Probiotics database: a potential source of fermented foods

Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda

The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.

Probiotic-fermented edible herbs as functional foods: A review of current status, challenges, and strategies

Recently, consumers have become increasingly interested in natural, health-promoting, and chronic disease-preventing medicine and food homology (MFH). There has been accumulating evidence that many herbal medicines, including MFH, are biologically active due to their biotransformation through the intestinal microbiota. The emphasis of scientific investigation has moved from the functionally active role of MFH to the more subtle role of biotransformation of the active ingredients in probiotic-fermented MFH and their health benefits. This review provides an overview of the current status of research on probiotic-fermented MFH. Probiotics degrade toxins and anti-nutritional factors in MFH, improve the flavor of MFH, and increase its bioactive components through their transformative effects. Moreover, MFH can provide a material base for the growth of probiotics and promote the production of their metabolites. In addition, the health benefits of probiotic-fermented MFH in recent years, including antimicrobial, antioxidant, anti-inflammatory, anti-neurodegenerative, skin-protective, and gut microbiome-modulating effects, are summarized, and the health risks associated with them are also described. Finally, the future development of probiotic-fermented MFH is prospected in combination with modern development technologies, such as high-throughput screening technology, synthetic biology technology, and database construction technology. Overall, probiotic-fermented MFH has the potential to be used in functional food for preventing and improving people's health. In the future, personalized functional foods can be expected based on synthetic biology technology and a database on the functional role of probiotic-fermented MFH.

Probiotic therapy, African fermented foods and food-derived bioactive peptides in the management of SARS-CoV-2 cases and other viral infections

The current paper focuses on the impact of probiotics, African fermented foods and bioactive peptides on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection severity and related viral infections. Using probiotics or bioactive peptides as therapeutic adjuncts appears superior to standard care alone. Probiotics play critical roles in innate and adaptive immune modulation by balancing the gut microbiota to combat viral infections, secondary bacterial infections and microbial dysbiosis. African fermented foods contain abundant potential probiotic microorganisms such as the lactic acid bacteria (LAB), Saccharomyces, and Bacillus. More so, fermented food-derived bioactive peptides play vital roles in preventing cardiovascular diseases, hypertension, lung injury, diabetes, and other COVID-19 comorbidities. Regularly incorporating potential probiotics and bioactive peptides into diets should enable a build-up of the benefits in the body system that may result in a better prognosis, especially in COVID-19 patients with underlying complexities. Despite the reported therapeutic potentials of probiotics and fermented foods, numerous setbacks exist regarding their application in disease management. These shortfalls underscore an evident need for more studies to evaluate the specific potentials of probiotics and traditional fermented foods in ameliorating SARS-CoV-2 and other viral infections.

FDF-DB: A Database of Traditional Fermented Dairy Foods and Their Associated Microbiota

BACKGROUND

Fermented foods are attracting increasing interest due to their nutritional and health benefits, including a positive impact on gut microbiota exerted by their associated microbes. However, information relative to traditional fermented dairy products, along with their autochthonous microbiota, is still fragmented and poorly standardized. Therefore, our aim was to collect and aggregate data useful for obtaining a comprehensive overview translated in a classical database interface that can be easily handled by users.

METHODS

a preliminary inventory was built up by systematically collecting data from publicly available resources for the creation of a list of traditional dairy foods produced worldwide, including additional metadata useful for stratifying, and collapsing subgroups.

RESULTS

we developed the Fermented Dairy Food Database (FDF-DB), a feasible resource comprising 1852 traditional dairy foods (cheeses, fermented milks, and yogurt) for which microbial content and other associated metadata such as geographical indication label, country/region of origin, technological aspects were gathered.

CONCLUSIONS

FDF-DB is a useful and user-friendly resource where taxonomic information and processing production details converge. This resource will be of great aid for researchers, food industries, stakeholders and any user interested in the identification of technological and microbiological features characterizing traditional fermented dairy products.

Comparative Metabolomic Analysis of Moromi Fermented Using Different Aspergillus oryzae Strains

Aspergillus oryzae (A. oryzae) is an important starter in the fermentation of koji and moromi. However, the effect of different A. oryzae strains on the quality of moromi has rarely been studied. For this reason, this study analyzed the physicochemical properties, enzyme activity, sensory quality, and metabolite profiles of moromi samples fermented using two strains (A. oryzae KCCM12012P (moromi-1) and KCCM12804P (moromi-2)), which were newly isolated from fermented soy foods, and compared them to those of a commercialized A. oryzae strain (control). Amino-type nitrogen contents of moromi-1 and moromi-2 samples were higher than that of control moromi, and their amylase and protease activities were also higher. Moreover, metabolite profiles of moromi were significantly altered according to strains. In particular, the levels of many amino acids, peptides, nucleotides, and acidic compounds were altered, which resulted in changes in the sensory quality of moromi. Although volatile compounds were not investigated, the results suggested that the quality of moromi was significantly different for newly isolated strains, especially A. oryzae KCCM12804P, and they were superior to the commercial strain in terms of taste-related substances. Therefore, these strains could be used as good starters to produce moromi and soy sauce with good sensory quality.

ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics

The use of probiotics to improve health via the modulation of gut microbiota has gained wide attention. The growing volume of investigations of probiotic microorganisms and commercialized probiotic products has created the need for a database to organize the health-promoting functions driven by probiotics reported in academic articles, clinical trials and patents. We constructed ProBioQuest to collect up-to-date literature related to probiotics from PubMed.gov, ClinicalTrials.gov and PatentsView. More than 2.8 million articles have been collected. Automated information technology-assisted procedures enabled us to collect the data continuously, providing the most up-to-date information. Statistical functions and semantic analyses are provided on the website as an advanced search engine, which contributes to the semantic tool of this database for information search and analyses. The semantic analytical output provides categorized search results and functions to enhance further analysis. A keyword bank is included which can display multiple tables of contents. Users can select keywords from different displayed categories to achieve easily filtered searches. Additional information on the searched items can be browsed via the link-out function. ProBioQuest is not only useful to scientists and health professionals but also to dietary supplement manufacturers and the general public. In this paper, the method we used to build this database-web system is described. Applications of ProBioQuest for several literature-based analyses of probiotics are included as examples of the various uses of this search engine. ProBioQuest can be accessed free of charge at http://kwanlab.bio.cuhk.edu.hk/PBQ/.

Recent advances in antiviral effects of probiotics: potential mechanism study in prevention and treatment of SARS-CoV-2

SARS-CoV-2 is responsible for coronavirus disease 2019 (COVID-19), progressively extended worldwide countries on an epidemic scale. Along with all the drug treatments suggested to date, currently, there are no approved management protocols and treatment regimens for SARS-CoV-2. The unavailability of optimal medication and effective vaccines against SARS-CoV-2 indicates the requirement for alternative therapies. Probiotics are living organisms that deliberate beneficial effects on the host when used sufficiently and in adequate amounts, and fermented food is their rich source. Probiotics affect viruses by antiviral mechanisms and reduce diarrhea and respiratory tract infection. At this point, we comprehensively evaluated the antiviral effects of probiotics and their mechanism with a particular focus on SARS-CoV-2. In this review, we suggested the conceptual and potential mechanisms of probiotics by which they could exhibit antiviral properties against SARS-CoV-2, according to the previous evidence concerning the mechanism of antiviral effects of probiotics. This study reviewed recent studies that speculate about the role of probiotics in the prevention of the SARS-CoV-2-induced cytokine storm through the mechanisms such as induction of anti-inflammatory cytokines (IL-10), downregulation of pro-inflammatory cytokines (TNF-α, IL-2, IL-6), inhibition of JAK signaling pathway, and act as HDAC inhibitor. Also, the recent clinical trials and their outcome have been reviewed.

Effects of Salt Treatment Time on the Metabolites, Microbial Composition, and Quality Characteristics of the Soy Sauce Moromi Extract

Salt is one of the most important factors for fermented foods, but the effect of salt treatment time on the quality of fermented foods has rarely been studied. In this study, the effect of different salt treatment times (0, 48, and 96 h) after the start of fermentation on the quality of the soy sauce moromi extract (SSME) was investigated. As the salt treatment time was delayed, the population of Aspergillus oryzae, Lactobacillaceae, and Enterococcaecea in SSME increased, whereas the population of Staphylococcaceae and Bacillaceae decreased, leading to changes in the enzymatic activity and metabolite profiles. In particular, the contents of amino acids, peptides, volatile compounds, acidic compounds, sugars, and secondary metabolites were significantly affected by the salt treatment time, resulting in changes in the sensory quality and appearance of SSME. The correlation data showed that metabolites, bacterial population, and sensory parameters had strong positive or negative correlations with each other. Moreover, based on metabolomics analysis, the salt treatment-time-related SSME metabolomic pathway was proposed. Although further studies are needed to elucidate the salt treatment mechanism in fermented foods, our data can be useful to better understand the effect of salt treatment time on the quality of fermented foods.

The Role of Gut Microbiota on Cholesterol Metabolism in Atherosclerosis

Hypercholesterolemia plays a causal role in the development of atherosclerosis and is one of the main risk factors for cardiovascular disease (CVD), the leading cause of death worldwide especially in developed countries. Current data show that the role of microbiota extends beyond digestion by being implicated in several metabolic and inflammatory processes linked to several diseases including CVD. Studies have reported associations between bacterial metabolites and hypercholesterolemia. However, such associations remain poorly investigated and characterized. In this review, the mechanisms of microbial derived metabolites such as primary and secondary bile acids (BAs), trimethylamine N-oxide (TMAO), and short-chain fatty acids (SCFAs) will be explored in the context of cholesterol metabolism. These metabolites play critical roles in maintaining cardiovascular health and if dysregulated can potentially contribute to CVD. They can be modulated via nutritional and pharmacological interventions such as statins, prebiotics, and probiotics. However, the mechanisms behind these interactions also remain unclear, and mechanistic insights into their impact will be provided. Therefore, the objectives of this paper are to present current knowledge on potential mechanisms whereby microbial metabolites regulate cholesterol homeostasis and to discuss the feasibility of modulating intestinal microbes and metabolites as a novel therapeutic for hypercholesterolemia.

Recent innovations in the production of selected specialty (non-traditional) beers

Customer demand for product diversity is the key driving force for innovations in the brewing industry. Specialty beers are regarded as a distinct group of beers different from two major types, lagers and ales, without established definitions or boundaries. Specialty beers, including low- to no-alcohol beer, low carbohydrate beer, gluten-free beer, sour beer, probiotic beer, and enriched beer, are exclusively brewed and developed keeping in mind their functionality, the health and wellbeing of the consumer, and emerging market trends. Compared with conventional beer-brewing, the production of specialty beers is technologically challenging and usually requires additional process steps, unique microorganisms, and special equipment, which in turn may incur additional costs. In addition, the maintenance of quality and stability of the products as well as consumer acceptability of the products are major challenges to successful commercialization. A harmonious integration of traditional brewing practices and modern technological approaches may hold potential for future developments. In the present review, latest developments in the fermentative production of selected specialty beers are discussed.

Cholesterol Reduction and Vitamin B12 Production Study on Enterococcus faecium and Lactobacillus pentosus Isolated from Yoghurt

The present study was aimed to test cholesterol reduction and vitamin B12 production abilities of the isolated lactic acid bacteria (LAB). Three LAB isolates, namely, Enterococcus faecium (EF), Enterococcus faecium (Chole1), and Lactobacillus pentosus (7MP), having probiotic potential, were isolated from yoghurt. These isolates were screened for bile salt hydrolase (BSH) activity, cholesterol reduction property in MRS broth, and the production of vitamin B12. The present study revealed that the isolate 7MP possesses the highest potential of (48%) cholesterol reduction compared to the other isolates. The isolates EF and Chole1 produced a good amount of (1 ng/mL) vitamin B12. These isolates were identified by 16S rRNA gene sequencing and confirmed by MALD_TOF analysis. Thus, the use of these LAB isolates for yoghurt-making can offer the value addition of lowering cholesterol and vitamin B12 fortification in fermented food.

Antiviral activity of fermented foods and their probiotics bacteria towards respiratory and alimentary tracts viruses

The recent COVID-19, a viral outbreak calls for a high demand for non-conventional antiviral agents that can reduce the risk of infections and promote fast recovery. Fermented foods and their probiotics bacteria have recently received increasing interest due to the reported potential of high antiviral activity. Several probiotics strains demonstrated broad range of antiviral activities and different mechanisms of action. This article will review the diversity, health benefits, interaction with immune system and antiviral activity of fermented foods and their probiotics bacteria. In addition, the mechanisms of action will be reviewed to determine the broad range potential antiviral activity against the respiratory and alimentary tracts viruses. The probiotics bacteria and bioactive compounds in fermented foods demonstrated antiviral activities against respiratory and alimentary tracts viruses. The mechanism of action was reported to be due to the stimulation of the immune system function via enhancing natural killers cell toxicity, enhance the production of pro-inflammatory cytokines, and increasing the cytotoxic of T lymphocytes (CD3⁺, CD16⁺, CD56⁺). However, further studies are highly recommended to determine the potential antiviral activity for traditional fermented foods.

FermFooDb: A database of bioactive peptides derived from fermented foods

Globally fermented foods are in demands due to their functional and nutritional benefits. These foods are sources of probiotic organisms and bioactive peptides, various amino acids, enzymes etc. that provides numerous health benefits. FermFooDb (https://webs.iiitd.edu.in/raghava/fermfoodb/) is a manually curated database of bioactive peptides derived from wide range of foods that maintain comprehensive information about peptides and process of fermentation. This database comprises of 2205 entries with following major fields, peptide sequence, Mass and IC50, food source, functional activity, fermentation conditions, starter culture, testing conditions of sequences in vitro or in vivo, type of model and method of analysis. The bioactive peptides in our database have wide range of therapeutic potentials that includes antihypertensive, ACE-inhibitory, antioxidant, antimicrobial, immunomodulatory and cholesterol lowering peptides. These bioactive peptides were derived from different types of fermented foods that include milk, cheese, yogurt, wheat and rice. Numerous, web-based tools have been integrated to retrieve data, peptide mapping of proteins, similarity search and multiple-sequence alignment. This database will be useful for the food industry and researchers to explore full therapeutic potential of fermented foods from specific cultures.

Fermented dairy products as delivery vehicles of novel probiotic strains isolated from traditional fermented Asian foods

The screening of novel probiotic strains from various food sources including fruits, vegetables, herbs, and traditional fermented foods, have been of growing concern recently. Most of these potential probiotic lactic acid bacteria isolates were distinguished from the commercial probiotics based on multiple therapeutic effects and functionalities. Recent in vitro and in vivo investigates have also verified the usage of probiotics to lower the risk of diseases. Application of these novel strains in fermented dairy products is also an emerging trend to improve the physical and quality characteristics, functional properties, and safety of dairy products. Moreover, since dairy products are one of the highest consumed products in the globe, the dispatch channels for fermented dairy products are already established. Therefore, incorporating novel probiotic strains into fermented dairy products might be the most feasible approach for their delivery. In this context, our aim is to discuss the feasibility of dairy products as delivery vehicles for novel probiotic strains. Thus, we summarize the scientific evidence that points to a dynamic future for the production of fermented dairy-based probiotics.

Screening of Bacteriocinogenic Lactic Acid Bacteria and Their Characterization as Potential Probiotics

Probiotics are living microorganisms used as nutritional additives that confer health benefits on the host. Their use in food products is very attractive, especially if they could also inhibit important foodborne pathogens. In this study, antimicrobial activity against several foodborne pathogens was screened for 280 lactic acid bacteria (LAB) isolated from different food products and the probiotic characteristics of bacteriocinogenic isolates were evaluated. Seven out of 280 LAB isolates were selected due to their bacteriocinogenic properties and identified by 16S rRNA gene sequence analysis as Pediococcus pentosaceus (n = 6) and Lactobacillus plantarum (n = 1). Virulence factors and antibiotic resistances were not detected for any of the isolates. Except for L. plantarum R23, all the isolates were able to survive through the simulated gastrointestinal tract conditions. Only P. pentosaceus CFF4 was able to adhere to Caco-2 cells after the simulated gastrointestinal tract passage. In conclusion, even though in vivo studies should be performed, P. pentosaceus CFF4, which was also able to inhibit the growth of foodborne pathogens in vitro, seems to be a potential probiotic to be used in the food industry.

An overview of yeast probiotics as cancer biotherapeutics: possible clinical application in colorectal cancer

The previous reports have established a strong link between diet, lifestyle, and gut microbiota population with the onset of the colorectal cancer (CRC). Administration of probiotics has become a particular interest in prevention and treatment of CRC. As potential dietary complements, probiotics might be able to lower the risk of CRC and manage the safety of traditional cancer therapies such as surgery, radiation therapy, and chemotherapy. This review investigates the promising effects of probiotics as biotherapeutics, with due attention to possible clinical application of yeast probiotics in prevention and treatment of CRC. In addition, various underlying anti-cancer mechanisms are covered here based on scientific evidence and findings from numerous experimental studies. Application of probiotics as biotherapeutics in CRC, however, needs to be approved by human clinical trials. It is of prime concern, to find potential probiotic strains, effective doses for administrations and regimes, and molecular mechanisms involved in prevention and treatment.