Guidance on the assessment of the toxigenic potential of Bacillus species used in animal nutrition

Genomic and Phenotypic Safety Assessment of Probiotic Bacillus coagulans Strain JBI-YZ6.3

Spore-forming Bacillus coagulans has been widely recognized as an important probiotic, which is commonly used in products for human consumption and animal feeds. B. coagulans exhibits beneficial traits from both Bacillus and lactic acid-producing Lactobacillus. The present study evaluated the safety of the newly isolated B. coagulans strain JBI-YZ6.3, using combined genomic and phenotypic analysis approaches. The taxonomic classification based on genome sequence and biochemical tests identified strain JBI-YZ6.3 as B. coagulans. Comprehensive genome-based analyses established JBI-YZ6.3 as a novel strain of B. coagulans. Antibiotic susceptibility testing showed that the strain JBI-YZ6.3 was sensitive to a panel of fourteen antibiotics, and no genes related to antibiotic resistance were found in its genome. The spores of strain JBI-YZ6.3 exhibited tolerance to acid and bile salts, as well as stability at ambient and elevated conditions of temperature and relative humidity. There were no homologs of Bacillus toxin genes identified in the genome of JBI-YZ6.3, and the strain exhibited no cytotoxicity towards Vero cells and human peripheral blood mononuclear cells. In conclusion, findings from this study support the safety of B. coagulans strain JBI-YZ6.3, which can be developed into new probiotic products for preventive and therapeutic benefits in human and animal hosts.

Bacillus Species as Direct-Fed Microbial Antibiotic Alternatives for Monogastric Production

Antibiotic growth promoters have been utilized for long time at subtherapeutic levels as feed supplements in monogastric animal rations. Because of their side-effects such as antibiotic resistance, reduction of beneficial bacteria in the gut, and dysbiosis, it is necessary to look for non-therapeutic alternatives. Probiotics play an important role as the key substitutes to antibacterial agents due to their many beneficial effects on the monogastric animal host. For instance, enhancement of the gut microbiota balance can contribute to improvement of feed utilization efficiency, nutrients absorption, growth rate, and economic profitability of livestock. Probiotics are defined as "live microorganisms that, when administered in adequate amounts, confer a health benefit on the host." They are available in diverse forms for use as feed supplements. Their utilization as feed additives assists in good digestion of feed ingredients and hence, making the nutrients available for promoting growth. Immunity can also be enhanced by supplementing probiotics to monogastrics diets. Moreover, probiotics can help in improving major meat quality traits and countering a variety of monogastric animals infectious diseases. A proper selection of the probiotic strains is required in order to confer optimal beneficial effects. The present review focuses on the general functional, safety, and technological screening criteria for selection of ideal Bacillus probiotics as feed supplements as well as their mechanism of action and beneficial effects on monogastric animals for improving production performance and health status.

Screening of Spore-Forming Bacteria with Probiotic Potential in Pristine Algerian Caves

The interest and exploration of biodiversity in subsurface ecosystems have increased significantly during the last 2 decades. The aim of this study was to investigate the in vitro probiotic properties of spore-forming bacteria isolated from deep caves. Two hundred fifty spore-forming microbes were enriched from sediment samples from 10 different pristine caves in Algeria at different depths. Isolates showing nonpathogenic profiles were screened for their potential to produce digestive enzymes (gliadinase and beta-galactosidase) in solid and liquid media, respectively. Different probiotic potentialities were studied, including (i) growth at 37°C, (ii) survival in simulated gastric juice, (iii) survival in simulated intestinal fluid, and (iv) antibiotic sensitivity and cell surface properties. The results showed that out of 250 isolates, 13 isolates demonstrated nonpathogenic character, probiotic potentialities, and ability to hydrolyze gliadin and lactose in solution. These findings suggest that a selection of cave microbes might serve as a source of interesting candidates for probiotics.

IMPORTANCE Previous microbial studies of subsurface ecosystems like caves focused mainly on the natural biodiversity in these systems. So far, only a few studies focused on the biotechnological potential of microbes in these systems, focusing in particular on their antibacterial potential, antibiotic production, and, to some extent, enzymatic potential. This study explores whether subsurface ecosystems can serve as an alternative source for microbes relevant to probiotics. The research focused on the ability of cave microbes to degrade two substrates (lactose and gliadin) that cause common digestive disorders. Since these enzymes may prove to be useful in food processing and in reducing the effect of lactose and gliadin digestion within intolerant patients, isolation of microbes such as in this study may expand the possibilities of developing alternative strategies to deal with these intolerances.

Virulence Factor Genes and Cytotoxicity of Streptococcus agalactiae Isolated from Bovine Mastitis in Poland

Streptococcus agalactiae can produce a wide variety of virulence factors, including toxins and proteins which facilitate adhesion to and colonization and invasion of the host cells. There are few reports on the characteristics of field isolates from bovine mastitis in Poland. Thus, the aim of this study was to determine the occurrence of types of hemolysis on blood agar, virulence factor genes, and cytotoxicity of S. agalactiae isolates derived from cows with mastitis across Poland. The study included 68 isolates. Virulence genes were tested using standard PCR, and cytotoxicity was determined using methylthiazol tetrazolium (MTT) and lactate dehydrogenase (LDH) tests. Among the tested isolates, 89.7% were β-hemolytic, 8.8% γ-hemolytic, and 1.5% alpha-hemolytic. The only genes detected in all isolates were the cfb, cspA, hylB, and sip genes. Cytotoxicity assessment based on the LDH test revealed that isolates were cytotoxic only to Vero cells. However, according to the results obtained from the MTT test, more than half of the isolates exhibited low cytotoxicity to both SK and Vero cells, whereas the other isolates showed moderate or no cytotoxicity to both cell lines. Our research confirms the prevalence of various virulence genes in S. agalactiae isolated from Polish dairy herds, which have previously been found in isolates recovered from human and animal infections. For the first time, the presence of bac- and scpB-positive isolates of S. agalactiae was determined in Polish dairy cattle, and the cytotoxicity of bovine isolates was assessed. IMPORTANCE We believe that this manuscript is one of the few reports on the characteristics of field S. agalactiae isolates derived from cases of bovine mastitis in cows in Poland in terms of the occurrence of virulence genes and cytotoxicity. For the first time, the presence of bac- and scpB-positive isolates of S. agalactiae was determined in Polish dairy cattle, and the cytotoxicity of bovine isolates was assessed.

Use of probiotics for formation of microflora of gastrointestinal tract of calves

The results of the use of probiotic strains of microorganisms of the Bacillus family for the correction and formation of the microflora of the gastrointestinal tract and the impact on metabolism in calves are presented. The aim of the study. To analyze the effect of probiotics on the microflora of the gastrointestinal tract in calves and biochemical parameters of blood in calves up to one month. Materials and methods. The research was conducted during 2020 in the conditions of Ukrainian farms for cattle breeding. Five experimental groups of five one-week-old calves were formed in each and one control group. Calves were kept separately in the same conditions on the same diet, but with feeding together with colostrum substitute probiotics of five grams per animal: Bacillus amyloliquefaciense, Bacillus mucilaginosus, Bacillus coagulans, Bacillus megaterium, Bacillus pumilus. The strains are deposited and produced by “Kronos Agro” Ukraine. Results. It was found that as a result of studies when feeding calves B. coagulans, B. pumilus and B. mucilaginosus the number of Lactobacillus sp. was 80 % higher than in the control group. The level of opportunistic pathogens in the experimental group with B. coagulans had minimal values. Animals in the group where B. mucilaginosus was given had a higher amount of Candida - up to 300 CFU/g and Enterobacteriaceae – 200 CFU/g; which is 50 % less compared to control groups, but more than in the experiment with B. coagulans. According to the results of biochemical examination of blood serum in calves, the absence of toxic effects of probiotic strains: Bacillus amyloliquefaciense, Bacillus mucilaginosus, Bacillus coagulans, Bacillus megaterium, Bacillus pumilus on the internal organs of animals was established. Conclusions. It was found that the maximum positive effect on the microflora of the gastrointestinal tract of calves up to 30 days of age had B. coagulans (1×109) when fed at a dose of 5 g per animal. The amount of Lactobacillus sp. was the maximum and reached 800 CFU/g, which is 80 % more than in the control group. At the same time, the level of opportunistic pathogens in the experimental group with B. coagulans had minimal indicators and was: Clostridium by 20 %, Escherichia coli – by 70 %, Enterobacteriaceae, Staphylococcus and Candida – 100 % less than the control. In the study of biochemical parameters, it was found that the activity of enzymes, protein and glucose levels in the serum of experimental animals fed with B. coagulans were within the physiological norm, indicating a normal metabolic process and no toxic effects.

Antimicrobial Activity of Lipopeptide Biosurfactants Against Foodborne Pathogen and Food Spoilage Microorganisms and Their Cytotoxicity

Lipopeptide biosurfactants produced by Bacillus sp. were assessed regarding their antimicrobial activity against foodborne pathogenic and food spoilage microorganisms. Both Gram-positive and Gram-negative bacteria were found not to be susceptible to these lipopeptides. However, mycosubtilin and mycosubtilin/surfactin mixtures were very active against the filamentous fungi Paecilomyces variotti and Byssochlamys fulva, with minimum inhibitory concentrations (MICs) of 1-16 mg/L. They were also active against Candida krusei, MIC = 16-64 mg/L. Moreover it was found that the antifungal activity of these lipopeptides was not affected by differences in isoform composition and/or purity. Furthermore their cytotoxicity tested on two different cell lines mimicking ingestion and detoxification was comparable to those of approved food preservatives such as nisin. Overall, for the first time here mycosubtilin and mycosubtilin/surfactin mixtures were found to have high antifungal activity against food relevant fungi at concentrations lower than their toxicity level hence, suggesting their application for extending the shelf-life of products susceptible to these moulds. In addition combining nisin with mycosubtilin or mycosubtiliin/surfactin mixtures proved to be an effective approach to produce antimicrobials with broader spectrum of action.

Selection of carbohydrate-active probiotics from the gut of carnivorous fish fed plant-based diets

The gastrointestinal microbiota plays a critical role on host health and metabolism. This is particularly important in teleost nutrition, because fish do not possess some of the necessary enzymes to cope with the dietary challenges of aquaculture production. A main difficulty within fish nutrition is its dependence on fish meal, an unsustainable commodity and a source of organic pollutants. The most obvious sustainable alternatives to fish meal are plant feedstuffs, but their nutritive value is limited by the presence of high levels of non-starch polysaccharides (NSP), which are not metabolized by fish. The composition of fish-gut microbial communities have been demonstrated to adapt when the host is fed different ingredients. Thus, we hypothesized that a selective pressure of plant-based diets on fish gut microbiota, could be a beneficial strategy for an enrichment of bacteria with a secretome able to mobilize dietary NSP. By targeting bacterial sporulating isolates with diverse carbohydrase activities from the gut of European sea bass, we have obtained isolates with high probiotic potential. By inferring the adaptive fitness to the fish gut and the amenability to industrial processing, we identified the best two candidates to become industrially valuable probiotics. This potential was confirmed in vivo, since one of the select isolates lead to a better growth and feed utilization efficiency in fish fed probiotic-supplemented plant-based diets, thus contributing for sustainable and more cost-effective aquaculture practices.

Safety and efficacy of Cinergy® Life B3 HiCon (Bacillus amyloliquefaciens NRRL B-50508, B. amyloliquefaciens NRRL B-50509 and Bacillus subtilis NRRL B-50510) as a feed additive for pigs for fattening and minor porcine species

The additive contains viable spores of two strains of Bacillus amyloliquefaciens and a single strain of Bacillus subtilis and is intended to be used with pigs for fattening and minor porcine species at a minimum inclusion level of 1.5 × 108 colony forming units (CFU)/kg complete feedingstuffs. The two bacterial species are considered suitable for the qualified presumption of safety (QPS) approach to safety assessment, which requires the identity of the strains to be established and evidence that they lack toxigenic potential and acquired antimicrobial resistance determinants for antibiotics of human and veterinary importance. The identity of the three active agents is established and the lack of toxigenic potential confirmed. The two B. amyloliquefaciens strains do not show resistance to relevant antibiotics, and are presumed safe for the target species, consumers and the environment. The B. subtilis strain showed a low level of resistance to streptomycin, for which acquired resistance genes were not identified. Therefore, it also complies with the QPS qualifications and is presumed safe for the target species, consumer and the environment. Since no other component give rise to concerns, Cinergy® Life B3 HiCon is also considered safe for the target species, consumers and the environment. In the absence of data, no conclusions can be made on the skin or eye irritancy or the potential for dermal sensitisation of the additive. Owing to the proteinaceous nature of the active agents, the additive is considered a potential respiratory sensitiser. However, the low dusting potential makes it unlikely that additive poses a risk for the respiratory system. Cinergy® Life B3 HiCon showed a potential to improve the feed to gain ratio in pigs for fattening given the additive at a minimum inclusion level of 1.5 × 108 CFU/kg complete feed. This conclusion is extrapolated to minor porcine species at the same application rate and for an equivalent growth phase.

Regulatory and Safety Requirements for Food Cultures

The increased use of food cultures to ferment perishable raw materials has potentiated the need for regulations to assess and assure the safety of food cultures and their uses. These regulations differ from country to country, all aimed at assuring the safe use of food cultures which has to be guaranteed by the food culture supplier. Here we highlight national differences in regulations and review a list of methods and methodologies to assess the safety of food cultures at strain level, at production, and in the final product.

Safety and efficacy of Probion Forte® (Bacillus subtilis KCCM 10941P and Bacillus coagulans KCCM 11093P) as a feed additive for chickens for fattening

Following a request from the European Commission, the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of Probion Forte^® when used in feed for chickens for fattening. Probion Forte^® is a preparation containing viable spores of a strain of Bacillus subtilis and Bacillus coagulans intended for use in feed for chickens for fattening at the minimum dose of 1 × 10⁸ and a maximum of 2 × 10⁸ colony-forming units (CFU)/kg feedingstuffs. In the view of the FEEDAP Panel, the identity of the bacterial strains is established as B. subtilis and B. coagulans and their susceptibility to relevant antibiotics is demonstrated. However, both bacterial strains belong to species capable of producing toxins. The absence of a toxigenic potential has not been demonstrated and, therefore, these strains do not qualify for a qualified presumption of safety (QPS) approach to safety assessment and separate studies on target animals and consumer safety are required. The data provided did not allow concluding on the safety for chickens for fattening or the consumers. Probion Forte^® is not a skin or eye irritant but should be considered a potential respiratory sensitiser. No conclusion can be drawn on the skin sensitisation potential of the additive. In the absence of evidence that the two active agents are not toxigenic, Probion Forte^® is considered as a hazard for those handling the additive. Probion Forte^® is considered safe for the environment. The FEEDAP Panel is not in the position to conclude on the efficacy of Probion Forte^® for chickens for fattening from the data provided.

Scientific Opinion on the update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA

EFSA is requested to assess the safety of a broad range of biological agents in the context of notification for market authorisation as sources of food and feed additives, food enzymes and plant protection products. The qualified presumption of safety (QPS) assessment was developed to provide a harmonised generic pre-assessment to support safety risk assessments performed by EFSA's scientific Panels. The safety of unambiguously defined biological agents (at the highest taxonomic unit appropriate for the purpose for which an application is intended), and the completeness of the body of knowledge are assessed. Identified safety concerns for a taxonomic unit are, where possible and reasonable in number, reflected as 'qualifications' in connection with a recommendation for a QPS status. The list of QPS recommended biological agents was reviewed and updated in the current opinion and therefore becomes the valid list. The 2016 update reviews previously assessed microorganisms including bacteria, yeasts and viruses used for plant protection purposes following an Extensive Literature Search strategy. The taxonomic units related to the new notifications received since the 2013 QPS opinion, were periodically evaluated for a QPS status and the results published as Statements of the BIOHAZ Panel. Carnobacterium divergens, Lactobacillus diolivorans, Microbacterium imperiale, Pasteuria nishizawae, Pediococcus parvulus, Bacillus flexus, Bacillus smithii, Xanthomonas campestris and Candida cylindracea were recommended for the QPS list. All taxonomic units previously recommended for the 2013 QPS list had their status reconfirmed as well their qualifications with the exception of Pasteuria nishizawae for which the qualification was removed. The exclusion of filamentous fungi and enterococci from the QPS evaluations was reconsidered but monitoring will be maintained and the status will be re-evaluated in the next QPS Opinion update. Evaluation of bacteriophages should remain as a case-by-case procedure and should not be considered for QPS status.

Microbiological and molecular characterization of commercially available probiotics containing Bacillus clausii from India and Pakistan

Probiotics are actively used for treatment of diarrhoea, respiratory infections, and prevention of infectious gastrointestinal diseases. The efficacy of probiotics is due to strain-specific features and the number of viable cells; however, several reports of deviations from the label in the actual content of strains in probiotic products are a matter of concern. Most of the available data on quality focuses on probiotic products containing lactobacilli and/or bifidobacteria, while very few data are available on spore-forming probiotics. The present study evaluates the label claims for spore count and species identification in five commercial probiotic products marketed in India and Pakistan that claim to contain Bacillus clausii: Tufpro, Ecogro, Enterogermina, Entromax, and Ospor. Bacterial enumeration from three batches was done by microbiological plating methods by two independent operators. Species identification was done using PCR amplification and sequence analysis of the 16S rRNA gene, and determination of the total amount of species present in the products was done using PCR-denaturing gradient gel electrophoresis (PCR-DGGE) analysis followed by DNA sequencing of the excised bands. Plate count methods demonstrated poor correlations between quantitative label indications and bacteria recovered from plates for Tufpro, Ecogro, and Ospor. The 16S rRNA analysis performed on bacteria isolated from plate counts showed that only Enterogermina and Ospor contained homogenous B. clausii. PCR-DGGE analysis revealed that only Enterogermina had a homogenous B. clausii population while other products had mixed bacterial populations. In conclusion, the current analysis clearly demonstrates that of the five analysed commercial probiotics, only Enterogermina followed the label claims.

Integrate genome-based assessment of safety for probiotic strains: Bacillus coagulans GBI-30, 6086 as a case study

Probiotics are microorganisms that confer beneficial effects on the host; nevertheless, before being allowed for human consumption, their safety must be verified with accurate protocols. In the genomic era, such procedures should take into account the genomic-based approaches. This study aims at assessing the safety traits of Bacillus coagulans GBI-30, 6086 integrating the most updated genomics-based procedures and conventional phenotypic assays. Special attention was paid to putative virulence factors (VF), antibiotic resistance (AR) genes and genes encoding enzymes responsible for harmful metabolites (i.e. biogenic amines, BAs). This probiotic strain was phenotypically resistant to streptomycin and kanamycin, although the genome analysis suggested that the AR-related genes were not easily transferrable to other bacteria, and no other genes with potential safety risks, such as those related to VF or BA production, were retrieved. Furthermore, no unstable elements that could potentially lead to genomic rearrangements were detected. Moreover, a workflow is proposed to allow the proper taxonomic identification of a microbial strain and the accurate evaluation of risk-related gene traits, combining whole genome sequencing analysis with updated bioinformatics tools and standard phenotypic assays. The workflow presented can be generalized as a guideline for the safety investigation of novel probiotic strains to help stakeholders (from scientists to manufacturers and consumers) to meet regulatory requirements and avoid misleading information.

Surfactins in natto: the surfactin production capacity of the starter strains and the actual surfactin contents in the products

Surfactin-type lipopeptides are suspected of being implicated in the rare food poisonings caused by Bacillus species outside the Bacillus cereus cluster. In order to get information on surfactin levels in actual human foods, bacilli from three commercial samples of a Japanese traditional bean product, natto, were isolated in order to clarify their potential to produce the suspect lipopeptides. The isolated bacilli were characterized as Bacillus subtilis. They were β-hemolytic and gave a positive signal in the PCR screen for genes associated with surfactin production, and their culture extracts were cytotoxic to boar sperm cells. Organic extracts of both Bacillus cultures and the natto samples were analyzed for their surfactin content using ultrahigh-performance liquid chromatography with high-resolution mass spectrometry. All the strains proved to be surfactin producers (15 to 39 μg/ml culture medium); the natto samples contained as much as 2.2 mg g(-1) of surfactins. This means that consumers can ingest at least approximately 80 to 100 mg of surfactins per single 50-g natto serving apparently without suffering any ill effects, indicating a very low human toxicity.