Metagenomics-based approach for studying and selecting bioprotective strains from the bacterial community of artisanal cheeses

A metagenome-based approach was used to assess the taxonomic affiliation and functional potential for bacteriocin production of the bacterial community in cow's milk artisanal cheeses from Northwestern Argentina. Three different samples were analyzed by high-throughput sequencing of the V4 region of the 16S rRNA gene and shotgun metagenomics. Taxonomic analysis showed that cheese A and C were quite similar whereas cheese B displayed a rather different bacterial composition. Overall, two families, Streptococceae and Enterococceae, dominated the artisanal cheese microbiota, being the former family prevalent in cheese B and the later family the most important in samples A and C. Besides the usual species associated to cheeses, a number of bacterial taxa that have not been previously found in Argentinean artisanal cheeses were reported in the present work such as Macrococcus caseolyticus and Streptococcus macedonicus Functional metagenomics analysis using the bacteriocin mining software BAGEL3, identified 2 ORFs encoding antimicrobial peptides in cheese B and 42 different peptides in sample C. The bacteriocin genes found showed good correlation with taxonomy. Based on the microbial diversity and functional features found through shotgun metagenomic sequencing, a culture-dependent approach was applied aiming to isolate bacteriocin-producing bacteria able to inhibit the growth of the foodborne pathogen Listeria monocytogenes. From 151 bacterial colonies derived from the cheese samples, 10 were associated to high anti-Listeria activity. Based on partial 16S rRNA gene sequencing and RAPD-PCR analysis, all bacteriocinogenic isolates were identified as Enterococcus faecium. Finally, we carried out a pilot experiment with L. monocytogenes-contaminated cheese using one of the enterococcal isolates as a bioprotective adjunct culture. The use of E. faecium CRL1879 during artisanal cheese manufacturing did not alter the main organoleptic properties of the cheese and ensured an efficient control of the foodborne pathogen up to 30 days. This finding supports the use of E. faecium CRL1879 as an adjunct culture in the cheese-making process with a combination of both safety and minimal processing.

Do Your Kids Get What You Paid for? Evaluation of Commercially Available Probiotic Products Intended for Children in the Republic of the Philippines and the Republic of Korea

A wide range of probiotic products is available on the market and can be easily purchased over the counter and unlike pharmaceutical drugs, their commercial distribution is not strictly regulated. In this study, ten probiotic preparations commercially available for children's consumption in the Republic of the Philippines (PH) and the Republic of Korea (SK) have been investigated. The analyses included determination of viable counts and taxonomic identification of the bacterial species present in each formulation. The status of each product was assessed by comparing the results with information and claims provided on the label. In addition to their molecular identification, safety assessment of the isolated strains was conducted by testing for hemolysis, biogenic amine production and antibiotic resistance. One out of the ten products contained lower viable numbers of recovered microorganisms than claimed on the label. Enterococcus strains, although not mentioned on the label, were isolated from four products. Some of these isolates produced biogenic amines and were resistant to one or several antibiotics. Metagenomic analyses of two products revealed that one product did not contain most of the microorganisms declared in its specification. The study demonstrated that some commercial probiotic products for children did not match their label claims. Infants and young children belong to the most vulnerable members of society, and food supplements including probiotics destined for this consumer group require careful checking and strict regulation before commercial distribution.

Use of Probiotics for the Management of Acute Gastroenteritis in Children: An Update

Since the publication of the 2014 European Society for Paediatric Gastroenterology, Hepatology, and Nutrition Working Group (WG) on Probiotics and Prebiotics guidelines for the management of acute gastroenteritis (AGE), new evidence concerning the efficacy of probiotics has become available. This document provides updated recommendations on the use of probiotics for the treatment of AGE in previously presumed healthy infants and children. A systematic literature search was performed. All pooled analyses were explicitly performed for the current report. The WG graded the recommendations and assessed the certainty of the supporting evidence using the Grading of Recommendations, Assessment Development, and Evaluations tool. The recommendations were formulated if at least 2 randomized controlled trials that used a given probiotic were available. Despite the large number of identified trials, the WG could not identify 2 randomized controlled trial of high quality for any strain that provided benefit when used for treating AGE. The WG made weak recommendations for (in descending order in terms of the number of trials evaluating any given strain): Saccharomyces boulardii (low to very low certainty of evidence); Lactobacillus rhamnosus GG (very low certainty of evidence); L reuteri DSM 17938 (low to very low certainty of evidence); and L rhamnosus 19070-2 and L reuteri DSM 12246 (very low certainty of evidence). The WG made a strong recommendation against L helveticus R0052 and L rhamnosus R0011 (moderate certainty of evidence) and a weak recommendation against Bacillus clausii strains O/C, SIN, N/R, and T (very low certainty of evidence).

Randomized, Placebo-Controlled, Double-Blind and Open-Label Studies in the Treatment and Prevention of Acute Diarrhea With Enterococcus faecium SF68

Enterococcus faecium SF68® (SF68) is a licensed pharmaceutical for treatment and prevention of diarrhea in Austria, Italy and Switzerland. However, as for other probiotics, evidence for its efficacy is based on small to medium-sized studies. Four unpublished studies on the treatment of acute diarrhea and the prevention of antibiotic-associated diarrhea were analyzed: one randomized, double blind, placebo-controlled trial (RCT) for treatment (n = 1,143), one open-label study for treatment (n = 5,093), one RCT for prevention (n = 1,397) and one open-label study for prevention (n = 4,340). Patients in the treatment-arm and the open-label studies received SF68 (b.i.d. for the prevention studies, t.i.d. for the treatment trials) for 7 days. Primary end points were time to resolution of diarrhea (treatment) and percentage of development of diarrhea (prevention). The primary endpoint of the treatment study was met with a decreased time to resolution of diarrhea in SF68-treated patients compared to controls (median 3 vs. 4 days, p < 0.001). Time to resolution of secondary symptoms was also significantly reduced. Preventive treatment with SF68 was more effective than placebo with development of diarrhea in 8.6 vs. 16.2% (p < 0.001). Results from the open-label studies were consistent with the RCTs. The incidence of adverse events were low (1.1 and 1.4% in the RCT and 4.7 and 7.4% in the open-label studies). SF68 is effective and safe in the treatment of acute diarrhea and prevention of antibiotic-associated diarrhea.

Live Biotherapeutic Products, A Road Map for Safety Assessment

Recent developments in the understanding of the relationship between the microbiota and its host have provided evidence regarding the therapeutic potential of selected microorganisms to prevent or treat disease. According to Directive 2001/83/EC, in the European Union (EU), any product intended to prevent or treat disease is defined as a medicinal product and requires a marketing authorization by competent authorities prior to commercialization. Even if the pharmaceutical regulatory framework is harmonized at the EU level, obtaining marketing authorisations for medicinal products remains very challenging for Live Biotherapeutic Products (LBPs). Compared to other medicinal products currently on the market, safety assessment of LBPs represents a real challenge because of their specific characteristics and mode of action. Indeed, LBPs are not intended to reach the systemic circulation targeting distant organs, tissues, or receptors, but rather exert their effect through direct interactions with the complex native microbiota and/or the modulation of complex host-microbiota relation, indirectly leading to distant biological effects within the host. Hence, developers must rely on a thorough risk analysis, and pharmaceutical guidelines for other biological products should be taken into account in order to design relevant non-clinical and clinical development programmes. Here we aim at providing a roadmap for a risk analysis that takes into account the specificities of LBPs. We describe the different risks associated with these products and their interactions with the patient. Then, from that risk assessment, we propose solutions to design non-clinical programmes and First in Human (FIH) early clinical trials appropriate to assess LBP safety.

Titration of supplemental Bacillus subtilis subsp. subtilis American Type Culture Collection PTA-125135 to broiler chickens fed diets of 2 different metabolizable energy concentrations

Bacillus subtilis subsp. subtilis American Type Culture Collection deposit number PTA-125135 has recently been studied by our laboratory as a potential probiotic strain for avian species. The objective of the present study was to evaluate growth performance and feed efficiency in broiler chickens in response to a dose titration of the Bacillus strain in feed. In addition to a nonsupplemented control, Bacillus spores were supplemented into broiler chicken diets at 4 levels, which were 8.1 × 10⁴, 1.6 × 10⁵, 2.4 × 10⁵, and 3.2 × 10⁵ CFU per g of feed. The titration was applied to two different dietary regimes of standard or low metabolizable energy (ME), which differed in ME by 22, 56, and 110 kcal/kg in starter, grower, and finisher dietary phases, respectively. All diets contained 249 g per metric ton of a previously patented synbiotic feed additive. Performance data were collected at day 14, 26, and 40 of age, and the effects of Bacillus and ME treatments were evaluated by factorial ANOVA. Treatment group means were further examined for significant (P < 0.05) pairwise differences among treatments and for significant (P < 0.05) linear and quadratic effects. At day 14 of age, significant linear effects for decreased feed conversion ratio (FCR) with higher CFU of Bacillus supplementation were observed within the standard ME diet. At day 26, a linear trend was observed for increased mortality with increased dose within the standard ME diet only. Bacillus supplementation at day 26 also significantly affected FCR and mortality-adjusted FCR, where supplementation with 3.2 × 10⁵ CFU per g feed produced lower FCR and mortality-adjusted FCR than supplementation with 1.6 × 10⁵ CFU per g feed. We conclude from linear effects related to feed efficiency observed at day 14 and from the significant separation of Bacillus treatment means within the titrated range of supplementation at day 26 that further evaluation for effects on performance should be made of doses at 2.4 × 10⁵, 3.2 × 10⁵, and greater CFU per g in feed.

Administration of Enterococcus faecium HS-08 increases intestinal acetate and induces immunoglobulin A secretion in mice

A probiotic is considered a live microbial feed supplement that has beneficial effects on the host. In this study, the probiotic property by which Enterococcus faecium HS-08 strengthens the immune system was investigated. Using a murine model, we evaluated the abilities of this strain to increase intestinal short-chain fatty acid contents and to induce the production of mucosal immunoglobulin A (IgA), which are crucial for mucosal immune systems. Various amounts (0%, 0.0038%, 0.038%, or 0.38%) of strain HS-08 cells were administered to BALB/cAJcl mice, which resulted in a dose-dependent increase of fecal IgA levels. A qRT-PCR analysis of Peyer's patch cells revealed that the gene expression of retinal-dehydrogenase, interleukin 6, B-cell-activating factor, and a proliferation-inducing ligand were increased, which leads to IgA secretion via a T-cell-independent mechanism. The administration of 0.038% and 0.38% of strain HS-08 cells also increased fecal acetate levels, which plays an important role for maintaining immune functions. This cecal floral analysis and the stability of strain HS-08 against gastrointestinal digestion suggest that this strain can inhabit the host intestine. In conclusion, the administration of E. faecium HS-08 increased intestinal acetate levels and enhanced IgA secretion, which may result in strengthening of the mucosal immune system.

The effect of synbiotic preparations on the intestinal microbiota and her metabolism in broiler chickens

The aim of the research was to determine the effect of newly elaborated synbiotic preparations on the count of dominant intestinal microorganisms, on the profile of fatty acids (short chain - SCFA and branched chain - BCFA), the lactic acid produced and the performance of chickens. The studies determined the composition of the dominant intestinal microbiota with use of the culture method. The fatty acid profile was also determined using the high-performance liquid chromatography method (HPLC). Moreover, the performance of chickens was determined such as the daily cumulative mortality rate, the feed conversion ratio (FCR) and the European Production Efficiency Factor (EPEF). It was found that synbiotics had a beneficial effect on parameters of the performance of chickens, and also resulted in increase in the count of beneficial bacteria and to the restriction in growth of potential pathogens in the gastrointestinal tract. Synbiotics caused an increase in the concentration of lactic acid and SCFA and a decrease in the concentration of BCFA in the broiler's excreta. These results showed a beneficial effect of the tested synbiotics on the intestinal microbiota, their metabolism and the performance of broiler chickens. The elaborated synbiotics can be successfully used as feed additives for broiler chickens.

Bacteriocins From LAB and Other Alternative Approaches for the Control of Clostridium and Clostridiodes Related Gastrointestinal Colitis

The gut microbiome is considered as a promising target for future non-conventional therapeutic treatment of inflammatory and infectious diseases. The search for appropriate safe and beneficial (lactic acid bacterial and other) putative probiotic strains and/or their antimicrobial metabolites represents a challenging approach for combating several problematic and emerging infections. The process of selecting suitable strains, especially of lactic acid bacteria (LAB) with superior properties, has been accelerated and intensified during the past two decades, also thanks to recent developments in lab techniques. Currently, special focus is on the potential of antimicrobial metabolites produced by some LAB strains and their application as active therapeutic agents. The vision is to develop a scientific basis for 'biotherapeutics' as alternative to conventional approaches in both human and veterinary medicine. Consequently, innovative and promising applications of LAB to the therapeutic practice are presently emerging. An overview of the existing literature indicates that some antimicrobial metabolites such as bacteriocins, widely produced by different bacterial species including LAB, are promising biotherapeutic agents for controlling infections caused by potential pathogens, such as Clostridium and Clostridiodes. Non-conventional, safe and well designed therapeutic treatments may contribute to the improvement of gut dysbiotic conditions. Thereby gut homeostasis can be restored and inflammatory conditions such as gastrointestinal colitis ameliorated. Combining the knowledge on the production, characterization and application of bacteriocins from probiotic LAB, together with their antibacterial properties, appears to be a promising and novel approach in biotherapy. In this overview, different scenarios for the control of Clostridium spp. by application of bacteriocins as therapeutic agents, also in synergistic combination with antibiotics, will be discussed.

Genetic and Biochemical Evidence That Enterococcus faecalis Gr17 Produces a Novel and Sec-Dependent Bacteriocin, Enterocin Gr17

Bacteriocins are ribosomally synthesized antibacterial peptides or proteins from microorganisms. We report a novel bacteriocin producing strain, Enterococcus faecalis Gr17, that was isolated from the Chinese traditional low-salt fermented whole fish product Suan yu. E. faecalis Gr17 displayed potent antibacterial activity against foodborne pathogenic and spoilage bacteria. The complete genome of E. faecalis Gr17 contained one circular chromosome and plasmid. The gene cluster of a novel bacteriocin designated enterocin Gr17 was identified. The enterocin Gr17 structural gene encodes a precursor of the bacteriocin. Two other transporter genes and an immunity gene within two divergent operons were identified as being associated with enterocin Gr17 secretion and protection. The novel enterocin Gr17 was purified by ammonium sulfate precipitation, cation exchange, gel filtration, and reverse-phase high-performance liquid chromatography. The molecular weight of enterocin Gr17 was 4,531.01 Da as determined by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and its mature amino acid sequence of enterocin Gr17 was RSYGNGVYCNNSKCWVNWGEAKENIIGIVISGWATGLAGMGR. Sequence alignment revealed that enterocin Gr17 is a class IIa bacteriocin with similarities to enterocin P. The merits of bactericidal activity, sensitivity to enzymes, and pronounced stability to chemicals, temperature (60°C, 30 min and 121°C, 15 min), and pH (2-10) indicated practicality and safety of enterocin Gr17 in the food industry. The complete genome information of E. faecalis Gr17 will improve the understanding of the biosynthetic mechanism of enterocin Gr17, which has potential value as a food biopreservative.

Pilot evaluation of Enterococcus faecium SF68 as adjunctive therapy for oclacitinib-responsive adult atopic dermatitis in dogs

OBJECTIVE

To evaluate the adjunctive effect of supplementation with Enterococcus faecium SF68 (FortiFlora; Purina Pro Plan Veterinary Diets) on oclacitinib (Apoquel, Zoetis) dose reduction, while maintaining or reducing the Pruritus Visual Analog Score and Canine Atopic Dermatitis Extent and Severity Index values in client-owned adult dogs with environmental atopic dermatitis.

MATERIALS AND METHODS

Enrolled dogs had exhibited control of atopic dermatitis on oclacitinib for at least 6 months before, and continuing throughout, the study. Dogs with non-seasonal pruritus were blindly randomised to receive either SF68 (1×10⁸ colony forming units/g orally twice daily) or placebo for 12 weeks. After 8 weeks of supplementation, oclacitinib dose was decreased by approximately 25%, aiming to maintain and reduce the clinical disease scores.

RESULTS

Supplementation with SF68 was associated with no difference in oclacitinib dose reduction versus placebo in 21 client-owned dogs with atopic dermatitis. Clinical disease scores were not different between groups at study completion.

CLINICAL SIGNIFICANCE

Further larger-scale studies are warranted to investigate optimal strain(s), dosing and duration of probiotic supplementation as an adjunctive strategy in management of canine atopic dermatitis.

Enterococci: Between Emerging Pathogens and Potential Probiotics

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

Toward rational selection criteria for selection of probiotics in pigs

An accurate understanding of properties of probiotics is a prerequisite for selecting probiotic organisms for use in swine production. This review aims to review selection criteria for probiotic organism in swine. The systematically investigated ecological history rather than the source of isolates should be regarded as the natural origin of probiotic strains, which helps to correct the inconsistencies arising from incorrect identification of the source. Moreover, in vivo studies are suggested as follow-up assessment to validate the characteristics of probiotic predicted by in vitro experiments. In addition, the intended probiotic effect depends on the age of the animal and disease prevention in young animals may require different probiotic strains when compared to growth promotion in older animals. With adequate selection criteria, the inclusion of probiotic in feed supplementation is a promising way to exert positive effects on sows, newborns, weanling animals and grower-finisher pigs. Both host-adapted probiotics and nomadic probiotics can be applied for pathogen inhibition but host adapted organisms appear to have a different mode of action. Host-adapted probiotic strains are likely to be associated with exclusive colonization while the nomadic or environmental strain exert better immune stimulating functions. Strains with potent enzymatic activity are fitter for grower pigs favoring feed digestion and enhancing growth performance.

Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective

Lactic acid bacteria (LAB) are representative members of multiple ecosystems on earth, displaying dynamic interactions within animal and plant kingdoms in respect with other microbes. This highly heterogeneous phylogenetic group has coevolved with plants, invertebrates, and vertebrates, establishing either mutualism, symbiosis, commensalism, or even parasitism-like behavior with their hosts. Depending on their location and environment conditions, LAB can be dominant or sometimes in minority within ecosystems. Whatever their origins and relative abundance in specific anatomic sites, LAB exhibit multifaceted ecological and functional properties. While some resident LAB permanently inhabit distinct animal mucosal cavities, others are provided by food and may transiently occupy the gastrointestinal tract. It is admitted that the overall gut microbiome has a deep impact on health and diseases. Here, we examined the presence and the physiological role of LAB in the healthy human and several animal microbiome. Moreover, we also highlighted some dysbiotic states and related consequences for health, considering both the resident and the so-called "transionts" microorganisms. Whether LAB-related health effects act collectively or follow a strain-specificity dogma is also addressed. Besides the highly suggested contribution of LAB to interplay with immune, metabolic, and even brain-axis regulation, the possible involvement of LAB in xenobiotic detoxification processes and metal equilibrium is also tackled. Recent technological developments such as functional metagenomics, metabolomics, high-content screening and design in vitro and in vivo experimental models now open new horizons for LAB as markers applied for disease diagnosis, susceptibility, and follow-up. Moreover, identification of general and more specific molecular mechanisms based on antioxidant, antimicrobial, anti-inflammatory, and detoxifying properties of LAB currently extends their selection and promising use, either as probiotics, in traditional and functional foods, for dedicated treatments and mostly for maintenance of normobiosis and homeostasis.