Viability and Composition Validation of Commercial Probiotic Products by Selective Culturing Combined with Next-Generation Sequencing

Characterization of probiotics isolated from dietary supplements and evaluation of metabiotic-antibiotic combinations as promising therapeutic options against antibiotic-resistant pathogens using time-kill assay

BACKGROUND

The global probiotics dietary supplements market size is continuously growing. To overcome probiotics' health concerns, metabiotics are recognized as a safer alternative. Aiming to deal with the escalating antimicrobial resistance, the current work demonstrates synergistic metabiotic-antibiotic combinations against antibiotic-resistant pathogens.

METHODS

The probiotic properties of lactic acid bacteria (LAB) strains isolated from 3 commercial dietary supplements were characterized in vitro. The combinations of the cell-free supernatants (CFS) of selected probiotic strains and conventional antibiotics against Staphylococcus aureus and Escherichia coli clinical isolates were evaluated using the time-kill assay. To our knowledge, the current literature lacks sufficient time-kill assay studies revealing the kinetics of such metabiotic-antibiotic combinations against S. aureus and E. coli.

RESULTS

Four LAB strains isolated from dietary supplements as well as two reference strains were included in this study. The isolated LAB strains were identified by MALDI-TOF mass spectrometry as follows: P2: Lactobacillus acidophilus, P3: Lactiplantibacillus plantarum, P4: Lacticaseibacillus rhamnosus, and P5: Pediococcus acidilactici. The identification matched with that annotated by the manufacturers, except for P3. The tested strains could resist the acidic environment at pH 3. Excluding P2, the examined strains showed less than 1 log reduction in survivors upon the addition of reconstituted skimmed milk to pepsin at pH 2 and displayed an acceptable tolerance to 0.3% ox-bile. All the strains tolerated pancreatin. The hydrophobicity and autoaggregation capacities ranged between 7-92% and 36-66%, respectively. P2 was excluded owing to its inferior probiotic potential. Although the remaining strains showed excellent growth at 0.2% phenol, their growth was reduced at higher concentrations. L. plantarum and P. acidilactici strains possessed bile salt hydrolysis activity. The time-kill assay revealed promising synergistic activities of the combinations of CFS of L. rhamnosus P4 with either ceftazidime or gentamicin against E. coli and with only ceftazidime against S. aureus, as well as CFS of P. acidilactici P5 and ceftazidime against S. aureus.

CONCLUSIONS

Strict identification and evaluation of the probiotic strains incorporated in dietary supplements is crucial to ensure their safety and efficacy. The CFS of probiotics could be utilized to formulate novel biotherapeutics targeting problematic pathogens. However, future in vivo studies are required to evaluate the appropriate treatment regimen.

A Shotgun Metagenomics Investigation into Labeling Inaccuracies in Widely Sold Probiotic Supplements in the USA

While probiotics are generally considered safe, concerns persist regarding the accuracy of labels on these supplements and their potential contribution to the spread of antibiotic resistance genes. Given that probiotics are predominantly ingested with a view towards obtaining particular health benefits. The objective of this study is to assess the composition of 50 widely available probiotic supplements in the USA using shotgun metagenome sequencing. The study also determines the potential resistome profile, and the functional characteristics of these products. This study finds that 67% of products does not contain any labeling inaccuracies. Antimicrobial Resistance Genes (ARGs) are identified in several products, particularly Bacillus-based products carrying between 10 and 56 genes. The risk posed by the presence of these ARGs requires further study. Functional analysis reveals differences in metabolic profiles among probiotic supplements, indicating the importance of strain-level selection for personalized probiotics. This study provides updated and comprehensive analysis to evaluate a snapshot of the USA market. The study demonstrates that label inaccuracies occur on approximately one third of popular dietary supplement products sold in the USA, supporting the need for improved approaches to marketing and quality control. Further, the risk of antibiotic resistance, especially in Bacillus-based formulations, should be assessed.

Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products

The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju. The genomes were constructed using GTDB and validated through PATRICK and TYGS. A FastTree 2 phylogenetic tree was constructed using several type strain sequences from relevant species. Bacteriocin and ribosomally synthesized polypeptide (RiPP) genes were discovered, and a safety check was performed to test for toxins, antibiotic resistance, and genetic drift genes. Except for two products with unclaimed species, the labeling was taxonomically correct. In three product formulations, Lactobacillus acidophilus, Limosilactobacillus reuteri, Lacticaseibacillus paracasei, and Bifidobacterium animalis exhibited two to three genomic alterations, while Streptococcus equinus was found in one. TYGS and GDTB discovered E. faecium and L. paracasei in distinctly different ways. All the bacteria tested had the genetic repertoire to tolerate GIT transit, although some exhibited antibiotic resistance, and one strain had two virulence genes. Except for Bifidobacterium strains, the others revealed a variety of bacteriocins and ribosomally synthesized polypeptides (RiPP), 92% of which were unique and non-homologous to known ones. Plasmids and mobile genetic elements are present in strains of L. reuteri (NPLps01.et_L.r and NPLps02.uf_L.r), Lactobacillus delbrueckii (NPLps01.et_L.d), Streptococcus thermophilus (NPLps06.ab_S.t), and E. faecium (NPLps07.nf_E.f). Our findings support the use of metagenomics to build better and efficient production and post-production practices for probiotic quality and safety assessment.

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

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

Single-cell rapid identification, in situ viability and vitality profiling, and genome-based source-tracking for probiotics products

Rapid expansion of the probiotics industry demands fast, sensitive, comprehensive, and low-cost strategies for quality assessment. Here, we introduce a culture-free, one-cell-resolution, phenome-genome-combined strategy called Single-Cell Identification, Viability and Vitality tests, and Source-tracking (SCIVVS). For each cell directly extracted from the product, the fingerprint region of D2O-probed single-cell Raman spectrum (SCRS) enables species-level identification with 93% accuracy, based on a reference SCRS database from 21 statutory probiotic species, whereas the C-D band accurately quantifies viability, metabolic vitality plus their intercellular heterogeneity. For source-tracking, single-cell Raman-activated Cell Sorting and Sequencing can proceed, producing indexed, precisely one-cell-based genome assemblies that can reach ~99.40% genome-wide coverage. Finally, we validated an integrated SCIVVS workflow with automated SCRS acquisition where the whole process except sequencing takes just 5 h. As it is >20-fold faster, >10-time cheaper, vitality-revealing, heterogeneity-resolving, and automation-prone, SCIVVS is a new technological and data framework for quality assessment of live-cell products.

3D printing of microencapsulated Lactobacillus rhamnosus for oral delivery

3D Printing is an innovative technology within the pharma and food industries that allows the design and manufacturing of novel delivery systems. Orally safe delivery of probiotics to the gastrointestinal tract faces several challenges regarding bacterial viability, in addition to comply with commercial and regulatory standpoints. Lactobacillus rhamnosus CNCM I-4036 (Lr) was microencapsulated in generally recognised as safe (GRAS) proteins, and then assessed for robocasting 3D printing. Microparticles (MP-Lr) were developed and characterised, prior to being 3D printed with pharmaceutical excipients. MP-Lr showed a size of 12.3 ± 4.1 µm and a non-uniform wrinkled surface determined by Scanning Electron Microscopy (SEM). Bacterial quantification by plate counting accounted for 8.68 ±0.6 CFU/g of live bacteria encapsulated within. Formulations were able to keep the bacterial dose constant upon contact with gastric and intestinal pH. Printlets consisted in oval-shape formulations (15 mm × 8 mm × 3.2 mm) of ca. 370 mg of total weight, with a uniform surface. After the 3D printing process, bacterial viability remained even as MP-Lr protected bacteria alongside the process (log reduction of 0.52, p>0.05) in comparison with non-encapsulated probiotic (log reduction of 3.05). Moreover, microparticle size was not altered during the 3D printing process. We confirmed the success of this technology for developing an orally safe formulation, GRAS category, of microencapsulated Lr for gastrointestinal vehiculation.

Analysis of the microbial content of probiotic products commercialized worldwide and survivability in conditions mimicking the human gut environment

Introduction

Probiotics are living microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Adequate number of living microbes, the presence of specific microorganisms, and their survival in the gastrointestinal (GI) environment are important to achieve desired health benefits of probiotic products. In this in vitro study, 21 leading probiotic formulations commercialized worldwide were evaluated for their microbial content and survivability in simulated GI conditions.

Methods

Plate-count method was used to determine the amount of living microbes contained in the products. Culture-dependent Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry and culture-independent metagenomic analysis through 16S and 18S rDNA sequencing were applied in combination for species identification. To estimate the potential survivability of the microorganisms contained in the products in the harsh GI environment, an in vitro model composed of different simulated gastric and intestinal fluids was adopted.

Results

The majority of the tested probiotic products were concordant with the labels in terms of number of viable microbes and contained probiotic species. However, one product included fewer viable microbes than those displayed on the label, one product contained two species that were not declared, and another product lacked one of the labeled probiotic strains. Survivability in simulated acidic and alkaline GI fluids was highly variable depending on the composition of the products. The microorganisms contained in four products survived in both acidic and alkaline environments. For one of these products, microorganisms also appeared to grow in the alkaline environment.

Conclusion

This in vitro study demonstrates that most globally commercialized probiotic products are consistent with the claims described on their labels with respect to the number and species of the contained microbes. Evaluated probiotics generally performed well in survivability tests, although viability of microbes in simulated gastric and intestinal environments showed large variability. Although the results obtained in this study indicate a good quality of the tested formulations, it is important to stress that stringent quality controls of probiotic products should always be performed to provide optimal health benefits for the host.

Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements

The market for the application of probiotics as a livestock health improvement supplement has increased in recent years. However, most of the available products are quality-controlled using low-resolution techniques and un-curated databases, resulting in misidentification and incorrect product labels. In this work, we deployed two workflows and compared results obtained by full-length 16S rRNA genes (16S) and metagenomic (Meta) data to investigate their reliability for the microbial composition of both liquid and solid forms of animal probiotic products using Oxford Nanopore long-read-only (without short-read). Our result revealed that 16S amplicon data permits to detect the bacterial microbiota even with the low abundance in the samples. Moreover, the 16S approach has the potential to provide species-level resolution for prokaryotes but not for assessing yeast communities. Whereas, Meta data has more power to recover of high-quality metagenome-assembled genomes that enables detailed exploration of both bacterial and yeast populations, as well as antimicrobial resistance genes, and functional genes in the population. Our findings clearly demonstrate that implementing these workflows with long-read-only monitoring could be applied to assessing the quality and safety of probiotic products for animals and evaluating the quality of probiotic products on the market. This would benefit the sustained growth of the livestock probiotic industry.

In Vitro Evaluation of Commercial Probiotic Products Containing Streptococcus salivarius K12 by Assessment of Probiotic Viability and Inhibitory Potency against Respiratory Pathogens

Upper respiratory infections (URI) are the most frequent illnesses, especially in children. The majority of those infections are prescribed broad-spectrum antibiotics, which are associated with various side effects and with the increase in multi-drug-resistant strains. A promising alternative approach is the administration of the probiotic strain Streptococcus salivarius K12 (SSK12) that colonizes the upper respiratory tract (URT) and produces the salivaricins A2 and B, which strongly antagonize the growth of key respiratory pathogens. However, since for food supplements no quality controls of the active probiotic ingredient are mandatory, the efficacy of commercial products containing SSK12 may vary. This study aimed to investigate the in vitro efficacy of several commercial SSK12-containing probiotics, positioned for the prevention of respiratory infections. The parameters evaluated to determine the in vitro efficacy included the viability of the probiotic bacterial strain and the minimum inhibitory dilution (MID) of the probiotic, determined by the agar spot method, against the pathogenic/potential pathogenic bacterial strains Streptococcus pyogenes FF22 and Micrococcus luteus T18. All tests were carried out both 12 and 24 months after manufacturing (AM) for each commercial product. The viability ranged from 9 × 108 to 4.4 × 109 CFU/serving at 12 months AM and from 8.5 × 107 to 2.8 × 109 CFU/serving at 24 months AM. The MID was, in general, positively correlated with the probiotic bacterium viability and varied between the commercial products, ranging from 10−5 to 10−7 at 12 months AM and from 10−4 to 10−7 at 24 months AM. Moreover, the inhibition zones related to the two indicator strains were variable in diameter for different products. The high variation of the in vitro efficacy of commercial products containing SSK12 may explain the different results reported in the literature regarding the clinical benefits of these preparations, and the determination of this parameter may be useful to evaluate the quality of probiotic products containing this bacterial strain.

Oxalobacter formigenes: A new hope as a live biotherapeutic agent in the management of calcium oxalate renal stones

Recent advances in understanding the association of gut microbiota with the host have shown evidence of certain bacterial therapeutic potentiality in preventing and treating metabolic diseases. Hyperoxaluria is a severe challenge in nephrology and has led to the novel gut eubiosis as current therapy. The human gut commensal, obligate anaerobic, and intestinal oxalate-degrading strains of Oxalobacter formigenes have drawn a promising significant interest for the next-generation probiotics (NGPs). This nonpathogenic, potential probiotic, and specialist oxalotrophic properties of O. formigenes give a new hope as a live biotherapeutic agent for calcium oxalate renal therapy. Numerous satisfactory outcomes of in vitro and in vivo studies were achieved on evaluating O. formigenes functionality, but the commercial production of this bacterium is yet to be achieved. This bacterium finds diverse application in dietary and endogenous oxalate degradation and the improvement of gut health, on which we concentrated our attention in this review. The relationship between good anaerobic gut bacterial dysbiosis and renal complications is comprehensively discussed to address the need for the development probiotic formulation. However, the commercial production of this bacteria on a broad scale is complex, with numerous obstacles, mainly because they are oxygen-sensitive and difficult to culture. This review will coherently present the current and available methodologies in producing, stabilizing, and delivering these NGPs to treat calcium stones. Moreover, the study presents the extensive work and key milestones achieved in the research on O. formigenes from tale to the truth.

Compositional Quality and Possible Gastrointestinal Performance of Marketed Probiotic Supplements

The local pharmacies and shops are brimming with various probiotic products that herald a range of health benefits. The poor quality of probiotic products in both dosage and species is symptomatic of this multi-billion-dollar market making it difficult for consumers to single out reliable ones. This study aims to fill the potential gap in the labeling accuracy of probiotic products intended for human consumption. We describe a combinatorial approach using classical culture-dependent technique to quantify and molecular techniques (16 s rRNA gene sequencing, multilocus sequence, and ribotyping) for strain recognition of the microbial contents. The full gamut of probiotic characteristics including acid, bile and lysozyme tolerances, adhesiveness, anti-pathogenicity, and degree of safeness were performed. Their capacity to endure gastro-intestinal (GIT) stresses and select drugs was assessed in vitro. Our results forced us to declare that the local probiotic market is essentially unregulated. Almost none of the probiotic products tested met the label claim. Some (11%) have no viable cells, and a quarter (27%) showing significant inter-batch variation. A lower microbial count was typical with undesirables constituting a quarter of the total (~ 27%). Half of the products contained antibiotic-resistant strains; the unregulated use of these probiotics carries the risk of spreading antibiotic resistance to gut pathobionts. Poor tolerance to gut conditions and mediocre functionalism make the case worse. The current regulatory systems do not take this discrepancy into account. We recommend an evidence-based regular market surveillance of marketed probiotics to ensure the authenticity of the claims and product effectiveness.

Microbiological Quality and Resistance to an Artificial Gut Environment of Two Probiotic Formulations

The quality control of probiotic products is the focus of numerous organizations worldwide. Several studies have highlighted the poor microbiological quality of many commercial probiotic formulations in terms of the identity of the contained microorganisms, viability, and purity, thus precluding the expected health benefits and representing a potential health risk for consumers. In this paper, we analyzed the contents of two probiotic formulations, one composed of an encapsulated mixture of lactobacilli and bifidobacteria, and one by a lyophilized yeast. The microorganisms contained in the products were quantified and identified using up-to-date methodologies, such as MALDI-TOF MS and metagenomic analysis. Moreover, as acid and bile tolerance is included among the criteria used to select probiotic microorganisms, in vitro tests were performed to evaluate the behavior of the formulations in conditions mimicking the harsh gastric environment and the intestinal fluids. Our results indicate the high quality of the formulations in terms of the enumeration and identification of the contained organisms, as well as the absence of contaminants. Moreover, both products tolerated the acidic conditions well, with encapsulation providing further protection for the microorganisms. A good tolerance to the simulated artificial intestinal conditions was also evidenced for both preparations.

Spotlight on the Compositional Quality of Probiotic Formulations Marketed Worldwide

On the worldwide market, a great number of probiotic formulations are available to consumers as drugs, dietary supplements, and functional foods. For exerting their beneficial effects on host health, these preparations should contain a sufficient amount of the indicated living microbes and be pathogen-free to be safe. Therefore, the contained microbial species and their amount until product expiry are required to be accurately reported on the labels. While commercial formulations licensed as drugs are subjected to rigorous quality controls, less stringent regulations are generally applied to preparations categorized as dietary supplements and functional foods. Many reports indicated that the content of several probiotic formulations does not always correspond to the label claims in terms of microbial identification, number of living organisms, and purity, highlighting the requirement for more stringent quality controls by manufacturers. The main focus of this review is to provide an in-depth overview of the microbiological quality of probiotic formulations commercialized worldwide. Many incongruences in the compositional quality of some probiotic formulations available on the worldwide market were highlighted. Even if manufacturers carry at least some of the responsibility for these inconsistencies, studies that analyze probiotic products should be conducted following recommended and up-to-date methodologies.

Authenticity of probiotic foods and dietary supplements: A pivotal issue to address

The market of probiotic foods and supplements is growing rapidly but frequently the commercialized products are not compliant with their labels in terms of claimed probiotic strain(s) and labeled number of viable probiotic cells, thus mining the authenticity of these probiotic products.In this review, we provide an up-to-date overview of: (i) the current regulatory aspects, (ii) the consistency of probiotic foods and supplements with their labels, (iii) the implications of mislabeling on the quality, safety and functionality of these products and (iv) the available and most promising methods to assess the authenticity of these products, taking into account the need to discriminate among the different physiological states probiotics might be in the carrier matrices. It arises that authenticity of probiotic foods and supplements is an urgent issue, of industrial and legislation relevance, that need to be addressed. A plethora of methods are available to reach this goal, each with its own advantages and disadvantages. Protocols that combine the use of propidium monoazide (PMA) with metagenomics or polyphasic approaches including the PMA real time PCR or flow cytometry (for the viability assessment) and the whole genome sequence analysis (for the identification and typing of the probiotic strain) are the most promising that should be standardized and used by producers and regulators.

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.