Recent systems biology approaches for probiotics use in health aspects: a review

In vitro and in vivo genome-based safety evaluation of Lacticaseibacillus rhamnosus LRa05

The aim of this study was to comprehensively evaluate the safety of Lacticaseibacillus rhamnosus LRa05 (hereinafter "LRa05") to determine its suitability for use as a probiotic in the food industry. First, we sequenced the genome of LRa05 and then determined whether it contained genes associated with antibiotic resistance, virulence, or pathogenicity. Second, we evaluated the safety of LRa05 in vitro by performing a hemolysis assay and examining its ability to produce biogenic amines, its antimicrobial susceptibility, its capacity to transfer antibiotic resistance genes, its genomic stability, and whether it contained potential virulence factors. Third, we investigated the pathogenicity of LRa05 in mice by oral gavage and intraperitoneal injection. A bioinformatics analysis revealed no evidence that the genome of LRa05 contains genes associated with virulence or antibiotic resistance. In addition, the results of in vitro experiments showed that LRa05 does not produce d-lactic acid or exhibit hemolytic activity and is sensitive to clinically relevant antibiotics. Furthermore, a pathogenicity test revealed that LRa05 exhibits no lethality or toxicity in mice. Taken together, these findings indicate that LRa05 is sufficiently safe to be explored as a potential probiotic for use in the food industry.

Comparing technology and regulatory landscape of probiotics as food, dietary supplements and live biotherapeutics

Application of beneficial microorganisms as probiotics targets a broad range of intended uses, from maintaining health and supporting normal bodily functions to curing and preventing diseases. Currently, three main regulatory fields of probiotic products can be defined depending on their intended use: the more similar probiotic foods and probiotic dietary supplements, and live biotherapeutic products. However, it is not always straightforward to classify a probiotic product into one of these categories. The regulatory nuances of developing, manufacturing, investigating and applying each category of probiotic products are not universal, and not always apparent to those unfamiliar with the various global probiotic regulatory guidelines. Various global markets can be significantly different regarding legislation, possible claims, market value and quality requirements for the development and commercialization of probiotic products. Furthermore, different probiotic product categories are also linked with variable costs at different stages of product development. This review outlines the current landscape comparing probiotic foods, probiotic dietary supplements, and live biotherapeutics as probiotic products from a regulatory lens, focusing on product development, manufacturing and production, and clinical research agenda. The aim is to inform and promote a better understanding among stakeholders by outlining the expectations and performance for each probiotic product category, depending on their intended use and targeted geographical region.

The future of functional food: Emerging technologies application on prebiotics, probiotics and postbiotics

This review was the first to gather literature about the effect of emerging technologies on probiotic, prebiotic, and postbiotic products. Applying emerging technologies to probiotic products can increase probiotic survival and improve probiotic properties (cholesterol attachment, adhesion to Caco-2 cells, increase angiotensin-converting enzyme (ACE) inhibitory, antioxidant, and antimicrobial activities, and decrease systolic blood pressure). Furthermore, it can optimize the fermentation process, produce or maintain compounds of interest (bacteriocin, oligosaccharides, peptides, phenolic compounds, flavonoids), improve bioactivity (vitamin, aglycones, calcium), and sensory characteristics. Applying emerging technologies to prebiotic products did not result in prebiotic degradation. Still, it contributed to higher concentrations of bioactive compounds (citric and ascorbic acids, anthocyanin, polyphenols, flavonoids) and health properties (antioxidant activity and inhibition of ACE, α-amylase, and α-glucosidase). Emerging technologies may also be applied to obtain postbiotics with increased health effects. In this way, current studies suggest that emerging food processing technologies enhance the efficiency of probiotics and prebiotics in food. The information provided may help food industries to choose a more suitable technology to process their products and provide a basis for the most used process parameters. Furthermore, the current gaps are discussed. Emerging technologies may be used to process food products resulting in increased probiotic functionality, prebiotic stability, and higher concentrations of bioactive compounds. In addition, they can be used to obtain postbiotic products with improved health effects compared to the conventional heat treatment.

Alterations in Faecal Microbiota and Elevated Levels of Intestinal IgA Following Oral Administration of Lacticaseibacillus casei in mice

The intestinal microbiota has been identified as a crucial regulator of the overall health, with studies describing its influence in a variety of disorders and developmental processes throughout the body. A widely accepted approach of influencing the microbiota and regulating its functionality in health or disease is the consumption of probiotics. In this study, we aimed to identify the impact of probiotic Lacticaseibacillus casei ATCC393 on the intestinal microbiota of mice and circulating soluble products of microbial origin or the immune system. Investigation of the gut microflora using next-generation sequencing analysis revealed alterations in the microbial populations following consumption of the probiotic. Abundance of taxa classified as Muribaculaceae was increased in lactobacilli-fed animals, while abundance of taxa classified as Lachnospiraceae and Oscillospiraceae was decreased. In addition, the composition of the intestinal microbiota was modified by the administration of L. casei, as evident by the clustering of test subjects when inspecting beta diversity, without however any significant effect on the alpha diversity of the animals. Finally, production of IgA in the intestinal lumen of mice that had received the microorganism was significantly increased, as was the concentration of lactic acid, while levels of acetic acid were noticeably lower in the L. casei group. The findings suggest that L. casei can be considered a potential candidate strain for the modulation of intestinal homeostasis and a component of dietary interventions aiming to improve overall health.

The role of the microbiome in gastrointestinal inflammation

The microbiome plays an important role in maintaining human health. Despite multiple factors being attributed to the shaping of the human microbiome, extrinsic factors such diet and use of medications including antibiotics appear to dominate. Mucosal surfaces, particularly in the gut, are highly adapted to be able to tolerate a large population of microorganisms whilst still being able to produce a rapid and effective immune response against infection. The intestinal microbiome is not functionally independent from the host mucosa and can, through presentation of microbe-associated molecular patterns (MAMPs) and generation of microbe-derived metabolites, fundamentally influence mucosal barrier integrity and modulate host immunity. In a healthy gut there is an abundance of beneficial bacteria that help to preserve intestinal homoeostasis, promote protective immune responses, and limit excessive inflammation. The importance of the microbiome is further highlighted during dysbiosis where a loss of this finely balanced microbial population can lead to mucosal barrier dysfunction, aberrant immune responses, and chronic inflammation that increases the risk of disease development. Improvements in our understanding of the microbiome are providing opportunities to harness members of a healthy microbiota to help reverse dysbiosis, reduce inflammation, and ultimately prevent disease progression.

Pro-biomics: Omics Technologies To Unravel the Role of Probiotics in Health and Disease

The comprehensive characterization of probiotic action has flourished during the past few decades, alongside the evolution of high-throughput, multiomics platforms. The integration of these platforms into probiotic animal and human studies has provided valuable insights into the holistic effects of probiotic supplementation on intestinal and extraintestinal diseases. Indeed, these methodologies have informed about global molecular changes induced in the host and residing commensals at multiple levels, providing a bulk of metagenomic, transcriptomic, proteomic, and metabolomic data. The meaningful interpretation of generated data remains a challenge; however, the maturation of the field of systems biology and artificial intelligence has supported analysis of results. In this review article, we present current literature on the use of multiomics approaches in probiotic studies, we discuss current trends in probiotic research, and examine the possibility of tailor-made probiotic supplementation. Lastly, we delve deeper into newer technologies that have been developed in the last few years, such as single-cell multiomics analyses, and provide future directions for the maximization of probiotic efficacy.

Probiotics and MicroRNA: Their Roles in the Host-Microbe Interactions

Probiotics are widely accepted to be beneficial for the maintenance of the gut homeostasis - the dynamic and healthy interactions between host and gut microorganisms. In addition, emerging as a key molecule of inter-domain communication, microRNAs (miRNAs) can also mediate the host-microbe interactions. However, a comprehensive description and summary of the association between miRNAs and probiotics have not been reported yet. In this review, we have discussed the roles of probiotics and miRNAs in host-microbe interactions and proposed the association of probiotics with altered miRNAs in various intestinal diseases and potential molecular mechanisms underlying the action of probiotics. Furthermore, we provided a perspective of probiotics-miRNA-host/gut microbiota axis applied in search of disease management highly associated with the gut microbiome, which will potentially prove to be beneficial for future studies.

Probiotic Pediococcus acidilactici strain from tomato pickle displays anti-cancer activity and alleviates gut inflammation in-vitro

The present study characterized the potential probiotic properties of Pediococcus acidilactici TMAB26 strain isolated from traditional Indian tomato pickle, and evaluated its possible therapeutic applications as an anti-cancer and anti-inflammatory agent in vitro. The 16S rRNA sequencing and primary screening demarcated TMAB26 strain as an ideal probiotic candidate, with distinctive properties of acid tolerance (58.02% at pH 2.5), bile tolerance (55.53% at 0.5%), and efficient adherence to the mucosal surface of the human intestinal cells in vitro, along with antagonistic, anti-inflammatory, and anti-cancer properties. The strain exhibited antagonism against standard intestinal pathogenic strains Staphylococcus aureus, Pseudomonas aeruginosa, Bacillus subtilis, E. coli, Klebsiella pneumonia, and Salmonella typhi with zones of inhibition in the range of 6-18 mm. The cytotoxicity evaluation of the probiotic isolate TMAB26 culture supernatant (1:1 dilution) showed significant cytotoxicity on HT-29 (94.91% ± 1.27) and Caco-2 (92.63% ± 0.63) cancer cells when compared to that of the peripheral blood mononuclear cells (PBMCs) alone. Furthermore, the strain culture supernatant reduced the mRNA levels of the proinflammatory cytokine tumor necrosis factor-alpha (TNF-α) by threefold, Interleukin-6 (IL-6) by eightfold and increased the mRNA levels of the anti-inflammatory cytokine Interleukin-10 (IL-10) in lipopolysaccharide (LPS) pretreated HT-29 and peripheral blood mononuclear cells (PBMCs), suggesting the potential role of TMAB26 isolate, i.e., Pediococcus acidilactici MTCC 13014 in alleviating gut inflammation.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02570-1.

Engineered Akkermansia muciniphila: A promising agent against diseases (Review)

Achieving a harmonious gut microbial ecosystem has been hypothesized to be a successful method for alleviating metabolic disorders. The administration of probiotics, such as Lactobacillus and Bifidobacteria, is a known traditional and safe pathway to regulate human commensal microbes. With advancements in genetic sequencing and genetic editing tools, more bacteria are able to function as engineered probiotics with multiple therapeutic properties. As one of the next-generation probiotic candidates, Akkermansia muciniphila (A. muciniphila) has been discovered to enhance the gut barrier function and moderate inflammatory responses, exhibit improved effects with pasteurization and display beneficial probiotic effects in individuals with obesity, type 2 diabetes, atherosclerosis and autism-related gastrointestinal disturbances. In view of this knowledge, the present review aimed to summarize the effects of A. muciniphila in the treatment of metabolic disorders and to discuss several mature recombination systems for the genetic modification of A. muciniphila. From gaining an enhanced understanding of its genetic background, ingested A. muciniphila is expected to be used in various applications, including as a diagnostic tool, and in the site-specific delivery of therapeutic drugs.

Isolation of a Leuconostoc mesenteroides Strain With Anti-Porcine Epidemic Diarrhea Virus Activities From Kefir Grains

Swine grown under commercial conditions are vulnerable to environmental exposure to several viruses, which may cause infectious diseases and spread easily and rapidly, resulting in significant economic losses in animal husbandry. Previous studies have suggested that probiotics seem to be a new and promising alternative to vaccinations to protect animals against potential viral infections. In this study, we used the Vero cell culture model of infection to study porcine epidemic diarrhea virus (PEDV). We screened lactic acid bacteria (LAB) with anti-PEDV potential from kefir grains, which are starter cultures used to ferment milk into kefir. Twenty-nine LAB strains were isolated and identified as Enterococcus durans, Lactobacillus kefiri, Lactococcus lactis, and Leuconostoc mesenteroides, according to 16S ribosomal RNA (rRNA) and rpoA gene sequence analyses. The anti-PEDV activities of the LAB intracellular extracts were compared, and the intracellular extracts of Ln. mesenteroides showed higher anti-PEDV activities than that of the other species. Among the Ln. mesenteroides strains, a strain designated YPK30 showed a higher growth rate than that of the other strains and was further evaluated for its anti-PEDV activity. The results showed that the intracellular extracts of Ln. mesenteroides YPK30 possessed in vitro prophylactic, therapeutic, and direct-inhibitory effects against PEDV in the Vero cell model. The expression levels of Type 1 interferon (IFN)-dependent genes, including Myxovirus resistance 1 (MX1) and interferon-stimulated gene 15 (ISG15), were significantly increased after treatment with intracellular extracts of Ln. mesenteroides YPK30 for 24 h. Such expression suggests that the anti-PEDV activity of Ln. mesenteroides YPK30 could be attributed to its up-regulatory effect on the expression of MX1 and ISG15 genes. These results suggested that Ln. mesenteroides YPK30 has the potential to provide some levels of host protection against PEDV infections.

Promising discovery of beneficial Escherichia coli in the human gut

Ingested dietary fibres are hydrolysed by colon microbiota to produce energy-providing short-chain fatty acids (SCFA) that stimulate anti-inflammatory effects. SCFA-producing bacteria were screened from bacteria isolated from human faeces using bromothymol blue as an acid indicator and gas chromatography for SCFA profiling. The beneficial functions (antagonistic activity, haemolytic activities, antibiotic susceptibility, mucus adherent percentage and toxin gene detection) were evaluated for the top five SCFA-producing bacteria isolated from three healthy volunteers that identified as Escherichia coli strains. They produced acetic, propionic, isobutyric, butyric, isovaleric, valeric and caproic acids at average concentrations of 15.9, 1.8, 1.1, 1.9, 1.8, 2.7 and 3.4 mM, respectively. The SCFA production by E. coli strains was rapidly increased during the first 8 h of incubation and gradually decreased after 16 h of incubation. All E. coli strains showed acid and bile tolerance, resulting in a survival rate greater than 70% with no haemolytic activity, mucus adherence greater than 40% and susceptibility to conventional antibiotics. Hence, the selected E. coli strains exhibited promising probiotic properties with neither enterotoxin nor LPS producibility was detected. The present results confirm the existence of friendly and harmless E. coli strains in human microbiota as potential probiotics.