Whole-genome analysis of probiotic product isolates reveals the presence of genes related to antimicrobial resistance, virulence factors, and toxic metabolites, posing potential health risks

Exploring the dark side of probiotics to pursue light: Intrinsic and extrinsic risks to be opportunistic pathogens

Probiotics, live microorganisms with multiple health benefits, have gained popularity for their roles in maintaining daily health and treating a variety of diseases. However, they have the potential to be opportunistic pathogens in some conditions. This review delves into the intrinsic and extrinsic risks associated with probiotics. Intrinsic risks involve the production of harmful substances, such as toxins and invasive factors, biofilm formation, bacteria emboli, antibiotic resistance with relevant genetic materials, genetic plasticity, and metabolic issues, while extrinsic risks include problems in regulatory oversight and public awareness, host health status and appropriately administration. It emphasizes the need for a balanced view of their therapeutic benefits and potential hazards, advocating for further research to understand the complex interactions between probiotics and the human microbiome, to optimize the safety and efficacy of probiotics.

Living Bacteria: A New Vehicle for Vaccine Delivery in Cancer Immunotherapy

Cancer vaccines, aimed at evolving the human immune system to eliminate tumor cells, have long been explored as a method of cancer treatment with significant clinical potential. Traditional delivery systems face significant challenges in directly targeting tumor cells and delivering adequate amounts of antigen due to the hostile tumor microenvironment. Emerging evidence suggests that certain bacteria naturally home in on tumors and modulate antitumor immunity, making bacterial vectors a promising vehicle for precision cancer vaccines. Live bacterial vehicles offer several advantages, including tumor colonization, precise drug delivery, and immune stimulation, making them a compelling option for cancer immunotherapy. In this review, we explore the mechanisms of action behind living bacteria-based vaccines, recent progress in popular bacterial chassis, and strategies for specific payload delivery and biocontainment to ensure safety. These approaches will lay the foundation for developing an affordable, widely applicable cancer vaccine delivery system. This review also discusses the challenges and future opportunities in harnessing bacterial-based vaccines for enhanced therapeutic outcomes in cancer treatment.

The Isolation, Identification, and Whole-Genome Sequencing of a Potential Probiotic, Clostridium butyricum YF1, Isolated from the Intestine of the Ricefield Eel (Monopterus albus)

Clostridium butyricum, recognized as a probiotic, is widely distributed in the intestines of various animals. In this study, the C. butyricum strain YF1 was isolated from the intestine of the ricefield eel (Monopterus albus) using an anaerobic culture method and was identified through morphological, physiological, biochemical, and 16S rRNA sequence analyses. Notably, C. butyricum YF1 exhibited a rapid growth rate and was found to produce ten types of short-chain fatty acids, particularly high-yield acetic acid and butyric acid. Additionally, YF1 demonstrated a high tolerance to elevated temperatures (70 °C), bile salts (0.1% to 0.5%), artificial intestinal fluid, and artificial gastric fluid, while being sensitive to most antibiotics. Further whole-genome sequencing revealed that C. butyricum YF1 has a total genome size of 4,314,266 bp and contains 3853 coding genes. Specifically, 82 tRNAs, 21 rRNAs, 288 repeat sequences, 13 prophages, and two gene islands were detected. Moreover, gene function analysis indicated that the highest number of genes were annotated to metabolic processes, and the butyric acid metabolism pathway was found to be complete. Meanwhile, 598 virulence genes and 186 resistance genes were predicted. In conclusion, the findings from this study contribute to probiotic development and provide innovative approaches for the sustainable and healthy cultivation of ricefield eels.

Probiotic Characteristics and Whole Genome Analysis of Lactiplantibacillus plantarum PM8 from Giant Panda (Ailuropoda melanoleuca) Milk

Milk is a rich source of probiotics, particularly lactic acid bacteria (LAB), which have been shown to promote gut health, support the immune system, enhance digestion, and prevent pathogen colonization. This study aimed to isolate and identify LAB strains from giant panda (Ailuropoda melanoleuca) milk, evaluate their probiotic properties, and analyze the genomic characteristics of a promising strain. Thirteen LAB strains were isolated from 12 samples of giant panda milk. Among all LAB strains, Lactiplantibacillus plantarum PM8 (PM8) demonstrated probiotic properties and safety features. It exhibited strong growth performance, high antipathogenic activity against four pathogens, and strong survival rates under simulated gastrointestinal conditions. PM8 also showed excellent adhesion capabilities to Caco-2 cells. Additionally, safety assessment revealed no hemolysin production and minimal antibiotic resistance, making it a promising candidate for probiotic applications. The genome of PM8 consists of 3,227,035 bp with a GC content of 44.60% and contains 3171 coding sequences, including 113 carbohydrate-active enzyme genes and genes related to exopolysaccharides synthesis, vitamin B biosynthesis, adhesion, antioxidant activity, and bile salt hydrolysis. Notably, it contains genes involved in nonribosomally synthesized secondary metabolite and bacteriocin production. The genomic safety analysis confirmed that PM8 lacks the capacity to transmit bacterial antimicrobial resistance and is non-pathogenic to both humans and animals. These findings suggest that PM8 holds considerable potential for enhancing gut health and supporting the development of safe probiotic products.

Isolation and Characterization of Lactic Acid Bacteria From "Trites" Having the Ability to Produce α-Glucosidase Inhibitors

Alpha-glucosidase inhibitors are one of the therapies used for treating type 2 diabetes by inhibiting the absorption of carbohydrates in the gastrointestinal tract. In addition to antimicrobial activity, some probiotic species show α-glucosidase inhibitor activity, making them potential alternative therapies for type 2 diabetes. This study aimed to characterize probiotics from "trites," a traditional food from North Sumatra, Indonesia, that exhibit α-glucosidase inhibition, potentially useful for type 2 diabetes treatment. The probiotic potential of the isolates was evaluated through antagonistic activity, acid tolerance, bile tolerance, and susceptibility to antimicrobial agents. α-Glucosidase inhibition was tested with acarbose as a control. The best-performing isolate, LBSU8, was identified as Pediococcus acidilactici through 16S rRNA gene sequencing. Gene analysis using genome sequencing for LBSU8 revealed antimicrobial secondary metabolites, including RiPPs, polyketide, and NRP, while capsular polysaccharide might contribute to its antidiabetic activity. Though no specific α-glucosidase inhibitory secondary metabolites were identified, enzymes like dTDP-glucose 4,6-dehydratase, transketolase, and glucose-1-phosphate thymidylyltransferase may contribute to this activity. P. acidilactici LBSU8 shows potential as an alternative diabetes therapy in the food and drug industries. Further studies are needed to elucidate the exact mechanism behind its α-glucosidase inhibitory activity and to explore its efficacy in clinical settings.

Comprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India

Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.

The Safety of Probiotics Intended for Use in Pregnant and Lactating Women: From a Desirable to a Required Task

During pregnancy, women undergo changes that affect virtually every organ, apparatus, or system, including the host microbiota. Most pregnancies progress smoothly despite the common presence of minor side-effects arising from such adaptations. However, some women may experience more serious complications, including gestational diabetes mellitus, preeclampsia, or preterm delivery. Probiotics are one of the products most used to try to prevent or treat any of the minor or severe symptoms or complications that women may experience during pregnancy or lactation; however, most of them have never been tested in such populations and, therefore, their efficacy and safety claims are frequently unsubstantiated. Overall, probiotic trials involving pregnant or lactating women have shown that these products are usually well-tolerated and safe although adverse effects may also exist. Therefore, health professionals attending pregnant or lactating women should be aware of their use and monitor their efficacy and safety. In conclusion, probiotics recommendations for pregnant or lactating women should be based on scientific evidence, opting exclusively for those products that have been designed for the specific target or condition that a pregnant or lactating woman may be experiencing or at risk of, and which efficacy and safety has already been convincingly tested in such populations.

Unlocking Probiotic Potential: Genomic Insights into Weissella paramesenteroides UFTM 2.6.1

Weissella, a genus of lactic acid bacteria, has diverse beneficial attributes including probiotic activity and biotechnological applications. Therefore, the investigation of the Weissella genus has garnered growing interest. In this study, we sequenced the complete genome of Weissella paramesenteroides UFTM 2.6.1 isolated from unpasteurized cow's milk from the Triângulo Mineiro region and performed probiogenomic analyses. Taxonomic characterization confirmed the identity of W. paramesenteroides. The genome comprises 1926 protein-coding genes, mainly related to cell metabolism, information storage and processing, and cellular processes and signaling. Ninety-nine unique genes associated with probiotic functions were identified in the genome of W. paramesenteroides UFTM 2.6.1, including genes involved in stress response, bacterial persistence in the gastrointestinal tract, and biosynthesis of vitamins. In silico analysis of bacteriocin-related genes identified Pediocin, and subsequent in vitro testing confirmed that W. paramesenteroides UFTM 2.6.1 exhibits antimicrobial activity against Listeria spp. Genomic characterization revealed the presence of the replicon pLCK4 and four prophage regions, one of which was intact. Moreover, no CRISPR-Cas array or associated Cas proteins were found, along with an absence of resistance and virulence genes, suggesting a safety aspect of the evaluated strain. Pan-genome analysis unveiled 204 exclusive genes in the genome of W. paramesenteroides UFTM 2.6.1, which includes metabolism and stress-associated genes. In general, the results indicate probiotic potential of W. paramesenteroides UFTM 2.6.1. Further studies are required to ensure the safety and beneficial effects of this bacterium in vivo, aiming for future applications in the food industry and animal and human medicine.

Marine Pediococcus pentosaceus E3 Probiotic Properties, Whole-Genome Sequence Analysis, and Safety Assessment

Probiotics play a significant role in enhancing health, and they are well known for bacteriocins production. Evaluating probiotics' whole-genome sequence provides insights into their consumption outcomes. Thus, genomic studies have a significant role in assessing the safety of probiotics more in-depth and offer valuable information regarding probiotics' functional diversity, metabolic pathways, and health-promoting mechanisms. Marine Pediococcus pentosaceus E3, isolated from shrimp gut, exhibited beneficial properties, indicating its potential as a probiotic candidate. Phenotypically, E3 strain was susceptible to most antibiotics assessed, tolerant to low pH and high bile salt conditions, and revealed no hemolysin activity. Interestingly, E3-neutralized CFS revealed significant antibacterial activity against pathogens under investigation. Therefore, the concentrated CFS was prepared and evaluated as a natural biopreservative and showed outstanding antimicrobial activity. Furthermore, integrated-based genome assessment has provided insight into probiotic characteristics at the genomic level. Whole-genome sequencing analysis revealed that the E3 genome possesses 1805 protein-coding genes, and the genome size was about 1.8 Mb with a G + C content of 37.28%. Moreover, the genome revealed the absence of virulence factors and clinically related antibiotic genes. Moreover, several genes consistent with probiotic microorganisms' features were estimated in the genome, including stress response, carbohydrate metabolism, and vitamin biosynthesis. In addition, several genes associated with survival and colonization within the gastrointestinal tract were also detected across the E3 genome. Therefore, the findings suggest that insights into the genetic characteristics of E3 guarantee the safety of the strain and facilitate future development of E3 isolate as a health-promoting probiotic and source of biopreservative.

Metatranscriptomic Analysis Reveals Actively Expressed Antimicrobial-Resistant Genes and Their Hosts in Hospital Wastewater

Antimicrobial resistance is a major global concern and economic threat, necessitating a reliable monitoring approach to understand its frequency and spread via the environment. Hospital wastewater serves as a critical reservoir for antimicrobial-resistant organisms; however, its role in resistance gene distribution and dissemination remains poorly understood. This study integrates metagenomic and metatranscriptomic analyses, elucidating the dynamics of antimicrobial resistance in hospital wastewater. Integrated metagenomic and metatranscriptomic sequencing were used to identify actively expressed antimicrobial-resistant genes and antimicrobial-resistant bacteria, offering comprehensive insights into antimicrobial resistance dynamics in hospital wastewater. Liquid chromatography-tandem mass spectrometry analysis revealed the presence of ampicillin, sulbactam, levofloxacin, sulfamethoxazole, and trimethoprim in the sample, which could apply selective pressure on antimicrobial resistance gene expression. While multidrug resistance genes were the most prevalent sequences in both metagenome-assembled genomes and plasmids, plasmid-derived sequences showed a high mRNA/DNA ratio, emphasizing the presence of functionally expressed antimicrobial resistance genes on plasmids rather than on chromosomes. The metagenomic and metatranscriptomic analyses revealed Serratia nevei MAG14 with high mRNA levels of antimicrobial resistance genes; moreover, multidrug-resistant Serratia sp., genetically related to MAG14, was isolated from the wastewater, supporting the phenotypic characterization of crucial antimicrobial-resistant bacteria and validating the genome analysis results. The findings underscore key genes and bacteria as targets for antimicrobial resistance surveillance in hospital wastewater to protect public and environmental health.

Genomic Characterization and Probiotic Properties of Lactiplantibacillus pentosus Isolated from Fermented Rice

The aim of the study was the preliminary genetic and phenotypic characterization of a potential probiotic strain of Lactiplantibacillus pentosus (strain krglsrbmofpi2) obtained from traditionally fermented rice. Genome sequencing revealed that the strain has a 3.7-Mb genome with a GC content of 46 and a total of 3192 protein-coding sequences. Using bioinformatic methods, we have successfully identified phage genes, plasmids, pathogenicity, antibiotic resistance and a variety of bacteriocins. Through comprehensive biochemical and biophysical analyses, we have gained valuable insights into its auto-aggregation, co-aggregation, antibiotic resistance, hydrophobicity, antioxidant activity and tolerance to simulated gastrointestinal conditions. The safety evaluation of the isolated L. pentosus was performed on the basis of its haemolytic activity. Our studies have shown that this strain has a strong antagonistic activity against the priority pathogens identified by the World Health Organization such as Vibrio cholerae, Clostridium perfringens, Salmonella enterica subsp. enterica ser. Typhi, Escherichia coli, Listeria monocytogenes and Staphylococcus aureus. It is essential to fully understand the genetic and functional properties of the L. pentosus strain before considering its use as a useful probiotic in the food industry.

Metagenomic analysis of the bacterial microbiome, resistome and virulome distinguishes Portuguese Serra da Estrela PDO cheeses from similar non-PDO cheeses: An exploratory approach

This study aimed to evaluate the microbiome, resistome and virulome of two types of Portuguese cheese using high throughput sequencing (HTS). Culture-dependent chromogenic methods were also used for certain groups/microorganisms. Eight samples of raw ewe's milk cheese were obtained from four producers: two producers with cheeses with a PDO (Protected Designation of Origin) label and the other two producers with cheeses without a PDO label. Agar-based culture methods were used to quantify total mesophiles, Enterobacteriaceae, Escherichia coli, Staphylococcus, Enterococcus and lactic acid bacteria. The presence of Listeria monocytogenes and Salmonella was also investigated. The selected isolates were identified by 16S rRNA gene sequencing and evaluated to determine antibiotic resistance and the presence of virulence genes. The eight cheese samples analyzed broadly complied with EC regulations in terms of the microbiological safety criteria. The HTS results demonstrated that Leuconostoc mesenteroides, Lactococcus lactis, Lactobacillus plantarum, Lacticaseibacillus rhamnosus, Enterococcus durans and Lactobacillus coryniformis were the most prevalent bacterial species in cheeses. The composition of the bacterial community varied, not only between PDO and non-PDO cheeses, but also between producers, particularly between the two non-PDO cheeses. Alpha-diversity analyses showed that PDO cheeses had greater bacterial diversity than non-PDO cheeses, demonstrating that the diversity of spontaneously fermented foods is significantly higher in cheeses produced without the addition of food preservatives and dairy ferments. Despite complying with microbiological regulations, both PDO and non-PDO cheeses harbored potential virulence genes as well as antibiotic resistance genes. However, PDO cheeses exhibited fewer of these virulence and antibiotic resistance genes compared to non-PDO cheeses. Therefore, the combination of conventional microbiological methods and the metagenomic approach could contribute to improving the attribution of the PDO label to this type of cheese.

Unveiling a Novel Antidote for Deoxynivalenol Contamination: Isolation, Identification, Whole Genome Analysis and In Vivo Safety Evaluation of Lactobacillus rhamnosus MY-1

Deoxynivalenol (DON) is a global contaminant found in crop residues, grains, feed, and animal and human food. Biodegradation is currently the best solution for addressing DON pollution. However, efficient detoxification bacteria or enzymes that can be applied in complex matrices are lacking. The aim of this study was to isolate a DON-detoxifying probiotic strain with a high degradation rate, a good safety profile, and a clear genetic background. One hundred and eight bacterial strains were isolated from 300 samples collected from a school farm and surrounding livestock farms. A new DON-degrading strain, Lactobacillus rhamnosus MY-1 (L. rhamnosus MY-1), with a degradation rate of 93.34% after 48 h and a comprehensive degradation method, was identified. Then, MY-1 at a concentration of 1 × 108 CFU/mL was administered to mice in a chronic intoxication experiment for 28 days. The experimental group showed significantly higher weight gain and exhibited good production performance compared to the control group. The length of the ileal villi in the experimental group was significantly longer than that in the control group. The expression of pro-inflammatory cytokines decreased, while the expression of anti-inflammatory factors increased in the experimental group. Whole-genome analysis revealed that most of the MY-1 genes were involved in carbohydrate metabolism and membrane transport, with a cluster of secondary metabolite genes encoding antimicrobial properties. In summary, this study successfully identified a Lactobacillus strain with good safety performance, high DON degradation efficiency, and a clear genetic background, providing a new approach for the treatment of DON contamination.

Role of Probiotics in the Treatment and Prevention of Common Gastrointestinal Conditions in Children

Probiotics are live microorganisms that confer health benefits to the host when administered in adequate amounts. Although recommendations for probiotic use should be strain-specific, many systematic reviews, including recommendations from different societies, recommend probiotic use in general, providing no relevant information for healthcare professionals regarding which probiotic to recommend for which clinical indication, at what dose, and for how long. This narrative review aimed to present the available evidence on the use of probiotics in the prevention and treatment of common gastrointestinal diseases in children, considering the strain and dose used. Furthermore, this study summarizes the evidence on the possible side effects and quality of products containing probiotics.

Benefits and concerns of probiotics: an overview of the potential genotoxicity of the colibactin-producing Escherichia coli Nissle 1917 strain

Recently, the mounting integration of probiotics into human health strategies has gathered considerable attention. Although the benefits of probiotics have been widely recognized in patients with gastrointestinal disorders, immune system modulation, and chronic-degenerative diseases, there is a growing need to evaluate their potential risks. In this context, new concerns have arisen regarding the safety of probiotics as some strains may have adverse effects in humans. Among these strains, Escherichia coli Nissle 1917 (EcN) exhibited traits of concern due to a pathogenic locus in its genome that produces potentially genotoxic metabolites. As the use of probiotics for therapeutic purposes is increasing, the effects of potentially harmful probiotics must be carefully evaluated. To this end, in this narrative review article, we reported the findings of the most relevant in vitro and in vivo studies investigating the expanding applications of probiotics and their impact on human well-being addressing concerns arising from the presence of antibiotic resistance and pathogenic elements, with a focus on the polyketide synthase (pks) pathogenic island of EcN. In this context, the literature data here discussed encourages a thorough profiling of probiotics to identify potential harmful elements as done for EcN where potential genotoxic effects of colibactin, a secondary metabolite, were observed. Specifically, while some studies suggest EcN is safe for gastrointestinal health, conflicting findings highlight the need for further research to clarify its safety and optimize its use in therapy. Overall, the data here presented suggest that a comprehensive assessment of the evolving landscape of probiotics is essential to make evidence-based decisions and ensure their correct use in humans.

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.

Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species

BACKGROUND

The gut microbiota is considered a rich source for potential novel probiotics. Enterococcus genus is a normal component of a healthy gut microbiota, suggesting its vital role. Nosocomial infections caused mainly by E. facalis and E. faecium have been attributed to the plasticity of the Enterococcus genomes. In this study, we assessed the probiotic and safety characteristics of two E. lactis strains isolated from the human gut microbiota using in-vitro and in silico approaches. Additionally, the safety of the E. lactis species was evaluated using comparative genomics analysis.

RESULTS

The two E. lactis strains 10NA and 50NA showed resistance to bile salts and acid tolerance with antibacterial activity against Escherichia coli, Salmonella typhi, and Clostridioides difficile. For safety assays, the two strains did not display any type of hemolysis on blood agar, and the survival of Caco-2 cells was not significantly different (P-value > 0.05) compared to the control using cell free supernatants at 100% (v/v), 50% (v/v), 10% (v/v), and 5% (v/v) concentrations. Regarding antibiotic susceptibility, both strains were sensitive to vancomycin, tetracycline, and chloramphenicol. Comprehensive whole-genome analysis revealed no concerning associations between virulence or antibiotic resistance genes and any of the identified mobile genetic elements. Comparative genome analysis with closely related E. faecium species genomes revealed the distinctive genomic safety of the E. lactis species.

CONCLUSIONS

Our two E. lactis strains showed promising probiotic properties in-vitro. Their genomes were devoid of any transferable antibiotic resistance genes. In silico comparative analysis confirmed the safety of the E. lactis species. These results suggest that E. lactis species could be a potential source for safer Enterococcus probiotic supplements.

ProbioMinServer: an integrated platform for assessing the safety and functional properties of potential probiotic strains

Motivation

ProbioMinServer is a platform designed to help researchers access information on probiotics regarding a wide variety of characteristics, such as safety (e.g. antimicrobial resistance, virulence, pathogenic, plasmid, and prophage genes) and functionality (e.g. functional classes, carbohydrate-active enzyme, and metabolite gene cluster profile). Because probiotics are functional foods, their safety and functionality are a crucial part of health care. Genomics has become a crucial methodology for investigating the safety and functionality of probiotics in food and feed. This shift is primarily attributed to the growing affordability of next-generation sequencing technologies. However, no integrated platform is available for simultaneously evaluating probiotic strain safety, investigating probiotic functionality, and identifying known phylogenetically related strains.

Results

Thus, we constructed a new platform, ProbioMinServer, which incorporates these functions. ProbioMinServer accepts whole-genome sequence files in the FASTA format. If the query genome belongs to the 25 common probiotic species collected in our database, the server performs a database search and analyzes the core-genome multilocus sequence typing. Front-end applications were implemented in JavaScript with a bootstrap framework, and back-end programs were implemented using PHP, Perl, and Python. ProbioMinServer can help researchers quickly and easily retrieve information on the safety and functionality of various probiotics.

Availability and implementation

The platform is available at https://probiomindb.imst.nsysu.edu.tw.

Probiotics Modulate Host Immune Response and Interact with the Gut Microbiota: Shaping Their Composition and Mediating Antibiotic Resistance

The consortium of microbes inhabiting the human body, together with their encoded genes and secreted metabolites, is referred to as the "human microbiome." Several studies have established a link between the composition of the microbiome and its impact on human health. This impact spans local gastrointestinal inflammation to systemic autoimmune disorders and neurodegenerative diseases such as Alzheimer's and Autism. Some of these links have been validated by rigorous experiments that identify specific strains as mediators or drivers of a particular condition. Consequently, the development of probiotics to compensate for a missing beneficial microbe(s) has advanced and become popular, especially in the treatment of irritable bowel diseases and to restore disrupted gut flora after antibiotic administration. The widespread use of probiotics is often advocated as a natural ecological therapy. However, this perception is not always accurate, as there is a potential for unexpected interactions when administering live microbial cultures. Here, we designed this research to explore the intricate interactions among probiotics, the host, and microbes through a series of experiments. Our objectives included assessing their immunomodulatory effects, response to oral medications, impact on microbial population dynamics, and mediation of antibiotic resistance. To achieve these goals, we employed diverse experimental protocols, including cell-based enzyme -linked immunosorbent assay (ELISA), antibiotic susceptibility testing, antimicrobial activity assays, computational prediction of probiotic genes responsible for antibiotic resistance, polymerase chain reaction (PCR)-based validation of predicted genes, and survival assays of probiotics in the presence of selected oral medications. Our findings highlight that more than half of the tested probiotics trigger an inflammatory response in the Caco-2 cell line, are influenced by oral medications, exhibit antibacterial activity, and possess genes encoding antimicrobial resistance. These results underscore the necessity for a reevaluation of probiotic usage and emphasize the importance of establishing regulations to govern probiotic testing, approval, and administration.

Potential of jackfruit inner skin fibre for encapsulation of probiotics on their stability against adverse conditions

The aim of this study was to investigate the impact of jackfruit inner skin fibre (JS) incorporated with whey protein isolate (WPI) and soybean oil (SO) as a wall material for probiotic encapsulation to improve probiotic stability against freeze-drying and gastrointestinal (GI) tract conditions. Bifidobacterium bifidum TISTR2129, Bifidobacterium breve TISTR2130, and Lactobacillus acidophilus TISTR1338 were studied in terms of SCFA production and the antibiotic-resistant profile and in an antagonistic assay to select suitable strains for preparing a probiotic cocktail, which was then encapsulated. The results revealed that B. breve and L. acidophilus can be used effectively as core materials. JS showed the most influential effect on protecting probiotics from freeze-drying. WPI:SO:JS at a ratio of 3.9:2.4:3.7 was the optimized wall material, which provided an ideal formulation with 83.1 ± 6.1% encapsulation efficiency. This formulation presented > 50% probiotic survival after exposure to gastro-intestinal tract conditions. Up to 77.8 ± 0.1% of the encapsulated probiotics survived after 8 weeks of storage at refrigeration temperature. This study highlights a process and formulation to encapsulate probiotics for use as food supplements that could provide benefits to human health as well as an alternative approach to reduce agricultural waste by increasing the value of jackfruit inner skin.

Probiotics: insights and new opportunities for Clostridioides difficile intervention

Clostridioides difficile infection (CDI) is a life-threatening disease caused by the Gram-positive, opportunistic intestinal pathogen C. difficile. Despite the availability of antimicrobial drugs to treat CDI, such as vancomycin, metronidazole, and fidaxomicin, recurrence of infection remains a significant clinical challenge. The use of live commensal microorganisms, or probiotics, is one of the most investigated non-antibiotic therapeutic options to balance gastrointestinal (GI) microbiota and subsequently tackle dysbiosis. In this review, we will discuss major commensal probiotic strains that have the potential to prevent and/or treat CDI and its recurrence, reassess the efficacy of probiotics supplementation as a CDI intervention, delve into lessons learned from probiotic modulation of the immune system, explore avenues like genome-scale metabolic network reconstructions, genome sequencing, and multi-omics to identify novel strains and understand their functionality, and discuss the current regulatory framework, challenges, and future directions.

Metatranscriptome deciphers the effects of non-antibiotic antimicrobial agents on antibiotic resistance and virulence factors in freshwater microcosms

The emergence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose health risks to the ecosystem and humans. Understanding how non-antibiotic antimicrobial agents drive the expression of ARGs and VFs in freshwater ecosystems, however, remains large challenges. Here, we employed freshwater microcosms and performed metatranscriptomic analysis to investigate the expression profiles of ARGs and VFs in response to pollutants of non-antibiotic antimicrobial agents, including silver nanoparticles (AgNPs) and azoxystrobin. Results showed that AgNPs significantly inhibited the total expression of ARGs and VFs and decreased the number of pathogenic microorganisms expressing these genes. Azoxystrobin increased the total expression of ARGs and VFs, as well as the number of pathogens expressing VFs, but concomitantly reduced the number of pathogens expressing ARGs. Two tested pollutants dramatically changed the expression profiles of ARGs and VFs, with distinct patterns: AgNPs displayed a negative effect, while azoxystrobin showed a positive effect on their expression profiles. Our findings provided a systematical insight to demonstrate that non-antibiotic antimicrobial agents with different mechanisms of action showed various effects on ARGs and VFs, and therefore represented different ecological risks.

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.

Beneficial, safety, and antioxidant properties of lactic acid bacteria: A next step in their evaluation as potential probiotics

The role of lactic acid bacteria (LAB) as probiotics as health promoting factors for human or veterinary practice has gained increasing interest during the last three decades. This is reflected in screening approaches of LAB strains in line with minimal requirements for a "probiotic" with regard to safety and functionality. The latter might also include natural antioxidant properties, thereby constituting an additional benefit in substituting synthetic antioxidants. The in vitro antioxidant assays conducted in this study included the scavenging of the 2,2-diphenyl-1-picrylhydrazil (DPPH) free radical, metal (Fe⁺²) ion chelation, determining the scavenging properties of the hydroxyl and superoxide radicals, and anti-lipid peroxidation. Analysis of DPPH free radical scavenging property for the microorganisms included in current study, showed Streptococcus salivarius ST59HK to exhibit the highest activity at a level of 85.24%. The greatest Fe⁺² chelation activity with 98.2% was recorded for Str. salivarius ST62HK while the lowest was recorded for Str. salivarius ST48HK at 71.5%. The greatest and minimal hydroxyl radical scavenging levels were detected for Str. salivarius ST59HK (98.6%) and Lactiplantibacillus plantarum ST63HK (35.60%), respectively. Superoxide anion radical scavenging activity was highly exhibited by Str. salivarius ST61HK (54.62%) and the least exhibited by Enterococcus faecium ST651ea (18.7%). Lastly, the strains Lactobacillus gasseri ST16HK and E. faecium ST7319ea showed the highest and lowest anti-lipid peroxidation levels with 69.43% and 26.15%, respectively. Anti-oxidative properties appear to be strain specific and thus some of these strains could be potentially applied as natural antioxidants in fermented food products.

Genomic and metabolic properties of Staphylococcus gallinarum FCW1 MCC4687 isolated from naturally fermented coconut water towards GRAS assessment

Staphylococcus gallinarum FCW1 was isolated from naturally fermented coconut-water and identified by biochemical and molecular methods. Probiotic characterization and safety assessment were conducted through a series of in vitro tests. A high survival rate was observed when the strain was tested for resistance to bile, lysozyme, simulated gastric and intestinal fluid, phenol, and different temperature and salt concentrations. The strain showed antagonism against some pathogens, was susceptible to all antibiotics tested except penicillin, and showed no hemolytic and DNase activity. Hydrophobicity, autoaggregation, biofilm formation, and antioxidation tests indicated that the strain possessed a high adhesive and antioxidant ability. Enzymatic activity was used to evaluate the metabolic capacities of the strain. In-vivo experiment on zebrafish was performed to check its safety status. The whole-genome sequencing indicated that the genome contained 2,880,305 bp with a GC content of 33.23%. The genome annotation confirmed the presence of probiotic-associated genes and genes for oxalate degradation, sulfate reduction, acetate metabolism, and ammonium transport in the FCW1 strain, adding to the theory that this strain may be helpful in treating kidney stones. This study revealed that the strain FCW1 might be an excellent potential probiotic in developing fermented coconut beverages and treating and preventing kidney stone disease.

Efficacies of Potential Probiotic Candidates Isolated from Traditional Fermented Korean Foods in Stimulating Immunoglobulin A Secretion

The aim of this study was to evaluate efficacies of selected lactic acid bacteria (LAB) in inducing immunoglobulin A (IgA) secretion. Twenty-five different LAB isolated from traditional fermented Korean foods were characterized for their probiotic properties and screened to identify those that could stimulate lamina propria cells (LPCs) from Peyer's patch to secret IgA in vitro. Among them, four strains (Lactiplantibacillus plantarum CJW55-10, Lactiplantibacillus pentosus CJW18-6, L. pentosus CJW56-11, and Pediococcus acidilactici CJN2696) were found to be strong IgA inducers. The number of IgA positive B cells and soluble IgA level were increased when LPCs were co-cultured with these LAB. Expression levels of toll-like receptor (TLR) such as TLR2 and TLR4 and secretion of interleuckin-6 were augmented in LPCs treated with these LAB. Further, we determined whether oral intake of these LAB enhanced IgA production in vivo. After one-week of daily oral administration, these LAB feed mice increased mucosal IgA and serum IgA. In conclusion, selected strains of LAB could induce systemic IgA secretion by activating lamina propria B cells in Peyer's patch and oral intake of selected strains of LAB can enhance systemic immunity by inducing mucosal IgA secretion.

Probiotics in the Sourdough Bread Fermentation: Current Status

Sourdough fermentation is an ancient technique to ferment cereal flour that improves bread quality, bringing nutritional and health benefits. The fermented dough has a complex microbiome composed mainly of lactic acid bacteria and yeasts. During fermentation, the production of metabolites and chemical reactions occur, giving the product unique characteristics and a high sensory quality. Mastery of fermentation allows adjustment of gluten levels, delaying starch digestibility, and increasing the bio-accessibility of vitamins and minerals. This review focuses on the main steps of sourdough fermentation, the microorganisms involved, and advances in bread production with functional properties. The impact of probiotics on human health, the metabolites produced, and the main microbial enzymes used in the bakery industry are also discussed.

Genome Investigation and Functional Annotation of Lactiplantibacillus plantarum YW11 Revealing Streptin and Ruminococcin-A as Potent Nutritive Bacteriocins against Gut Symbiotic Pathogens

All nutrient-rich feed and food environments, as well as animal and human mucosae, include lactic acid bacteria known as Lactobacillus plantarum. This study reveals an advanced analysis to study the interaction of probiotics with the gastrointestinal environment, irritable bowel disease, and immune responses along with the analysis of the secondary metabolites’ characteristics of Lp YW11. Whole genome sequencing of Lp YW11 revealed 2297 genes and 1078 functional categories of which 223 relate to carbohydrate metabolism, 21 against stress response, and the remaining 834 are involved in different cellular and metabolic pathways. Moreover, it was found that Lp YW11 consists of carbohydrate-active enzymes, which mainly contribute to 37 glycoside hydrolase and 28 glycosyltransferase enzyme coding genes. The probiotics obtained from the BACTIBASE database (streptin and Ruminococcin-A bacteriocins) were docked with virulent proteins (cdt, spvB, stxB, and ymt) of Salmonella, Shigella, Campylobacter, and Yersinia, respectively. These bacteria are the main pathogenic gut microbes that play a key role in causing various gastrointestinal diseases. The molecular docking, dynamics, and immune simulation analysis in this study predicted streptin and Ruminococcin-A as potent nutritive bacteriocins against gut symbiotic pathogens.

Integrated genome based evaluation of safety and probiotic characteristics of Lactiplantibacillus plantarum YW11 isolated from Tibetan kefir

The comparative genomic analysis of Lactiplantibacillus plantarum YW11 (L. plantarum YW11) isolated from Tibetan kefir involves comparison of the complete genome sequences of the isolated strain with other closely related L. plantarum strains. This type of analysis can be used to identify the genetic diversity among strains and to explore the genetic characteristics of the YW11 strain. The genome of L. plantarum YW11 was found to be composed of a circular single chromosome of 4,597,470 bp with a G + C content of 43.2%. A total of 4,278 open reading frames (ORFs) were identified in the genome and the coding density was found to be 87.8%. A comparative genomic analysis was conducted using two other L. plantarum strains, L. plantarum C11 and L. plantarum LMG21703. Genomic comparison revealed that L. plantarum YW11 shared 72.7 and 75.2% of gene content with L. plantarum C11 and L. plantarum LMG21703, respectively. Most of the genes shared between the three L. plantarum strains were involved in carbohydrate metabolism, energy production and conversion, amino acid metabolism, and transcription. In this analysis, 10 previously sequenced entire genomes of the species were compared using an in-silico technique to discover genomic divergence in genes linked with carbohydrate intake and their potential adaptations to distinct human intestinal environments. The subspecies pan-genome was open, which correlated with its extraordinary capacity to colonize several environments. Phylogenetic analysis revealed that the novel genomes were homogenously grouped among subspecies of l Lactiplantibacillus. L. plantarum was resistant to cefoxitin, erythromycin, and metronidazole, inhibited pathogens including Listeria monocytogenes, Clostridium difficile, Vibrio cholera, and others, and had excellent aerotolerance, which is useful for industrial operations. The comparative genomic analysis of L. plantarum YW11 isolated from Tibetan kefir can provide insights into the genetic characteristics of the strain, which can be used to further understand its role in the production of kefir.

Probiogenomic In-Silico Analysis and Safety Assessment of Lactiplantibacillus plantarum DJF10 Strain Isolated from Korean Raw Milk

The whole genome sequence of Lactiplantibacillus plantarum DJF10, isolated from Korean raw milk, is reported, along with its genomic analysis of probiotics and safety features. The genome consists of 29 contigs with a total length of 3,385,113 bp and a GC content of 44.3%. The average nucleotide identity and whole genome phylogenetic analysis showed the strain belongs to Lactiplantibacillus plantarum with 99% identity. Genome annotation using Prokka predicted a total of 3235 genes, including 3168 protein-coding sequences (CDS), 59 tRNAs, 7 rRNAs and 1 tmRNA. The functional annotation results by EggNOG and KEGG showed a high number of genes associated with genetic information and processing, transport and metabolism, suggesting the strain's ability to adapt to several environments. Various genes conferring probiotic characteristics, including genes related to stress adaptation to the gastrointestinal tract, biosynthesis of vitamins, cell adhesion and production of bacteriocins, were identified. The CAZyme analysis detected 98 genes distributed under five CAZymes classes. In addition, several genes encoding carbohydrate transport and metabolism were identified. The genome also revealed the presence of insertion sequences, genomic islands, phage regions, CRISPR-cas regions, and the absence of virulence and toxin genes. However, the presence of hemolysin and antibiotic-resistance-related genes detected in the KEGG search needs further experimental validation to confirm the safety of the strain. The presence of two bacteriocin clusters, sactipeptide and plantaricin J, as detected by the BAGEL 4 webserver, confer the higher antimicrobial potential of DJF10. Altogether, the analyses in this study performed highlight this strain's functional characteristics. However, further in vitro and in vivo studies are required on the safety assurance and potential application of L. plantarum DJF10 as a probiotic agent.

Functional and Safety Characterization of Weissella paramesenteroides Strains Isolated from Dairy Products through Whole-Genome Sequencing and Comparative Genomics

Strains belonging to the Weissella genus are frequently recovered from spontaneously fermented foods. Their functional, microbial-modulating, and probiotic traits enhance not only the sensorial properties but also the nutritional value, beneficial effects, and safety of fermented products. Sporadic cases of opportunistic pathogenicity and antibiotic resistance have deprived safety status from all Weissella species, which thus remain understudied. Our study increased the number of available high-quality and taxonomically accurate W. paramesenteroides genomes by 25% (9 genomes reported, leading to a total of 36 genomes). We conducted a phylogenetic and comparative genomic analysis of the most dominant Weissella species (W. cibaria, W. paramesenteroides, W. viridescens, W. soli, W. koreensis, W. hellenica and W. thailadensis). The phylogenetic tree corroborated species assignment but also revealed phylogenetic diversity within the Weissella species, which is likely related to the adaptation of Weissella in different niches. Using robust alignment criteria, we showed the overall absence of resistance and virulence genes in Weissella spp., except for one W. cibaria isolate carrying blaTEM-181. Enrichment analysis showed the association of Weissella species several CAZymes, which are essential for biotechnological applications. Additionally, the combination of CAZyme metabolites with probiotics can potentially lead to beneficial effects for hosts, such as the inhibition of inflammatory processes and the reduction of cholesterol levels. Bacteriocins and mobile genetic elements MGEs (Inc11 plasmid and ISS1N insertion sequence) were less abundant, however W. thailadensis and W. viridescens showed significant association with specific bacteriocin-encoding genes. Lastly, an analysis of phenotypic traits underlined the need to carefully evaluate W. cibaria strains before use as food additives and suggested the possibility of employing W. paramesenteroides and W. hellenica in the fermentation process of vegetable products. More studies providing high-resolution characterization of Weissella strains from various sources are necessary to elucidate the safety of Weissella spp. and exploit their beneficial characteristics.

A metagenome-wide association study of the gut microbiota in recurrent aphthous ulcer and regulation by thalidomide

Recurrent aphthous ulcer (RAU), one of the most common diseases in humans, has an unknown etiology and is difficult to treat. Thalidomide is an important immunomodulatory and antitumor drug and its effects on the gut microbiota still remain unclear. We conducted a metagenomic sequencing study of fecal samples from a cohort of individuals with RAU, performed biochemical assays of cytokines, immunoglobulins and antimicrobial peptides in serum and saliva, and investigated the regulation effects of thalidomide administration and withdrawal. Meanwhile we constructed the corresponding prediction models. Our metagenome-wide association results indicated that gut dysbacteriosis, microbial dysfunction and immune imbalance occurred in RAU patients. Thalidomide regulated gut dysbacteriosis in a species-specific manner and had different sustainable effects on various probiotics and pathogens. A previously unknown association between gut microbiota alterations and RAU was found, and the specific roles of thalidomide in modulating the gut microbiota and immunity were determined, suggesting that RAU may be affected by targeting gut dysbacteriosis and modifying immune imbalance. In-depth insights into sophisticated networks consisting of the gut microbiota and host cells may lead to the development of emerging treatments, including prebiotics, probiotics, synbiotics, and postbiotics.

Long-Read 16S rRNA Amplicon and Metagenomic Data of Swine Feed-Additive Probiotics Product

Swine feed-additive probiotics products play a major role in swine performance and welfare by promoting gut health. Here, we present two types of data, including a full-length 16S rRNA amplicon sequence data and a long-read metagenomic sequence data obtained from the same commercial probiotic product.

Comparative Genomics and Pan-Genome Driven Prediction of a Reduced Genome of Akkermansia muciniphila

Akkermanisia muciniphila imparts important health benefits and is considered a next-generation probiotic. It is imperative to understand the genomic diversity and metabolic potential of the species for safer applications as probiotics. As it resides with both health-promoting and pathogenic bacteria, understanding the evolutionary patterns are crucial, but this area remains largely unexplored. Moreover, pan-genome has previously been established based on only a limited number of strains and without careful strain selection. The pan-genomics have become very important for understanding species diversity and evolution. In the current study, a systematic approach was used to find a refined pan-genome profile of A. muciniphila by excluding too-diverse strains based on average nucleotide identity-based species demarcation. The strains were divided into four phylogroups using a variety of clustering techniques. Horizontal gene transfer and recombination patterns were also elucidated. Evolutionary patterns revealed that different phylogroups were expanding differently. Furthermore, a comparative evaluation of the metabolic potential of the pan-genome and its subsections was performed. Lastly, the study combines functional annotation, persistent genome, and essential genes to devise an approach to determine a minimal genome that can systematically remove unwanted genes, including virulent factors. The selection of one strain to be used as a chassis for the prediction of a reduced genome was very carefully performed by analyzing several genomic parameters, including the number of unique genes and the resistance and pathogenic potential of the strains. The strategy could be applied to other microbes, including human-associated microbiota, towards a common goal of predicting a minimal or a reduced genome.

Development of Resistance to Clarithromycin and Amoxicillin-Clavulanic Acid in Lactiplantibacillus plantarum In Vitro Is Followed by Genomic Rearrangements and Evolution of Virulence

Ensuring the safety of the use of probiotics is a top priority. Obviously, in addition to studying the beneficial properties of lactic acid bacteria, considerable attention should be directed to assessing the virulence of microorganisms as well as investigating the possibility of its evolution under conditions of selective pressure. To assess the virulence of probiotics, it is now recommended to analyze the genomes of bacteria in relation to the profiles of the virulome, resistome, and mobilome as well as the analysis of phenotypic resistance and virulence in vitro. However, the corresponding procedure has not yet been standardized, and virulence analysis of strains in vivo using model organisms has not been performed. Our study is devoted to testing the assumption that the development of antibiotic resistance in probiotic bacteria under conditions of selective pressure of antimicrobial drugs may be accompanied by the evolution of virulence. In this regard, special attention is required for the widespread in nature commensals and probiotic bacteria actively used in pharmacology and the food industry. As a result of step-by-step selection from the Lactiplantibacillus plantarum 8p-a3 strain isolated from the "Lactobacterin" probiotic (Biomed, Russia), the L. plantarum 8p-a3-Clr-Amx strain was obtained, showing increased resistance simultaneously to amoxicillin-clavulanic acid and clarithromycin (antibiotics, the combined use of which is widely used for Helicobacter pylori eradication) compared to the parent strain (MIC8p-a3-Clr-Amx of 20 μg/mL and 10 μg/mL, and MIC8p-a3 of 0.5 μg/mL and 0.05 μg/mL, respectively). The results of a comparative analysis of antibiotic-resistant and parental strains indicate that the development of resistance to the corresponding antimicrobial drugs in L. plantarum in vitro is accompanied by the following: (i) significant changes in the genomic profile (point mutations as well as deletions, insertions, duplications, and displacement of DNA sequences) associated in part with the resistome and mobilome; (ii) changes in phenotypic sensitivity to a number of antimicrobial drugs; and (iii) an increase in the level of virulence against Drosophila melanogaster, a model organism for which L. plantarum is considered to be a symbiont. The data obtained by us indicate that the mechanisms of adaptation to antimicrobial drugs in L. plantarum are not limited to those described earlier and determine the need for comprehensive studies of antibiotic resistance scenarios as well as the trajectories of virulence evolution in probiotic bacteria in vivo and in vitro to develop a standardized system for detecting virulent strains of the corresponding microorganisms. IMPORTANCE Ensuring the safety of the use of probiotics is a top priority. We found that increased resistance to popular antimicrobial drugs in Lactiplantibacillus plantarum is accompanied by significant changes in the genomic profile and phenotypic sensitivity to a number of antimicrobial drugs as well as in the level of virulence of this bacterium against Drosophila. The data obtained in our work indicate that the mechanisms of antibiotic resistance in this bacterium are not limited to those described earlier and determine the need for comprehensive studies of the potential for the evolution of virulence in lactic acid bacteria in vivo and in vitro and to develop a reliable control system to detect virulent strains among probiotics.

Genomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential

The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a wide variety of ecological niches, from fermented foodstuffs to host-associated microenvironments. Lc. paracasei SP5 is a novel strain, originally isolated from kefir grains that presents desirable probiotic and biotechnological attributes. In this study, we applied genomic tools to further characterize the probiotic and biotechnological potential of the strain. Firstly, whole genome sequencing and assembly, were performed to construct the chromosome map of the strain and determine its genomic stability. Lc. paracasei SP5 carriers several insertion sequences, however, no plasmids or mobile elements were detected. Furthermore, phylogenomic and comparative genomic analyses were utilized to study the nomadic attributes of the strain, and more specifically, its metabolic capacity and ability to withstand environmental stresses imposed during food processing and passage through the gastrointestinal (GI) tract. More specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzyme (CAZymes) analyses provided evidence for the ability of the stain to utilize an array of carbohydrates as growth substrates. Consequently, genes for heat, cold, osmotic shock, acidic pH, and bile salt tolerance were annotated. Importantly bioinformatic analysis showed that the novel strain does not harbor acquired antimicrobial resistance genes nor virulence factors, in agreement with previous experimental data. Putative bacteriocin biosynthesis clusters were identified using BAGEL4, suggesting its potential antimicrobial activity. Concerning microbe-host interactions, adhesins, moonlighting proteins, exopolysaccharide (EPS) biosynthesis genes and pilins mediating the adhesive phenotype were, also, pinpointed in the genome of Lc. paracasei SP5. Validation of this phenotype was performed by employing a microbiological method and confocal microscopy. Conclusively, Lc. paracasei SP5 harbors genes necessary for the manifestation of the probiotic character and application in the food industry. Upcoming studies will focus on the mechanisms of action of the novel strain at multiple levels.

Whole genome sequencing for the risk assessment of probiotic lactic acid bacteria

Probiotic bacteria exhibit beneficial effects on human and/or animal health, and have been widely used in foods and fermented products for decades. Most probiotics consist of lactic acid bacteria (LAB), which are used in the production of various food products but have also been shown to have the ability to prevent certain diseases. With the expansion of applications for probiotic LAB, there is an increasing concern with regard to safety, as cases with adverse effects, i.e., severe infections, transfer of antimicrobial resistance genes, etc., can occur. Currently, in vitro assays remain the primary way to assess the properties of LAB. However, such methodologies are not meeting the needs of strain risk assessment on a high-throughput scale, in the context of the evolving concept of food safety. Analyzing the complete genetic information, including potential virulence genes and other determinants with a negative impact on health, allows for assessing the safe use of the product, for which whole-genome sequencing (WGS) of individual LAB strains can be employed. Genomic data can also be used to understand subtle differences in the strain level important for beneficial effects, or protect patents. Here, we propose that WGS-based bioinformatics analyses are an ideal and cost-effective approach for the initial in silico microbial risk evaluation, while the technique may also increase our understanding of LAB strains for food safety and probiotic property evaluation.

Assessments of Probiotic Potentials of Lactiplantibacillus plantarum Strains Isolated From Chinese Traditional Fermented Food: Phenotypic and Genomic Analysis

The lack of rapid and effective approaches to determine the health benefits of strains is one of the main challenges affecting the selection of probiotics from large numbers of candidates. In this study, the probiotic potential of 44 Lactiplantibacillus plantarum strains isolated from different Chinese traditional fermented foods was evaluated, including acid and bile salt resistance, adhesion ability, survival in simulated human gastrointestinal transit, antioxidant activity, bile salt hydrolase (BSH) activity, and antibacterial activity. All tested L. plantarum strains showed high antioxidant capacity, BSH activity, and antibacterial activity. Among the strains, B652, C232, D444, and E932 were identified as the best comprehensive performed strains, which were selected for whole-genome sequencing, in order to provide clear information and identify key genes responsible for functional characteristics in vitro. It demonstrated that the antioxidant activity, adhesion activity, and ability to survive in the simulated gastric environment were found to be closely correlated with antioxidant enzyme encoding genes, cell-surface protein-encoding genes, and stress response genes, respectively. The numbers of functional genes present in strains might decide their performance in probiotic profile evaluation. The outcome of the study could support the development of a novel approach for the screening and identification of probiotics.

Consumer's acceptability and health consciousness of probiotic and prebiotic of non-dairy products

Human gut microbiota is a protective agent of intestinal and systemic health, and its modulation is of great interest for human wellbeing. In the world of biotics, besides probiotics, prebiotics, and synbiotics, also appears the denomination of "postbiotics" and "psychobiotics". Fermented dairy products are, traditionally, the major source of probiotics. Nevertheless, due to the increasing number of lactose-intolerant individuals and strict vegetarians, there is a need for innovative non-dairy products. Non-dairy biotics are being included in the normal diet and due to technological advances, many products are created using non-conventional food matrices like kombucha tea, herbal tea, baking mix, and cereal-based products. The microorganisms most used as probiotics in many of the non-dairy products are strains belonging to the genera Bifidobacterium, Enterococcus, Lactobacillus, Lactococcus, Streptococcus, and Bacillus, and some yeast strains namely Saccharomyces cerevisiae var. boulardii. Recently, several other yeasts have been described as having probiotic properties. This review describes gut-derived effects in humans of possible microorganisms, such as yeasts, and bacteria, isolated from non-dairy fermented and non-fermented foods and beverages. The microorganisms responsible for the processing of these non-dairy fermented products, together with the prebiotics, form a class of nutrients that have been proven to be beneficial for our gut health.