factors. In addition, these strains exhibited a low level of autoaggregation ability (37.2–66.3%) and hydrophobicity, as well as a high survival rate in gastrointestinal condition in vitro. Therefore, the safety and high gastrointestinal viability of E. faecalis MG5206 and E. faecium MG5232 suggests that both the strains could be utilized in food as potential probiotics in the future.

Multi-Strain Probiotics: Synergy among Isolates Enhances Biological Activities

The use of probiotics for health benefits is becoming popular because of the quest for safer products with protective and therapeutic effects against diseases and infectious agents. The emergence and spread of antimicrobial resistance among pathogens had prompted restrictions over the non-therapeutic use of antibiotics for prophylaxis and growth promotion, especially in animal husbandry. While single-strain probiotics are beneficial to health, multi-strain probiotics might be more helpful because of synergy and additive effects among the individual isolates. This article documents the mechanisms by which multi-strain probiotics exert their effects in managing infectious and non-infectious diseases, inhibiting antibiotic-resistant pathogens and health improvement. The administration of multi-strain probiotics was revealed to effectively alleviate bowel tract conditions, such as irritable bowel syndrome, inhibition of pathogens and modulation of the immune system and gut microbiota. Finally, while most of the current research focuses on comparing the effects of multi-strain and single-strain probiotics, there is a dearth of information on the molecular mechanisms of synergy among multi-strain probiotics isolates. This forms a basis for future research in the development of multi-strain probiotics for enhanced health benefits.

The mechanisms and safety of probiotics against toxigenic clostridium difficile

INTRODUCTION

Toxigenic Clostridium difficile (C. difficile) is the main cause of antibiotic-associated diarrhea and can induce pseudomembranous colitis and infrequent toxic megacolon, which are potentially fatal. The standard antibiotic therapy for C. difficile infection (CDI) is limited by antibiotics' broad spectrum and further disruptive effects on indigenous microbiota. Probiotics may offer a prospective and alternative strategy for the prevention and treatment of CDI.

AREAS COVERED

In this article, the mechanisms implying the probiotic effect against C. difficile and the safety profile highlighting the patient groups with inappropriate application of probiotics were reviewed from 2015 to 2020.

EXPERT OPINION

Although many strains with ability against C. difficile have been reported, the usage of probiotics for CDI prevention and/or treatment is scarce since the number of clinical trials is not sufficient to prove probiotics' efficacy and safety in CDI treatment, especially for premature infant and immunocompromised patient. Especially, there are few well-defined clinical studies supporting safety of probiotics for CDI. A few strains from Lactobacillus and Saccharomyces genus have been studied more extensively than other probiotic strains through clinical trials for CDI. Thus, more clinical intervention studies regarding the benefit and the comprehensive safety assessments of probiotics for CDI are needed.

Enterococcus faecalis Isolated From Infant Feces Inhibits Toxigenic Clostridioides (Clostridium) difficile

Clostridioides (Clostridium) difficile infection is implicated as a major cause of antibiotic-associated diarrhea in hospitals worldwide. Probiotics, especially lactic acid bacteria, are the most frequently used alternative treatment. This study aims to identify potential probiotic enterococci strains that act against C. difficile strains and exert a protective effect on colon adenocarcinoma cells (HT-29 cells). To this end, nine Enterococcus strains isolated from the feces of breast-fed infants were investigated. They were identified as E. faecalis by 16s rRNA sequencing and MALDI-TOF. The probiotic properties including their viabilities in simulated gastrointestinal condition, cell adhesion ability, and their safety were evaluated. All strains exhibited more tolerance toward both pepsin and bile salts and adhered more tightly to HT-29 cells compared with the reference probiotic strain Lactobacillus plantarum ATCC 14917. Polymerase chain reaction (PCR) results exhibited that six of nine strains carried at least one virulence determinant gene; however, none exhibited virulence phenotypes or carried transferable antibiotic resistance genes. These strains did not infect Galleria mellonella when compared to pathogenic E. faecalis strain (p < 0.05). Moreover, their antibacterial activities against C. difficile were examined using agar well-diffusion, spore production, and germination tests. The six safe strains inhibited spore germination (100 - 98.20% ± 2.17%) and sporulation, particularly in C. difficile ATCC 630 treated with E. faecalis PK 1302. Furthermore, immunofluorescence assay showed that the cytopathic effects of C. difficile of HT-29 cells were reduced by the treatment with the cell-free supernatant of E. faecalis strains. These strains prevented rounding of HT-29 cells and preserved the F-actin microstructure and tight junctions between adjacent cells, which indicated their ability to reduce the clostridial cytopathic effects. Thus, the study identified six E. faecalis isolates that have anti-C. difficile activity. These could be promising probiotics with potential applications in the prevention of C. difficile colonization and treatment of C. difficile infection.

Non-antibiotic therapy for Clostridioides difficile infection: a review

Clostridioides difficile infection (CDI) is a common infectious disease that is mainly caused by antibiotics. Antibiotic therapy is still the dominant treatment for CDI, although it is accompanied by side effects. Probiotics, fecal microbiota transplantation (FMT), engineered microorganisms, bacteriophages, diet, natural active substances, nanoparticles and compounds are examples of emerging non-antibiotic therapies that have received a great amount of attention. In this review, we collected data about different non-antibiotic therapies for CDI and provided a comprehensive analysis and detailed comparison of these therapies. The mechanism of action, therapeutic efficacy, and the strengths and weaknesses of these non-antibiotic therapies have been investigated to provide a basis for the reasonable alternative of non-antibiotic therapies for CDI. In summary, probiotics and FMT are currently the best choice for non-antibiotic therapy for CDI.

Rumen fermentation and microbial community composition influenced by live Enterococcus faecium supplementation

Supplementation of appropriate probiotics can improve the health and productivity of ruminants while mitigating environmental methane production. Hence, this study was conducted to determine the effects of Enterococcus faecium SROD on in vitro rumen fermentation, methane concentration, and microbial population structure. Ruminal samples were collected from ruminally cannulated Holstein–Friesian cattle, and 40:60 rice straw to concentrate ratio was used as substrate. Fresh culture of E. faecium SROD at different inclusion rates (0, 0.1%, 0.5%, and 1.0%) were investigated using in vitro rumen fermentation system. Addition of E. faecium SROD had a significant effect on total gas production with the greatest effect observed with 0.1% supplementation; however, there was no significant influence on pH. Supplementation of 0.1% E. faecium SROD resulted in the highest propionate (P = 0.005) but the lowest methane concentration (P = 0.001). In addition, acetate, butyrate, and total VFA concentrations in treatments were comparatively higher than control. Bioinformatics analysis revealed the predominance of the bacterial phyla Bacteroidetes and Firmicutes and the archaeal phylum Euryarchaeota. At the genus level, Prevotella (15–17%) and Methanobrevibacter (96%) dominated the bacterial and archaeal communities of the in vitro rumen fermenta, respectively. Supplementation of 0.1% E. faecium SROD resulted in the highest quantities of total bacteria and Ruminococcus flavefaciens, whereas 1.0% E. faecium SROD resulted in the highest contents of total fungi and Fibrobacter succinogenes. Overall, supplementation of 0.1% E. faecium SROD significantly increased the propionate and total volatile fatty acids concentrations but decreased the methane concentration while changing the microbial community abundance and composition.

Probiotics for Prevention and Treatment of Clostridium difficile Infection

Probiotics have been claimed as a valuable tool to restore the balance in the intestinal microbiota following a dysbiosis caused by, among other factors, antibiotic therapy. This perturbed environment could favor the overgrowth of Clostridium difficile and, in fact, the occurrence of C. difficile-associated infections (CDI) is being increasing in recent years. In spite of the high number of probiotics able to in vitro inhibit the growth and/or toxicity of this pathogen, its application for treatment or prevention of CDI is still scarce since there are not enough well-defined clinical studies supporting efficacy. Only a few strains, such as Lactobacillus rhamnosus GG and Saccharomyces boulardii have been studied in more extent. The increasing knowledge about the probiotic mechanisms of action against C. difficile, some of them reviewed here, makes promising the application of these live biotherapeutic agents against CDI. Nevertheless, more effort must be paid to standardize the clinical studied conducted to evaluate probiotic products, in combination with antibiotics, in order to select the best candidate for C. difficile infections.