Development and utility of the FDA 'GutProbe' DNA microarray for identification, genotyping and metagenomic analysis of commercially available probiotics

Whole genome sequencing of promising Lactobacillus delbrueckii subsp. bulgaricus strains isolated from Egyptian dairy products for probiotic characteristics

Probiotics are living microorganisms that, when given in an adequate dose, have a healthy impact on human well-being. With global interest in self-care, dietary supplements especially probiotics is expanding rapidly due to their supported health effects. In this study, a total of twenty-two samples were collected from dairy products in Egypt's markets, firstly isolated then identified and screened for probiotic properties under stressful conditions as NaCl, acid and bile salt conditions. After evaluation of the antimicrobial effect against widespread gram negative and gram positive human infecting bacteria, besides the antiviral assessment against (SARS-CoV-2) virus which has disturbed the world, the antibiotic susceptibility test was done. Only three promising isolates were subjected for whole genome sequence with high-output next generation technology and the obtained data was subjected to a full bioinformatics analysis. The results obtained stated the advance of our isolates to tolerate the stress factors that can struggle in the human gut as well as the antimicrobial effects. All these bright characteristics were confirmed and illustrated in detail through different and reliable genome analysis tools. Our isolates were founded to have stable genome through containing mobile genetic elements like phages and CRISPR clusters that confirm the safety and quality for human health.

Complete genome sequencing and probiotic characterization of promising lactic acid bacterial strains isolated from dairy products in Egyptian markets

BACKGROUND

Probiotics refer to live bacteria that, when administered in a sufficiently, exert a beneficial influence on human health. Due to the probiotics' beneficial health advantages, dietary supplements are expanding rapidly as a self-care interest worldwide. It may be beneficial to administer probiotic strains resistant to antibiotics concurrently with an antibiotic treatment. Our study investigates nineteen dairy products collected from Egyptian markets, isolated, identified and underwent a characterization for probiotic features under demanding circumstances as NaCl, acid and bile salt environments. The antibiotic sensitivity test was performed later to the antimicrobial assessment against widespread both negative and positive gram-stained bacteria infecting humans, along with the antiviral evaluation against (SARS-CoV-2), the virus that has disturbed the world recently.

RESULTS

Out of nineteen investigated isolates, five potential probiotic isolates were examined for probiotic characteristics. Our tested samples were of dairy origin (yogurt, cottage-cheese and sour milk) in Egypt, were identified as Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus and Pediococcus acidilactici. These promising isolates had withstood stressful factors, such as NaCl, acid, bile salts, and the antimicrobial advance. The genomes were characterized for the physiology, safety, and efficacy of these isolates for probiotic qualities plus the presence of mobile genetic components and prophages that influence the genome's flexibility. They lack virulence factors and pathogenicity, rather than the lack of antibiotic resistance genes.

CONCLUSION

Three promising isolates underwent complete genome sequencing with high-throughput second generation technology followed by comprehensive bioinformatic analysis. The results showed that our isolates possess traits enabling resilience to antimicrobial effects and stress factors that might cause problems in the human gut. Several trustworthy genomic analysis methods were used to confirm and provide detailed illustrations of all traits. Genomic analyses confirmed the presence of stable genomes due to including mobile genetic components such as phages and CRISPR clusters, which validate their quality and safe usage for human health.

Microbiota-targeted interventions and clinical implications for maternal-offspring health: An umbrella review of systematic reviews and meta-analyses of randomised controlled trials

Background

Microbes in the human body are the determinants of life-long health and disease. Microbiome acquisition starts in utero and matures during early childhood through breastfeeding. However, maternal gut dysbiosis affects the maternal-offspring microbiome interplay. Lines of evidence on dysbiosis-targeted interventions and their effect on maternal-offspring health and gut microbiome are inconsistent and inconclusive. Therefore, this study summarised studies to identify the most common microbiota-targeted intervention during pregnancy and lactation and to comprehensively evaluate its effects on maternal and offspring health.

Methods

This umbrella review was conducted by systematically searching databases such as PubMed and the Web of Science from inception to 2 September 2023. The quality was assessed using the Assessment of Multiple Systematic Reviews-2 checklist. The Grading of Recommendations Assessment, Development, and Evaluation was used for grading the strength and certainty of the studies. The overlap of primary studies was quantified by the corrected covered area score.

Results

A total of 17 systematic reviews and meta-analyses with 219 randomised controlled trials, 39 113 mothers, and 20 915 infants were included in this study. About 88% of studies had moderate and above certainty of evidence. Probiotics were the most common and effective interventions at reducing gestational diabetes risk (fasting blood glucose with the mean difference (MD) = -2.92, -0.05; I2 = 45, 98.97), fasting serum insulin (MD = -2.3, -2.06; I2 = 45, 77), glycated haemoglobin (Hb A1c) = -0.16; I2 = 0.00)), Homeostatic Model Assessment of insulin resistance (HOMA-IR) (MD = -20.55, -0.16; I2 = 0.00, 72.00), and lipid metabolism (MD = -5.47, 0.98; I2 = 0.00, 90.65). It was also effective in preventing and treating mastitis (risk ratio (RR) = 0.49; I2 = 2.00), relieving anxiety symptoms (MD = -0.99, 0.01; I2 = 0.00, 70.00), depression in lactation (MD = -0.46, -0.22; I2 = 0.00, 74.00) and reducing recto-vaginal bacterial colonisation (odds ratio (OR) = 0.62; I2 = 4.80), and with no adverse events. It also effectively remodelled the infant gut microbiome (MD = 0.89; I2 = 95.01) and prevented infant allergies. However, studies on pregnancy outcomes and preeclampsia incidences are limited.

Conclusions

Our findings from high-quality studies identify that probiotics are the most common microbiome interventions during pregnancy and lactation. Probiotics have a strong impact on maternal and offspring health through maintaining gut microbiome homeostasis. However, further studies are needed on the effect of microbiota-targeted interventions on maternal cardiometabolic health, pregnancy, and neonatal outcomes.

Registration

This umbrella review was registered with PROSPERO, CRD42023437098.

The Antimicrobial Effect of Various Single-Strain and Multi-Strain Probiotics, Dietary Supplements or Other Beneficial Microbes against Common Clinical Wound Pathogens

The skin is the largest organ in the human body and is colonized by a diverse microbiota that works in harmony to protect the skin. However, when skin damage occurs, the skin microbiota is also disrupted, and pathogens can invade the wound and cause infection. Probiotics or other beneficial microbes and their metabolites are one possible alternative treatment for combating skin pathogens via their antimicrobial effectiveness. The objective of our study was to evaluate the antimicrobial effect of seven multi-strain dietary supplements and eleven single-strain microbes that contain probiotics against 15 clinical wound pathogens using the agar spot assay, co-culturing assay, and agar well diffusion assay. We also conducted genera-specific and species-specific molecular methods to detect the DNA in the dietary supplements and single-strain beneficial microbes. We found that the multi-strain dietary supplements exhibited a statistically significant higher antagonistic effect against the challenge wound pathogens than the single-strain microbes and that lactobacilli-containing dietary supplements and single-strain microbes were significantly more efficient than the selected propionibacteria and bacilli. Differences in results between methods were also observed, possibly due to different mechanisms of action. Individual pathogens were susceptible to different dietary supplements or single-strain microbes. Perhaps an individual approach such as a 'probiogram' could be a possibility in the future as a method to find the most efficient targeted probiotic strains, cell-free supernatants, or neutralized cell-free supernatants that have the highest antagonistic effect against individual clinical wound pathogens.

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.

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

The consumption of dietary supplements to treat health complications or to improve overall health conditions has become a globally increasing trend that leads to the development of a large number of health-related novel products and expands the associated manufacturing industries around the world. In the current study, we applied selective culturing combined with next-generation sequencing to examine the microbial viability in terms of its culturability on culture medium, composition, and possible contamination in the selected 17 commercial probiotic products sold in the mainland China market. Additionally, the relative abundance of each individual bacterial content was also evaluated by using the generated sequencing reads. The tested probiotic product samples were subjected to Illumina HiSeq-2000 sequencing platform and thoroughly analyzed by the in-house developed bioinformatics pipeline. The comprehensive culturing and sequencing analysis revealed both viability and composition inaccuracy among the several tested probiotic products, however, no contaminant was identified during the analysis. Among the total, five probiotic products (29.41%) were found with an inaccurate or lower colony-forming unit (CFU) counts on culture media while four probiotic products (23.52%) have inaccurately labeled classification. This study provides an ideal qualitative and quantitative assessment approach, which can be used as a diagnostic tool for the accurate assessment of commercial probiotic supplements.

Database and Bioinformatics Studies of Probiotics

Probiotics have been widely explored for health benefits, animal cares, and agricultural applications. Recent advances in microbiome, microbiota, and microbial dark matter research have fueled greater interests in and paved ways for the study of the mechanisms of probiotics and the discovery of new probiotics from uncharacterized microbial sources. A probiotics database named PROBIO was developed to facilitate these efforts and the need for the information on the known probiotics, which provides the comprehensive information about the probiotic functions of 448 marketed, 167 clinical trial/field trial, and 382 research probiotics for use or being studied for use in humans, animals, and plants. The potential applications of the probiotics data are illustrated by several literature-reported investigations, which have used the relevant information for probing the function and mechanism of the probiotics and for discovering new probiotics. PROBIO can be accessed free of charge at http://bidd2.nus.edu.sg/probio/homepage.htm .

Current Status of the Preharvest Application of Pro- and Prebiotics to Farm Animals to Enhance the Microbial Safety of Animal Products

The selection of microorganisms that act as probiotics and feed additives that act as prebiotics is an ongoing research effort, but a sizable range of commercial pro-, pre- and synbiotic (combining pro- and prebiotics) products are already available and being used on farms. A survey of the composition of commercial products available in the United States revealed that Lactobacillus acidophilus, Enterococcus faecium, and Bacillus subtilis were the three most common species in probiotic products. Of the nearly 130 probiotic products (also called direct-fed microbials) for which information was available, about 50 also contained yeasts or molds. The focus on these particular bacteria and eukaryotes is due to long-standing ideas about the benefits of such strains, research data on effectiveness primarily in laboratory or research farm settings, and regulations that dictate which microorganisms or feed additives can be administered to farm animals. Of the direct-fed microbials, only six made a claim relating to food safety or competitive exclusion of pathogens. None of the approximately 50 prebiotic products mentioned food safety in their descriptions. The remainder emphasized enhancement of animal performance such as weight gain or overall animal health. The reason why so few products carry food safety-related claims is the difficulties in establishing unambiguous cause and effect relationships between the application of such products in varied and constantly changing farm environments and improved food safety of the end product.

Genotyping by PCR and High-Throughput Sequencing of Commercial Probiotic Products Reveals Composition Biases

Recent advances in microbiome research have brought renewed focus on beneficial bacteria, many of which are available in food and dietary supplements. Although probiotics have historically been defined as microorganisms that convey health benefits when ingested in sufficient viable amounts, this description now includes the stipulation “well defined strains,” encompassing definitive taxonomy for consumer consideration and regulatory oversight. Here, we evaluated 52 commercial dietary supplements covering a range of labeled species using plate counting and targeted genotyping. Strain identities were assessed using methods recently published by the United States Pharmacopeial Convention. We also determined the relative abundance of individual bacteria by high-throughput sequencing (HTS) of the 16S rRNA sequence using paired-end 2 × 250 bp Illumina MiSeq technology. Using these methods, we tested the hypothesis that products do contain the quantitative and qualitative list of labeled microbial species. We found that 17 samples (33%) were below label claim for CFU prior to their expiration dates. A multiplexed-PCR scheme showed that only 30/52 (58%) of the products contained a correctly labeled classification, with issues encompassing incorrect taxonomy, missing species, and un-labeled species. The HTS revealed that many blended products consisted predominantly of Lactobacillus acidophilus and Bifidobacterium animalis subsp. lactis. These results highlight the need for reliable methods to determine the correct taxonomy and quantify the relative amounts of mixed microbial populations in commercial probiotic products.

CAZyChip: dynamic assessment of exploration of glycoside hydrolases in microbial ecosystems

BACKGROUND

Microorganisms constitute a reservoir of enzymes involved in environmental carbon cycling and degradation of plant polysaccharides through their production of a vast variety of Glycoside Hydrolases (GH). The CAZyChip was developed to allow a rapid characterization at transcriptomic level of these GHs and to identify enzymes acting on hydrolysis of polysaccharides or glycans.

RESULTS

This DNA biochip contains the signature of 55,220 bacterial GHs available in the CAZy database. Probes were designed using two softwares, and microarrays were directly synthesized using the in situ ink-jet technology. CAZyChip specificity and reproducibility was validated by hybridization of known GHs RNA extracted from recombinant E. coli strains, which were previously identified by a functional metagenomic approach. The GHs arsenal was also studied in bioprocess conditions using rumen derived microbiota.

CONCLUSIONS

The CAZyChip appears to be a user friendly tool for profiling the expression of a large variety of GHs. It can be used to study temporal variations of functional diversity, thereby facilitating the identification of new efficient candidates for enzymatic conversions from various ecosystems.

Culture-Independent Metagenomic Surveillance of Commercially Available Probiotics with High-Throughput Next-Generation Sequencing

Millions of people consume dietary supplements either following a doctor's recommendation or at their own discretion to improve their overall health and well-being. This is a rapidly growing trend, with an associated and expanding manufacturing industry to meet the demand for new health-related products. In this study, we examined the contents and microbial viability of several popular probiotic products on the United States market. Culture-independent methods are proving ideal for fast and efficient analysis of foodborne pathogens and their associated microbial communities but may also be relevant for analyzing probiotics containing mixed microbial constituents. These products were subjected to next-generation whole-genome sequencing and analyzed by a custom in-house-developed k-mer counting method to validate manufacturer label information. In addition, the batch variability of respective products was examined to determine if any changes in their formulations and/or the manufacturing process occurred. Overall, the products we tested adhered to the ingredient claims and lot-to-lot differences were minimal. However, there were a few discrepancies in the naming of closely related Lactobacillus and Bifidobacterium species, whereas one product contained an apparent Enterococcus contaminant in two of its three lots. With the microbial contents of the products identified, we used traditional PCR and colony counting methods to comparatively assess our results and verify the viability of the microbes in these products with regard to the labeling claims. Of all the supplements examined, only one was found to be inaccurate in viability. Our use of next-generation sequencing as an analytical tool clearly demonstrated its utility for quickly analyzing commercially available products containing multiple microbes to ensure consumer safety. IMPORTANCE The rapidly growing supplement industry operates without a formal premarket approval process. Consumers rely on product labels to be accurate and true. Those products containing live microbials report both identity and viability on most product labels. This study used next-generation sequencing technology as an analytical tool in conjunction with classic culture methods to examine the validity of the labels on supplement products containing live microbials found in the United States marketplace. Our results show the importance of testing these products for identity, viability, and potential contaminants, as well as introduce a new culture-independent diagnostic approach for testing these products. Podcast: A podcast concerning this article is available.

Validating bifidobacterial species and subspecies identity in commercial probiotic products

BACKGROUND

The ingestion of probiotics to attempt to improve health is increasingly common; however, quality control of some commercial products can be limited. Clinical practice is shifting toward the routine use of probiotics to aid in prevention of necrotizing enterocolitis in premature infants, and probiotic administration to term infants is increasingly common to treat colic and/or prevent atopic disease. Since bifidobacteria dominate the feces of healthy breast-fed infants, they are often included in infant-targeted probiotics.

METHODS

We evaluated 16 probiotic products to determine how well their label claims describe the species of detectable bifidobacteria in the product. Recently developed DNA-based methods were used as a primary means of identification, and were confirmed using culture-based techniques.

RESULTS

We found that the contents of many bifidobacterial probiotic products differ from the ingredient list, sometimes at a subspecies level. Only 1 of the 16 probiotics perfectly matched its bifidobacterial label claims in all samples tested, and both pill-to-pill and lot-to-lot variation were observed.

CONCLUSION

Given the known differences between various bifidobacterial species and subspecies in metabolic capacity and colonization abilities, the prevalence of misidentified bifidobacteria in these products is cause for concern for those involved in clinical trials and consumers of probiotic products.

Application of metagenomic sequencing to food safety: detection of Shiga Toxin-producing Escherichia coli on fresh bagged spinach

Culture-independent diagnostics reduce the reliance on traditional (and slower) culture-based methodologies. Here we capitalize on advances in next-generation sequencing (NGS) to apply this approach to food pathogen detection utilizing NGS as an analytical tool. In this study, spiking spinach with Shiga toxin-producing Escherichia coli (STEC) following an established FDA culture-based protocol was used in conjunction with shotgun metagenomic sequencing to determine the limits of detection, sensitivity, and specificity levels and to obtain information on the microbiology of the protocol. We show that an expected level of contamination (∼10 CFU/100 g) could be adequately detected (including key virulence determinants and strain-level specificity) within 8 h of enrichment at a sequencing depth of 10,000,000 reads. We also rationalize the relative benefit of static versus shaking culture conditions and the addition of selected antimicrobial agents, thereby validating the long-standing culture-based parameters behind such protocols. Moreover, the shotgun metagenomic approach was informative regarding the dynamics of microbial communities during the enrichment process, including initial surveys of the microbial loads associated with bagged spinach; the microbes found included key genera such as Pseudomonas, Pantoea, and Exiguobacterium. Collectively, our metagenomic study highlights and considers various parameters required for transitioning to such sequencing-based diagnostics for food safety and the potential to develop better enrichment processes in a high-throughput manner not previously possible. Future studies will investigate new species-specific DNA signature target regimens, rational design of medium components in concert with judicious use of additives, such as antibiotics, and alterations in the sample processing protocol to enhance detection.