Safety evaluation of HOWARU ® Restore ( Lactobacillus acidophilus NCFM, Lactobacillus paracasei Lpc-37, Bifidobacterium animalis subsp. lactis Bl-04 and B. lactis Bi-07) for antibiotic resistance, genomic risk factors, and acute toxicity

Genome sequence and evaluation of safety and probiotic potential of Lacticaseibacillus paracasei LC86 and Lacticaseibacillus casei LC89

Aim

A comprehensive safety assessment of potential probiotic strains was essential for their application in the food industry. This article systematically evaluated the probiotic characteristics, whole-genome sequence analysis and safety of Lacticaseibacillus paracasei LC86 and Lacticaseibacillus casei LC89.

Methods

Firstly, the two strains of lactic acid bacteria selected were identified. Secondly, whole-genome sequencing was performed on LC86 and LC89, and their antibiotic resistance, pathogenicity, and virulence genes were analyzed. We tested various properties of the two strains, included tolerance, cell adhesion, hemolytic activity, catalase activity, gelatin hydrolysis, arginine hydrolysis ability, bile salt hydrolysis capacity, mucin degradation, bioamine, D-/L-lactic acid production and antibiotic susceptibility, to confirm the safety of LC86 and LC89 both in vitro and in vivo. Additionally, we studied the acute toxicity of LC86 and LC89 in mice through a 14-day oral gavage experiment.

Results

The two strains selected were identified as Lacticaseibacillus paracasei and Lacticaseibacillus casei. The genomes of both LC86 and LC89 were devoid of virulence, antibiotic resistance and pathogenicity genes. LC86 and LC89 exhibited good tolerance to temperature, artificial gastric fluid and artificial intestinal fluid; they were non-hemolytic, their catalase activity, gelatin hydrolysis, arginine hydrolysis and bile salt hydrolysis were all negative. They exhibited the capability to break down proteins and demonstrated sensitivity to a range of antibiotics. The oral LD50 for both LC86 and LC89 in mice was >2 × 1010 CFU/kg.

Conclusion

The experimental results above demonstrated the probiotic characteristics and safety of LC86 and LC89, indicating their potential as candidates for probiotics for human and animal applications.

Mechanism of Action and Beneficial Effects of Probiotics in Amateur and Professional Athletes

Probiotics are live microorganisms that, when administered in adequate amounts, provide health benefits to the host. According to the International Society of Sports Nutrition (ISSN), probiotic supplementation can optimize the health, performance, and recovery of athletes at all stages of their careers. Recent research suggests that probiotics can improve immune system functions, reduce gastrointestinal distress, and increase gut permeability in athletes. Additionally, probiotics may provide athletes with secondary health benefits that could positively affect athletic performance through enhanced recovery from fatigue, improved immune function, and maintenance of healthy gastrointestinal tract function. The integration of some probiotic strains into athletes' diets and the consumption of multi-strain compounds may lead to an improvement in performance and can positively affect performance-related aspects such as fatigue, muscle pain, body composition, and cardiorespiratory fitness. In summary, probiotics can be beneficial for athletes at all stages of their careers, from amateur to professional. This paper reviews the progress of research on the role of probiotic supplementation in improving energy metabolism and immune system functions, reducing gastrointestinal distress, and enhancing recovery from fatigue in athletes at different levels.

Rapid and Accurate Quantification of Viable Lactobacillus Cells in Infant Formula by Flow Cytometry Combined with Propidium Monoazide and Signal-Enhanced Fluorescence In Situ Hybridization

Lactobacillus is an important member of the probiotic bacterial family for regulating human intestinal microflora and preserving its normalcy, and it has been widely used in infant formula. An appropriate and feasible method to quantify viable Lactobacilli cells is urgently required to evaluate the quality of probiotic-fortified infant formula. This study presents a rapid and accurate method to count viable Lactobacilli cells in infant formula using flow cytometry (FCM). First, Lactobacillus cells were specifically and rapidly stained by oligonucleotide probes based on a signal-enhanced fluorescence in situ hybridization (SEFISH) technique. A DNA-binding fluorescent probe, propidium monoazide (PMA), was then used to accurately recognize viable Lactobacillus cells. The entire process of this newly developed PMA-SEFISH-FCM method was accomplished within 2.5 h, which included pretreatment, dual staining, and FCM analysis; thus, this method showed considerably shorter time-to-results than other rapid methods. This method also demonstrated a good linear correlation (R2 = 0.9994) with the traditional plate-based method with a bacterial recovery rate of 91.24%. To the best of our knowledge, the present study is the first report of FCM combined with PMA and FISH for the specific detection of viable bacterial cells.

Lactobacillus acidophilus NCFM and Lactiplantibacillus plantarum Lp-115 inhibit Helicobacter pylori colonization and gastric inflammation in a murine model

Purpose

To determine the role of Lactobacillus strains and their combinations in inhibiting the colonization of H. pylori and gastric mucosa inflammation.

Methods

Human gastric adenocarcinoma AGS cells were incubated with H. pylori and six probiotic strains (Lactobacillus acidophilus NCFM, L. acidophilus La-14, Lactiplantibacillus plantarum Lp-115, Lacticaseibacillus paracasei Lpc-37, Lacticaseibacillus rhamnosus Lr-32, and L. rhamnosus GG) and the adhesion ability of H. pylori in different combinations was evaluated by fluorescence microscopy and urease activity assay. Male C57BL/6 mice were randomly divided into five groups (uninfected, H. pylori, H. pylori+NCFM, H. pylori+Lp-115, and H. pylori+NCFM+Lp-115) and treated with two lactobacilli strains (NCFM and Lp-115) for six weeks. H. pylori colonization and tissue inflammation statuses were determined by rapid urease test, Hematoxylin-Eosin (HE) staining, immunohistochemistry, and qRT-PCR and ELISA.

Results

L. acidophilus NCFM, L. acidophilus La-14, L. plantarum Lp-115, L. paracasei Lpc-37, L. rhamnosus Lr-32, and L. rhamnosus GG reduced H. pylori adhesion and inflammation caused by H. pylori infection in AGS cells and mice. Among all probiotics L. acidophilus NCFM and L. plantarum, Lp-115 showed significant effects on the H. pylori eradication and reduction of inflammation in-vitro and in-vivo. Compared with the H. pylori infection group, the mRNA and protein expression levels of IL-8 and TNF-α in the six Lactobacillus intervention groups were significantly reduced. The changes in the urease activity (ureA and ureB) for 1-7h in each group showed that L. acidophilus NCFM, L. acidophilus La-14, L. plantarum Lp-115, and L. rhamnosus GG effectively reduced the colonization of H. pylori. We observed a higher ratio of lymphocyte and plasma cell infiltration into the lamina propria of the gastric mucosa and neutrophil infiltration in H. pylori+NCFM+Lp-115 mice. The infiltration of inflammatory cells in lamina propria of the gastric mucosa was reduced in the H. pylori+NCFM+Lp-115 group. Additionally, the expression of IFN-γ was decreased significantly in the NCFM and Lp-115 treated C57BL/6 mice.

Conclusions

L. acidophilus NCFM and L. plantarum Lp-115 can reduce the adhesion of H. pylori and inhibit the gastric inflammatory response caused by H. pylori infection.

Emerging pre-clinical safety assessments for potential probiotic strains: a review

Probiotics are amply studied and applied dietary supplements of greater consumer acceptance. Nevertheless, the emerging evidence on probiotics-mediated potential risks, especially among immunocompromised individuals, necessitates careful and in-depth safety studies. The traditional probiotic safety evaluation methods investigate targeted phenotypic traits, such as virulence factors and antibiotic resistance. However, the rapid innovation in omics technologies has offered an impactful means to ultimately sequence and unknot safety-related genes or their gene products at preliminary levels. Further validating the genome features using an array of phenotypic tests would provide an absolute realization of gene expression dynamics. For safety studies in animal models, the in vivo toxicity evaluation guidelines of chemicals proposed by the Organization for Economic Co-operation and Development (OECD) have been meticulously adopted in probiotic research. Future research should also focus on coupling genome-scale safety analysis and establishing a link to its transcriptome, proteome, or metabolome for a fine selection of safe probiotic strains. Considering the studies published over the years, it can be inferred that the safety of probiotics is strain-host-dose-specific. Taken together, an amalgamation of in silico, in vitro, and in vivo approaches are necessary for a fine scale selection of risk-free probiotic strain for use in human applications.

Considerations for determining safety of probiotics: A USP perspective

A history of safe use is a backbone of safety assessments for many current probiotic species, however, there is no global harmonization regarding requirements for establishing probiotic safety for use in foods and supplements. As probiotic manufacturers are increasingly seeking to use new strains, novel species, and next-generation probiotics, justification based on a significant history of use may be challenged. There are efforts underway by a variety of stakeholders, including the United States Pharmacopeia (USP), to develop best practices guidelines for assessing the quality and safety of probiotics. A current initiative of the USP seeks to provide expert advice specific to safety considerations for probiotics. Toward this goal, this review provides a helpful summary guide to global regulatory guidelines. We question the suitability of traditional animal toxicology studies designed for testing chemicals for relevance in assessing probiotic safety. This includes discussion of the use of excessive dose levels, the length of repeated dose toxicity studies needed, and the most suitable animal species used in toxicology studies. In addition, the importance of proper manufacturing practices with regard to final product safety are also included. Thus, an outline of essential parameters of a comprehensive safety assessment for a probiotic are provided.

Lactic acid bacteria: prominent player in the fight against human pathogens

INTRODUCTION

The human microbiome is a unique repository of diverse bacteria. Over 1000 microbial species reside in the human gut, which predominantly influences the host's internal environment and plays a significant role in host health. Lactic acid bacteria have long been employed for multiple purposes, ranging from food to medicines. Lactobacilli, which are often used in commercial food fermentation, have improved to the point that they might be helpful in medical applications.

AREAS COVERED

This review summarises various clinical and experimental evidence on efficacy of lactobacilli in treating a wide range of infections. Both laboratory based and clinical studies have been discussed.

EXPERT OPINION

Lactobacilli are widely accepted as safe biological treatments and host immune modulators (GRAS- Generally regarded as safe) by the US Food and Drug Administration and Qualified Presumption of Safety. Understanding the molecular mechanisms of lactobacilli in the treatment and pathogenicity of bacterial infections can help with the prediction and development of innovative therapeutics aimed at pathogens which have gained resistance to antimicrobials. To formulate effective lactobacilli based therapy significant research on the effectiveness of different lactobacilli strains and its association with demographic distribution is required. Also, the side effects of such therapy needs to be evaluated.

The effect of probiotics on functional constipation in adults: A randomized, double-blind controlled trial

BACKGROUND

Two formulations were developed in the form of an oral sachet containing probiotics, and their efficacy and safety were evaluated in adults with functional constipation.

METHODS

One formulation with Lactobacillus acidophilus, Bifidobacterium bifidum and Lactobacillus rhamnosus (3 billion Colony Forming Units - CFU); and another with Lactobacillus acidophilus, Bifidobacterium bifidum, Lactobacillus rhamnosus, Lactobacillus paracasei, Bifidobacterium longum, Bifidobacterium lactis, Lactobacillus casei, Bifidobacterium animallis (8 billion CFU). The participants were randomized in a 3-arm parallel study and one oral sachet was auto-administered once a day for 30 days.

RESULTS

Primary outcomes were improvement in increasing the frequency of weekly bowel movements and improvement in stool quality. Secondary outcomes were number of adverse events. In the first week one observed an increase in stool frequency and in the quality of stools, showing an improvement in constipation. No statistically significant differences were observed between the three treatment groups in relation to these outcomes (P ≥ .05). Only one adverse event was observed in a patient of group 2, related to abdominal pain.

CONCLUSION

The two probiotic cocktails were effective in improving the symptoms of functional constipation, by increasing both the weekly frequency of evacuation and stool quality, and were deemed safe. Clinicaltrials.gov number: NCT04437147.

Bifidobacterium animalis subsp. lactis Bi-07 supports lactose digestion in vitro and in randomized, placebo- and lactase-controlled clinical trials

BACKGROUND

Probiotics may alleviate lactose maldigestion.

OBJECTIVES

The objective was to select a probiotic with high lactase activity and compare it with lactase and placebo in clinical trials.

METHODS

Bacterial cultures were screened for lactase activity in a model of the upper gastrointestinal (GI) tract. Bifidobacterium animalis subsp. lactis Bi-07 (Bi-07) counts were adjusted in subsequent experiments to correspond to 4500 Food Chemicals Codex (FCC) units of lactase, the amount in the European Food Safety Authority (EFSA)-approved health claim. Two crossover clinical trials, Booster Alpha and Booster Omega, were performed in participants with lactose intolerance, where 2 × 1012 CFUs Bi-07, 4662 FCC lactase, or placebo was consumed simultaneously with a lactose challenge, with 1-wk washouts between challenges. The trial designs were identical except for the source of lactose. Breath hydrogen concentration (BHC) was measured to assess the effect of the investigational products on lactose digestion, for which incremental area under the curve (iAUC) was the primary outcome. Peak BHC, cumulative BHC, and GI symptoms were secondary outcomes.

RESULTS

Bi-07 was superior to placebo in reducing BHC [iAUC, parts per million (ppm) ∙ h] in both trials (Booster Alpha: geometric least square mean ratio: 0.462; 95% CI: 0.249, 0.859; P = 0.016; Booster Omega: 0.227; 95% CI: 0.095, 0.543; P = 0.001). Lactase was superior to placebo in Booster Alpha (0.190; 95% CI: 0.102, 0.365; P < 0.001) but not Booster Omega (0.493; 95% CI: 0.210, 1.156; P = 0.102). Noninferiority of Bi-07 compared with lactase was observed in Booster Omega (0.460; 95% CI: 0.193, 1.096; P = 0.079; CI upper limit < 1.25 noninferiority margin). Odds of abdominal pain (compared with placebo: 0.32, P = 0.036) and flatulence (compared with placebo: 0.25, P = 0.007) were lower with lactase in Booster Alpha. Increased odds of nausea were seen with Bi-07 (compared with placebo: 4.0, P = 0.005) in Booster Omega.

CONCLUSIONS

Bi-07 has high lactase activity, and in 2 clinical trials, it supported lactose digestion in individuals with lactose intolerance.These trials were registered at clinicaltrials.gov as NCT03659747 (Booster Alpha) and NCT03814668 (Booster Omega).

Microbiota analysis for risk assessment: evaluation of hazardous dietary substances and its potential role on the gut microbiome variability and dysbiosis

The expansion of fields related to probiotics, microbiome‐targeted interventions and an evolving landscape for implementation across policy, industry and end users, signifies an era of important clinical translational changes. Characteristics and perception of traditional probiotics stemmed from the historical long‐term use of fermented products. Although the distinction between probiotic microorganisms and fermentation‐associated microbes is important, it is often confused as not all fermented foods are probiotic supplements. Current innovation in area of biotechnology and bioinformatics is emerging outside of the classical definitions and new probiotics will emerge from novel sources, challenging scientific as well as regulatory instructions. At the same time, the search for individual and group microbiome signatures – biomarkers in order to predict disease incidence, progression and response to treatment is a key area of microbiological and multidisciplinary research, enabled by efficient and powerful processing of large data sets. However, the regulation of marketed beneficial microbes and probiotics differs among countries and the basic level of classification, which depend on probiotic classification is not globally harmonised. At the same time, the regulation is very demanding to evaluate the safety of products on the market, so that only those products with scientific evidence benefits can obtain positive recognition in ways of health claims. Collaborative experimental and theoretical approaches and case studies have assisted the progress in this crosscutting area of research. There is a requirement to clearly specify criteria and provide details about ways and approaches of achieving those criteria with the intention that manufacturers can benefit from a transparent way of communicating product quality to end users.

An Open-label, Multicenter Study to Assess the Efficacy and Safety of a Novel Probiotic Blend in Patients With Functional Gastrointestinal Symptoms

GOAL

A novel 5-strain (Bl-04, Bi-07, HN019, NCFM, and Lpc-37) probiotic blend was developed and its safety and efficacy were evaluated in patients with functional gastrointestinal (GI) symptoms.

BACKGROUND

These strains administered together have not previously been investigated.

STUDY

Patients aged 18 to 75 years with functional GI symptoms were eligible for inclusion in a single-arm, open-label, multicenter study (NCT04155801). An oral capsule containing the novel probiotic blend was administered once daily for 30 days. The primary efficacy endpoint was patient-reported improvement in overall GI well-being at day 30. Secondary efficacy endpoints included changes in GI symptoms assessed using the GI Health Symptom Questionnaire. Incidence of treatment-emergent adverse events was recorded at all visits.

RESULTS

Of 188 enrolled patients, 72.3% were female and mean (SD) age was 44.1 (13.4) years. At day 30, 85.1% of patients achieved the primary endpoint, a positive response signifying improvement in overall GI well-being. Improvements from baseline were reported at day 30 in diarrhea frequency (baseline frequency≥3 to 4 d/wk) and severity (baseline severity≥5/10) for 75.8% and 87.3% of patients, respectively. Over the same time period, constipation frequency (baseline frequency≥3 to 4 d/wk) and severity (baseline severity≥5/10) improved in 73.6% and 80.4% of patients, respectively. Most patients reported improvements at day 30 in frequency and severity of straining, urgency, abdominal pain/discomfort, bloating, and distention. Improvements reported at day 30 were generally observable at day 14. No safety signals were identified.

CONCLUSION

A novel 5-strain probiotic blend improved functional GI symptoms and was safe.

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.

A genome guided evaluation of the Lab4 probiotic consortium

In this study, we present the draft genome sequences of the Lab4 probiotic consortium using whole genome sequencing. Draft genome sequences were retrieved and deposited for each of the organisms; PRJNA559984 for B. bifidum CUL20, PRJNA482335 for Lactobacillus acidophilus CUL60, PRJNA482434 for Lactobacillus acid. Probiogenomic in silico analyses confirmed existing taxonomies and identified the presence putative gene sequences that were functionally related to the performance of each organism during in vitro assessments of bile and acid tolerability, adherence to enterocytes and susceptibility to antibiotics. Predictions of genomic stability identified no significant risk of horizontal gene transfer in any of the Lab4 strains and the absence of both antibiotic resistance and virulence genes. These observations were supported by the outcomes of acute phase and repeat dose tolerability studies in Wistar rats where challenge with high doses of Lab4 did not result in any mortalities, clinical/histopathological abnormalities nor indications of systemic toxicity. Detection of increased numbers of lactobacilli and bifidobacteria in the faeces of supplemented rats implied an ability to survive transit through the gastrointestinal tract and/or impact upon the intestinal microbiota composition. In summary, this study provides in silico, in vitro and in vivo support for probiotic functionality and the safety of the Lab4 consortium.

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.

Safety Assessment of Bacillus subtilis MB40 for Use in Foods and Dietary Supplements

With the growing popularity of probiotics in dietary supplements, foods, and beverages, it is important to substantiate not only the health benefits and efficacy of unique strains but also safety. In the interest of consumer safety and product transparency, strain identification should include whole-genome sequencing and safety assessment should include genotypic and phenotypic studies. Bacillus subtilis MB40, a unique strain marketed for use in dietary supplements, and food and beverage, was assessed for safety and tolerability across in silico, in vitro, and in vivo studies. MB40 was assessed for the absence of undesirable genetic elements encoding toxins and mobile antibiotic resistance. Tolerability was assessed in both rats and healthy human volunteers. In silico and in vitro testing confirmed the absence of enterotoxin and mobile antibiotic resistance genes of safety concern to humans. In rats, the no-observed-adverse-effect level (NOAEL) for MB40 after repeated oral administration for 14 days was determined to be 2000 mg/kg bw/day (equivalent to 3.7 × 10¹¹ CFU/kg bw/day). In a 28 day human tolerability trial, 10 × 10⁹ CFU/day of MB40 was well tolerated. Based on genome sequencing, strain characterization, screening for undesirable attributes and evidence of safety by appropriately designed safety evaluation studies in rats and humans, Bacillus subtilis MB40 does not pose any human health concerns under the conditions tested.

Epigenetics: A New Frontier in Probiotic Research

Research into the benefits of probiotics has progressed beyond interventional studies to identifying the underlying molecular mechanisms. Health-promoting effector molecules produced by probiotics are well documented and have been linked to specific genes and even individual nucleotides. However, the factors controlling the expression of these molecules are poorly understood and we argue that epigenetic influences likely play an important role in mediating the health-promoting attributes of probiotics. Here, we review established epigenetic regulation of important microbial genetic systems involved in health promotion, safety, and industrialization to provide evidence that the same regulation occurs in probiotic organisms. We advocate for studies combining genomic and meta-epigenomic data to better understand the mode of action of probiotics, their associated microbiomes, and their effects on consumers.

Fecal Recovery of Probiotics Administered as a Multi-Strain Formulation during Antibiotic Treatment

The present study aimed to investigate whether probiotic recovery is affected when consumed together with antibiotics. Fecal samples were collected from an earlier antibiotic associated diarrhea, randomized, placebo-controlled study with a product consisting of a combination of Lactobacillus acidophilus NCFM, Lactobacillus paracasei Lpc-37, and Bifidobacterium lactis Bi-07, B. lactis Bl-04 at equal numbers and at a total dose of 10¹⁰ CFU. Fecal samples were collected during the screening visit (T0), i.e., at the time of antibiotic prescription, and then on the last day of the antibiotic treatment (T1) as well as seven days after the subject had stopped taking the antibiotic treatment (T2) and at two weeks after completing antibiotic treatment and one week after probiotic/placebo consumption stopped (T3). Samples were analyzed for the presence of the four administered strains. The study was registered at clinicaltrials.gov as NCT01596829. Detection levels of all four strains were significantly increased from T0 to T1 and returned to baseline level from T2 to T3. There were also significantly more subjects with detectable levels of L. paracasei Lpc-37, B. lactis Bi-07, and B. lactis Bl-04 at T1 and T2 compared to T0 and T3, and compared to placebo. Each of the four strains could be detected in the feces of patients apparently unaffected by the simultaneous consumption of antibiotics.

Safety assessment of the candidate oral probiotic Lactobacillus crispatus YIT 12319: Analysis of antibiotic resistance and virulence-associated genes

Lactobacillus crispatus YIT 12319 (LcY) was isolated from the oral cavity of a healthy subject as a new candidate probiotic with potential benefits for oral health. As a safety assessment of LcY, we performed an antibiotic susceptibility test and virulence-associated gene analysis using a draft genome sequence. Susceptibility to 15 antibiotics was analyzed according to the standard method of the International Dairy Federation/International Organization for Standardization, as recommended by the European Food Safety Authority. The results showed that the minimum inhibitory concentrations of LcY were not higher than those of other L. crispatus strains, which have not acquired resistance to any antibiotics, suggesting that LcY had no externally acquired transmissible antibiotic resistance genes. Analysis of virulence-associated genes using the draft genome of LcY found that there were fewer potential virulence-associated genes in LcY than in other probiotics. These findings suggest that LcY could be a candidate probiotic based on its safety profile.

Safety profiles of beneficial lactic acid bacteria isolated from dairy systems

This study aimed to assess the safety aspects of 15 lactic acid bacteria (LAB) strains previously isolated from a dairy environment with relation to their beneficial features. LAB strains were assessed using phenotypic methods according to their production of virulence factors at 25 °C and 37 °C, as well as by examining their potential resistance to 15 antibiotics. Polymerase chain reaction (PCR) was also used to identify the presence of 50 genes associated with virulence factors and antibiotic resistance in the strains. None of the strains presented hemolytic activity or the production of gelatinase, lipase, deoxyribonuclease, or the tested biogenic amines. Based on the disk diffusion assay, all strains were resistant to oxacillin and sulfa/trimethoprim. Further, some were resistant to gentamicin (14), clindamycin (11), vancomycin (9), rifampicin (8), erythromycin (5), tetracycline (4), ampicillin (2), and chloramphenicol (1); no strain was resistant to imipenem. Regarding virulence- and antibiotic-resistance-related genes, 19 out of 50 tested genes were present in some strains; there was a variable association of expression. Based on the obtained data, the isolates presented relatively safe characteristics and behavior, findings that should lead to further studies to assess their potential usage as beneficial cultures in the food industry.

Droplet Digital PCR Is an Improved Alternative Method for High-Quality Enumeration of Viable Probiotic Strains

Traditional microbiological enumeration methods have long been employed as the standard evaluation procedure for probiotic microorganisms. These methods are labor intensive, have long-time to results and inherently have a high degree of variability – up to 35%. As clinical probiotic and microbiome science continues to grow and develop, it is increasingly important that researchers thoroughly define and deliver the targeted probiotic dose. Furthermore, to establish high quality commercial products, the same dosage level must be administered to consumers. An ISO method for the use of flow cytometry has been established which does speed up the time to results and reduce variability, but the method has not yet gained widespread adoption across the probiotic industry. This is possibly due to expertise needed to implement and maintain a new testing platform in an established quality system. In this study we compare enumeration using plate counts and flow cytometry to the use of droplet digital PCR (ddPCR), which in addition to giving faster time to results than plate count and less variability than both plate count and flow cytometry, has additional benefits such as strain-specific counts. Use of ddPCR gives the ability to design primers to target deletions and single base pair differences which will allow for strain profiling in microbiome analyses. We demonstrate that ddPCR probiotic enumeration results are positively correlated to both plate count and flow cytometry results and should be considered a viable, next generation enumeration method for the evaluation of probiotics.

"Physicochemical, immunomodulatory and safety aspects of milks fermented with Lactobacillus paracasei isolated from kefir"

The use of Lactobacillus paracasei strains isolated from kefir grains as starters for the development of functional dairy products was evaluated. The physicochemical and immunomodulatory properties of milks fermented with L. paracasei CIDCA8339, CIDCA83123 and CIDCA83124 were analyzed. The three strains produced bioactive metabolites during fermentation, since the fermented milk supernatants were able to downregulate >75% of the induced innate immune response in vitro. Although all strains presented absence of hemolytic activity and susceptibility to antibiotics, L. paracasei CIDCA8339 presented more attractive probiotic and technological properties. Mice consuming the fermented milk with L. paracasei CIDCA 8339 did not present significant modifications in sIgA levels or TNF-α, TGF-β and IL-10 mRNA expression in ileum. Additionally, a decrease of INF-γ level in ileum and no microbiological translocation to liver and spleen was observed. These results demonstrate that L. paracasei CIDCA8339 represents a safe promising potential probiotic strain for the development of functional foods.

The Production and Delivery of Probiotics: A Review of a Practical Approach

To successfully deliver probiotic benefits to the consumer, several criteria must be met. Here, we discuss the often-forgotten challenges in manufacturing the strains and incorporating them in consumer products that provide the required dose at the end of shelf life. For manufacturing, an intricate production process is required that ensures both high yield and stability and must also be able to meet requirements such as the absence of specific allergens, which precludes some obvious culture media ingredients. Reproducibility is important to ensure constant high performance and quality. To ensure this, quality control throughout the whole production process, from raw materials to the final product, is essential, as is the documentation of this quality control. Consumer product formulation requires extensive skill and experience. Traditionally, probiotic lactic acid bacteria and bifidobacteria have been incorporated in fermented dairy products, with limited shelf life and refrigerated storage. Currently, probiotics may be incorporated in dietary supplements and other "dry" food matrices which are expected to have up to 24 months of stability at ambient temperature and humidity. With the right choice of production process, product formulation, and strains, high-quality probiotics can be successfully included in a wide variety of delivery formats to suit consumer requirements.

Transcriptional and Functional Analysis of Bifidobacterium animalis subsp. lactis Exposure to Tetracycline

Commercial probiotic bacteria must be tested for acquired antibiotic resistance elements to avoid potential transfer to pathogens. The European Food Safety Authority recommends testing resistance using microdilution culture techniques previously used to establish inhibitory thresholds for the Bifidobacterium genus. Many Bifidobacterium animalis subsp. lactis strains exhibit increased resistance to tetracycline, historically attributed to the ribosomal protection gene tet(W). However, some strains that harbor genetically identical tet(W) genes show various inhibition levels, suggesting that other genetic elements also contribute to observed differences. Here, we adapted several molecular assays to confirm the inhibition of B. animalis subsp. lactis strains Bl-04 and HN019 and employed RNA sequencing to assess the transcriptional differences related to genomic polymorphisms. We detected specific stress responses to the antibiotic by correlating ATP concentration to number of viable genome copies from droplet digital PCR and found that the bacteria were still metabolically active in high drug concentrations. Transcriptional analyses revealed that several polymorphic regions, particularly a novel multidrug efflux transporter, were differentially expressed between the strains in each experimental condition, likely having phenotypic effects. We also found that the tet(W) gene was upregulated only during subinhibitory tetracycline concentrations, while two novel tetracycline resistance genes were upregulated at high concentrations. Furthermore, many genes involved in amino acid metabolism and transporter function were upregulated, while genes for complex carbohydrate utilization, protein metabolism, and clustered regularly interspaced short palindromic repeat(s) (CRISPR)-Cas systems were downregulated. These results provide high-throughput means for assessing antibiotic resistances of two highly related probiotic strains and determine the genetic network that contributes to the global tetracycline response.IMPORTANCEBifidobacterium animalis subsp. lactis is widely used in human food and dietary supplements. Although well documented to be safe, B. animalis subsp. lactis strains must not contain transferable antibiotic resistance elements. Many B. animalis subsp. lactis strains have different resistance measurements despite being genetically similar, and the reasons for this are not well understood. In the current study, we sought to examine how genomic differences between two closely related industrial B. animalis subsp. lactis strains contribute to different resistance levels. This will lead to a better understanding of resistance, identify future targets for analysis of transferability, and expand our understanding of tetracycline resistance in bacteria.

Effectiveness of Multistrain Versus Single-strain Probiotics: Current Status and Recommendations for the Future

Probiotics are investigated as single-strain and multistrain products. In the market, however, there is an increasing tendency to work with multistrain probiotics, in particular, products with a high number of different strains. There are some thoughts behind this: more strains imply more chances of success; it can mean a broader spectrum of efficacy, and there is often the hope that there are at least additive and, potentially, even synergistic effects. The present review did not find convincing evidence that these assumptions are valid. There is, however, also no strong evidence that the assumptions are incorrect and/or that there is antagonistic activity between strains in a combination. We suggest that, to answer these questions, structured research is conducted. Starting with a systematic review of meta-analyses that have compared single-strain and multistrain probiotic efficacy, dedicated human studies need to be performed, comparing single-strain and multistrain probiotics to each other and placebo. In vitro and animal studies can provide indications and may help understand mechanisms. For human, animal, and in vitro studies, it is recommended to work with the simple setup of 2 single strains, a 2-strain combination, and placebo. It is also important in such research to take into consideration the doses, as a combination product will have a higher total dose.

Ricci A, Allende A, Bolton D, Chemaly M, Davies R, Fernández Escámez PS, Girones R, Koutsoumanis K, Lindqvist R, Nørrung B, Robertson L, Ru G, Sanaa M, Simmons M, Skandamis P, Snary E, Speybroeck N, Ter Kuile B, Threlfall J, Wahlström H, Cocconcelli PS, Peixe L, Maradona MP, Querol A, Suarez JE, Sundh I, Vlak J, Barizzone F, Correia S, Herman L. Update of the list of QPS-recommended biological agents intentionally added to food or feed as notified to EFSA 8: suitability of taxonomic units notified to EFSA until March 2018

The qualified presumption of safety (QPS) was developed to provide a harmonised generic pre‐evaluation procedure to support safety risk assessments of biological agents performed by EFSA's Scientific Panels. The identity, body of knowledge, safety concerns and antimicrobial resistance of valid taxonomic units were assessed. Safety concerns identified for a taxonomic unit are, where possible and reasonable in number, reflected by ‘qualifications’ which should be assessed at the strain level by the EFSA's Scientific Panels. During the current assessment, no new information was found that would change the previously recommended QPS taxonomic units and their qualifications. The Panel clarified that the qualification ‘for production purpose only’ implies the absence of viable cells of the production organism in the final product and can also be applied for food and feed products based on microbial biomass. Between September 2017 and March 2018, the QPS notification list was updated with 46 microorganisms from applications for market authorisation. From these, 28 biological agents already had QPS status, 15 were excluded of the QPS exercise from the previous QPS mandate (10 filamentous fungi and one bacteriophage) or from further evaluations within the current mandate (two notifications of Streptomyces spp. and one of Escherichia coli), and one was excluded where confirmatory data for the risk assessment of a plant protection product (PPP) was requested (Pseudomonas sp.). Three taxonomic units were (re)evaluated: Paracoccus carotinifaciens and Paenibacillus lentus had been previously evaluated in 2008 and 2014, respectively, and were now re‐evaluated within this mandate, and Yarrowia lipolytica, which was evaluated for the first time. P. carotinifaciens and P. lentus cannot be granted QPS status due to lack of scientific knowledge. Y. lipolytica is recommended for QPS status, but only for production purpose.