Probiotics genomics

Endospore production of Bacillus spp. for industrial use

The increased occurrence of antibiotic resistance and the harmful use of pesticides are a major problem of modern times. A ban on the use of antibiotics as growth promoters in animal breeding has put a focus on the probiotics market. Probiotic food supplements are versatile and show promising results in animal and human nutrition. Chemical pesticides can be substituted by biopesticides, which are very effective against various pests in plants due to increased research. What these fields have in common is the use of spore-forming bacteria. The endospore-forming Bacillus spp. belonging to this group offer an effective solution to the aforementioned problems. Therefore, the biotechnological production of sufficient qualities of such endospores has become an innovative and financially viable field of research. In this review, the production of different Bacillus spp. endospores will be reviewed. For this purpose, the media compositions, cultivation conditions and bioprocess optimization methods of the last 20 years are presented and reflected.

Effect of Bacillus coagulans SNZ 1969 on the Improvement of Bowel Movement in Loperamide-Treated SD Rats

Bacillus coagulans SNZ 1969 (B. coagulans SNZ 1969) is a spore-forming bacterium reported to be effective in attenuating constipation. However, there is no study on whether B. coagulans SNZ 1969 could improve constipation through mucin secretion and changes in intestinal hormones. To address this knowledge gap, rats were orally administrated with various treatments for four weeks. The normal control (NOR) group received saline only. There were four constipation-induced groups. The LOP group received only loperamide (LOP), a constipation-inducing agent. The BIS group received both LOP and Bisacodyl (BIS, a constipation treatment agent). The SNZ-L group received both LOP and B. coagulans SNZ 1969 at 1 × 10⁸ CFU/day. The SNZ-H group received LOP and B.coagulans SNZ 1969 at 1 × 10¹⁰ CFU/day. As indicators of constipation improvement, fecal pellet weight, fecal water content, gastrointestinal transit time, and intestinal motility were measured. Mucus secretion in the colon was determined by histological colon analysis and mucin-related gene expressions. Gastrointestinal (GI) hormones were also measured. SNZ-L and SNZ-H groups showed significantly increased fecal weights, fecal water contents, and intestinal motility than the LOP group. SNZ-L and SNZ-H groups also showed higher secretion of mucin in the colon and mRNA expression levels of Mucin 2 and Aquaporin 8 than the LOP group. The SNZ-H group showed significantly increased substance P but significantly decreased somatostatin and vasoactive intestinal peptide than the LOP group. The results of this study suggest that B. coagulans SNZ 1969 intake could attenuate constipation through mucin secretion and alteration of GI hormones.

One Health Probiotics as Biocontrol Agents: One Health Tomato Probiotics

Tomato (Lycopersicon esculentum) is one of the most popular and valuable vegetables in the world. The most common products of its industrial processing in the food industry are juice, tomato paste, various sauces, canned or sun-dried fruits and powdered products. Tomato fruits are susceptible to bacterial diseases, and bacterial contamination can be a risk factor for the safety of processed tomato products. Developments in bioinformatics allow researchers to discuss target probiotic strains from an existing large number of probiotic strains for any link in the soil-plant-animal-human chain. Based on the literature and knowledge on the "One Health" concept, this study relates to the suggestion of a new term for probiotics: "One Health probiotics", beneficial for the unity of people, animals, and the environment. Strains of Lactiplantibacillus plantarum, having an ability to ferment a broad spectrum of plant carbohydrates, probiotic effects in human, and animal health, as well as being found in dairy products, vegetables, sauerkraut, pickles, some cheeses, fermented sausages, fish products, and rhizospheric soil, might be suggested as one of the probable candidates for "One Health" probiotics (also, for "One Health-tomato" probiotics) for the utilization in agriculture, food processing, and healthcare.

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

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

Lactic Acid Bacteria: Food Safety and Human Health Applications

Research on lactic acid bacteria has confirmed how specific strains possess probiotic properties and impart unique sensory characteristics to food products. The use of probiotic lactic acid bacteria (LAB) in many food products, thus confers various health benefits to humans when they are frequently consumed in adequate amounts. The advent of functional food or the concept of nutraceuticals objectively places more emphasis on seeking alternatives to limit the use of medications thus promoting the regular consumption of fermented foods. Probiotic use has thus been recommended to fulfill the role of nutraceuticals, as no side effects on human health have been reported. Probiotics and lactic acid bacteria can boost and strengthen the human immune system, thereby increasing its resistance against numerous disease conditions. Consumer safety and confidence in dairy and fermented food products and the desire of the food industry to meet the sensory and health needs of consumers, has thus increased the demand for probiotic starter cultures with exceptional performance coupled with health benefiting properties. The potential of probiotic cultures and lactic acid bacteria in many industrial applications including fermented food products generally affects product characteristics and also serves as health-promoting foods for humans. The alleviation of lactose intolerance in many populations globally has been one of the widely accepted health claims attributed to probiotics and lactic acid bacteria, although many diseases have been treated with probiotic lactic acid bacteria and have been proven with scientific and clinical studies. The aim of our review was to present information related to lactic acid bacteria, the new classification and perspectives on industrial applications with a special emphasis on food safety and human health.

Application of Bacillus coagulans in Animal Husbandry and Its Underlying Mechanisms

In recent decades, probiotics have attracted widespread attention and their application in healthcare and animal husbandry has been promising. Among many probiotics, Bacillus coagulans (B. coagulans) has become a key player in the field of probiotics in recent years. It has been demonstrated to be involved in regulating the balance of the intestinal microbiota, promoting metabolism and utilization of nutrients, improving immunity, and more importantly, it also has good industrial properties such as high temperature resistance, acid resistance, bile resistance, and the like. This review highlights the effects of B. coagulans in animal husbandry and its underlying mechanisms.

Growth Mode and Carbon Source Impact the Surfaceome Dynamics of Lactobacillus rhamnosus GG

Bacterial biofilms have clear implications in disease and in food applications involving probiotics. Here, we show that switching the carbohydrate source from glucose to fructose increased the biofilm formation and the total surface-antigenicity of a well-known probiotic, Lactobacillus rhamnosus GG. Surfaceomes (all cell surface-associated proteins) of GG cells grown with glucose and fructose in planktonic and biofilm cultures were identified and compared, which indicated carbohydrate source-dependent variations, especially during biofilm growth. The most distinctive differences under these conditions were detected with several surface adhesins (e.g., MBF, SpaC pilus protein and penicillin-binding proteins), enzymes (glycoside hydrolases, PrsA, PrtP, PrtR, and HtrA) and moonlighting proteins (glycolytic, transcription/translation and stress-associated proteins, r-proteins, tRNA synthetases, Clp family proteins, PepC, PepN, and PepA). The abundance of several known adhesins and candidate moonlighters, including enzymes acting on casein-derived peptides (ClpP, PepC, and PepN), increased in the biofilm cells grown on fructose, from which the surface-associated aminopeptidase activity mediated by PepC and PepN was further confirmed by an enzymatic assay. The mucus binding factor (MBF) was found most abundant in fructose grown biofilm cells whereas SpaC adhesin was identified specifically from planktonic cells growing on fructose. An additional indirect ELISA indicated both growth mode- and carbohydrate-dependent differences in abundance of SpaC, whereas the overall adherence of GG assessed with porcine mucus indicated that the carbon source and the growth mode affected mucus adhesion. The adherence of GG cells to mucus was almost completely inhibited by anti-SpaC antibodies regardless of growth mode and/or carbohydrate source, indicating the key role of the SpaCBA pilus in adherence under the tested conditions. Altogether, our results suggest that carbon source and growth mode coordinate mechanisms shaping the proteinaceous composition of GG cell surface, which potentially contributes to resistance, nutrient acquisition and cell-cell interactions under different conditions. In conclusion, the present study shows that different growth regimes and conditions can have a profound impact on the adherent and antigenic features of GG, thereby providing new information on how to gain additional benefits from this probiotic.

Structural Characterization of the Lactobacillus Plantarum FlmC Protein Involved in Biofilm Formation

Lactobacillus plantarum is one of the most predominant species in the human gut microbiota of healthy individuals. We have previously characterized some probiotic features of L. plantarum LM3, as the high resistance to different stress, the binding ability toward some extracellular matrix proteins and plasminogen and the immunomodulatory role of the surface expressed adhesin EnoA1. We have also identified the flmA, flmB and flmC genes, coding for putative proteins named FlmA, FlmB and FlmC, whose null mutations partially impaired biofilm development; the L. plantarum LM3–6 strain, carrying a deletion in flmC, showed a high rate of autolysis, supporting the hypothesis that FlmC might be involved in cell wall integrity. Here, we report the in-silico characterization of ΔTM-FlmC, a portion of the FlmC protein. The protein has been also expressed, purified and characterized by means of CD spectroscopy, ICP-mass and UHPLC-HRMS. The obtained experimental data validated the predicted model unveiling also the presence of a bound lipid molecule and of a Mg(II) ion. Overall, we provide strong evidences that ΔTM-FlmC belongs to the LytR-CpsA-Psr (LCP) family of domains and is involved in cell envelope biogenesis.

Potential Use of Bacillus coagulans in the Food Industry

Probiotic microorganisms are generally considered to beneficially affect host health when used in adequate amounts. Although generally used in dairy products, they are also widely used in various commercial food products such as fermented meats, cereals, baby foods, fruit juices, and ice creams. Among lactic acid bacteria, Lactobacillus and Bifidobacterium are the most commonly used bacteria in probiotic foods, but they are not resistant to heat treatment. Probiotic food diversity is expected to be greater with the use of probiotics, which are resistant to heat treatment and gastrointestinal system conditions. Bacillus coagulans (B. coagulans) has recently attracted the attention of researchers and food manufacturers, as it exhibits characteristics of both the Bacillus and Lactobacillus genera. B. coagulans is a spore-forming bacterium which is resistant to high temperatures with its probiotic activity. In addition, a large number of studies have been carried out on the low-cost microbial production of industrially valuable products such as lactic acid and various enzymes of B. coagulans which have been used in food production. In this review, the importance of B. coagulans in food industry is discussed. Moreover, some studies on B. coagulans products and the use of B. coagulans as a probiotic in food products are summarized.

Immobilized lipase from Lactobacillus plantarum in meat degradation and synthesis of flavor esters

Microbial lipases owing to their broad substrate specificity are widely used in various industrial applications like food processing, organic synthesis, detergent formulation and oil manufacturing. In the current study the immobilized lipase from Lactobacillus plantarum was found novel in degrading meat which can be applied in medical field and also in synthesizing different short chain fatty acid esters like 2,3,4-hydroxybenzyl acetates and triazole ester which makes a great impingement in natural flavor industry. The 4-hydroxybenzyl acetate obtained can also be used in cosmetics.

Comparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis

BACKGROUND

Lactobacillus crispatus is a ubiquitous micro-organism encountered in a wide range of host-associated habitats. It can be recovered from the gastrointestinal tract of animals and it is a common constituent of the vaginal microbiota of humans. Moreover, L. crispatus can contribute to the urogenital health of the host through competitive exclusion and the production of antimicrobial agents. In order to investigate the genetic diversity of this important urogenital species, we performed a comparative genomic analysis of L. crispatus.

RESULTS

Utilizing the completed genome sequence of a strain ST1 and the draft genome sequences of nine other L. crispatus isolates, we defined the scale and scope of the pan- and core genomic potential of L. crispatus. Our comparative analysis identified 1,224 and 2,705 ortholog groups present in all or only some of the ten strains, respectively. Based on mathematical modeling, sequencing of additional L. crispatus isolates would result in the identification of new genes and functions, whereas the conserved core of the ten strains was a good representation of the final L. crispatus core genome, estimated to level at about 1,116 ortholog groups. Importantly, the current core was observed to encode bacterial components potentially promoting urogenital health. Using antibody fragments specific for one of the conserved L. crispatus adhesins, we demonstrated that the L. crispatus core proteins have a potential to reduce the ability of Gardnerella vaginalis to adhere to epithelial cells. These findings thereby suggest that L. crispatus core proteins could protect the vagina from G. vaginalis and bacterial vaginosis.

CONCLUSIONS

Our pan-genome analysis provides insights into the intraspecific genome variability and the collective molecular mechanisms of the species L. crispatus. Using this approach, we described the differences and similarities between the genomes and identified features likely to be important for urogenital health. Notably, the conserved genetic backbone of L. crispatus accounted for close to 60% of the ortholog groups of an average L. crispatus strain and included factors for the competitive exclusion of G. vaginalis, providing an explanation on how this urogenital species could improve vaginal health.

Microbial characterization of probiotics--advisory report of the Working Group "8651 Probiotics" of the Belgian Superior Health Council (SHC)

When ingested in sufficient numbers, probiotics are expected to confer one or more proven health benefits on the consumer. Theoretically, the effectiveness of a probiotic food product is the sum of its microbial quality and its functional potential. Whereas the latter may vary much with the body (target) site, delivery mode, human target population, and health benefit envisaged microbial assessment of the probiotic product quality is more straightforward. The range of stakeholders that need to be informed on probiotic quality assessments is extremely broad, including academics, food and biotherapeutic industries, healthcare professionals, competent authorities, consumers, and professional press. In view of the rapidly expanding knowledge on this subject, the Belgian Superior Health Council installed Working Group "8651 Probiotics" to review the state of knowledge regarding the methodologies that make it possible to characterize strains and products with purported probiotic activity. This advisory report covers three main steps in the microbial quality assessment process, i.e. (i) correct species identification and strain-specific typing of bacterial and yeast strains used in probiotic applications, (ii) safety assessment of probiotic strains used for human consumption, and (iii) quality of the final probiotic product in terms of its microbial composition, concentration, stability, authenticity, and labeling.

Genomic diversity and versatility of Lactobacillus plantarum, a natural metabolic engineer

In the past decade it has become clear that the lactic acid bacterium Lactobacillus plantarum occupies a diverse range of environmental niches and has an enormous diversity in phenotypic properties, metabolic capacity and industrial applications. In this review, we describe how genome sequencing, comparative genome hybridization and comparative genomics has provided insight into the underlying genomic diversity and versatility of L. plantarum. One of the main features appears to be genomic life-style islands consisting of numerous functional gene cassettes, in particular for carbohydrates utilization, which can be acquired, shuffled, substituted or deleted in response to niche requirements. In this sense, L. plantarum can be considered a "natural metabolic engineer".