In silico genomic analysis of the potential probiotic Lactiplantibacillus pentosus CF2-10N reveals promising beneficial effects with health promoting properties

Comparative genome analysis of the immunomodulatory ability of Lactiplantibacillus plantarum and Lactiplantibacillus pentosus from Japanese pickles

Lactic acid bacteria (LAB) are pivotal in food preservation and exhibit immunomodulatory effects on interleukin-10 (IL-10) and interleukin-12 (IL-12) production. Lactiplantibacillus plantarum (L. plantarum) and Lactiplantibacillus pentosus (L. pentosus) from fermented food are known for their effect; however, a comprehensive comparative genome analysis is needed to identify the linked genes. Here, we investigated the immunomodulatory capability at the genome level of L. plantarum and L. pentosus strains isolated from Japanese pickles at the genome level, and we further identified their immunomodulation-associated genes using the potential-gene (PG) index derived from the Calinski-Harabasz (CH) index. The results revealed an immunostimulatory clade with strain-specific IL-10 and IL-12 induction and identified key genes via the PG index. Both genes across two species were shown to encode the enzyme TagF2, which is crucial for synthesizing poly-glycerol-3-phosphate type wall teichoic acid (poly-GroP WTA), indicating that TagF2 plays a potential role as an effective microbe-associated-molecular-pattern. In vivo analyses confirmed the IL-10-inducing ability of one strain, reinforcing the IL-10-stimulating capacity of its poly-GroP WTA. Subpotential genes in L. plantarum TagF2-possessing strains were linked to host‒cell interactions, suggesting that such strains play potential probiotic roles. Collectively, the PG index effectively identified immunomodulation-related genes, thus paving the way for the use of the PG index to detect potential health benefit-associated genes in other LAB species.

IMPORTANCE

Lactic acid bacteria are pivotal in food preservation and exhibit immunomodulatory effects on interleukin-10 (IL-10) and interleukin-12 (IL-12) production. Lactiplantibacillus plantarum and Lactiplantibacillus pentosus from fermented food are known for such effect, yet comprehensive comparative genome analysis is needed to elucidate the linked genes of the two species. The significance of our research is in observing the immunostimulatory clade with strain-specific cytokine induction and identifying key immunostimulation-related genes encoding enzymes that are crucial for synthesizing a potentially effective microbe-associated-molecular-pattern using the potential-gene index across two species. The further in vivo validation reinforced the interleukin-10-stimulating capacity of the identified pattern, and the detected sub-potential genes in Lactiplantibacillus plantarum key-gene possessing strains implied the utility of potential-gene index in detecting potential health-benefit-associated genes in other lactic acid bacteria species.

Gut Microbiota: An Immersion in Dysbiosis, Associated Pathologies, and Probiotics

The importance of the microbiome, particularly the gut microbiota and its implications for health, is well established. However, an increasing number of studies further strengthen the link between an imbalanced gut microbiota and a greater predisposition to different diseases. The gut microbiota constitutes a fundamental ecosystem for maintaining human health. Its alteration, known as dysbiosis, is associated with a wide range of conditions, including intestinal, metabolic, immunological, or neurological pathologies, among others. In recent years, there has been a substantial increase in knowledge about probiotics-bacterial species that enhance health or address various diseases-with numerous studies reporting their benefits in preventing or improving these conditions. This review aims to analyze the most common pathologies resulting from an imbalance in the gut microbiota, as well as detail the most important and known gut probiotics, their functions, and mechanisms of action in relation to these conditions.

Whole Genome Analysis of Limosilactobacillus fermentum MCC0552 for Probiotic Functionalities and Comparative Genomic Study with Reference Strains

Limosilactobacillus fermentum MCC0552, a potential probiotic was isolated from a dairy source. L. fermentum MCC0552 has been proven earlier to enhance immuno-modulatory response by alleviating inflammatory and diabetic effects. The objective of this study is to analyse the whole genome sequence of L. fermentum MCC0552 for probiotic functionalities and to compare it with the reference strains. The general genomic features of L. fermentum strain MCC0552 were analysed and a phylogenetic dendrogram was generated by considering the genome sequences of reference strains (L. fermentum IFO 3956, F-6, MTCC 5898 and ATCC 14931 or B1 28) which elucidates their evolutionary lineage. Functional analysis of MCC0552 reveals that the strain possess vitamin biosynthesis gene (thiamine and riboflavin) and mucin binding protein (mubp) with comparatively larger in size. HPLC analysis suggests that the strain MCC0552 synthesises class B vitamins (B1, B2, B6, B9 and B12) which increases its significance in nutritional and nutraceutical applications. Genomic island (GI) prediction shows 19 GI in strain MCC0552 genome were identified. GI regions possessed CRISPR cluster genes, mainly type IE, cas2 and type III-A, nucleotide sugar biosynthesis gene, TA system genes, heavy metal associated genes, etc. On further analysis, the strain exhibited the presence of 2 intact prophage regions which ensure its supplementary probiotic attribute. Thus, the present study elaborates on the probiotic potential of strain MCC0552 at the genome level, revealing its remarkable genomic potential and presenting novel prospects for utilising its unique genetic features in diverse scientific fields.

Emulsifier-modified sunflower oil-sunflower wax oleogel as growth modulator of probiotics

The efficiency of oleogel as an oral delivery vehicle of probiotics depends on the chemical composition and gelator used. However, the gelators, which are surfactant in nature often interact with the probiotics and alter the therapeutic outcome. Keeping this perspective in mind, here we have developed oleogel of sunflower oil containing 5% (w/w) of sunflower wax and different emulsifiers, namely Span80 (S), Tween 80(T), stearyl alcohol (SA), and Span60 (SP), and checked their influence on probiotics in-vitro. Using confocal laser scanning microscopy, it was found that adding different emulsifiers changed the length and arrangement of the gelator network. SA and SP-modified oleogels, used at a concentration of 0.05% (w/v), demonstrated enhanced growth and metabolic activity of Lactiplantibacillus pentosus, which was employed as a model probiotic. Furthermore, the mucin adhesion test and scanning electron microscopy confirmed the negligible effect of those oleogels on the activity and morphology of the probiotic, respectively. When the secretome of such probiotics was applied to the colonic cell line, no negative effects were seen. This study implied that sunflower oil-sunflower wax oleogels modified using different emulsifiers can modulate probiotic growth.

Bacteriocin Mining in Lactiplantibacillus pentosus PCZ4 with Broad-Spectrum Antibacterial Activity and Its Biopreservative Effects on Snakehead Fish

Some lactic acid bacteria (LAB) produce antibacterial substances such as bacteriocins, making them promising candidates for food preservation. In our study, Lactiplantibacillus pentosus PCZ4-a strain with broad-spectrum antibacterial activity-was isolated from traditional fermented kimchi in Sichuan. Whole-genome sequencing of PCZ4 revealed one chromosome and three plasmids. Through BAGEL4 mining, classes IIa and IIb bacteriocin plantaricin S were identified. Additionally, two new antibacterial peptides, Bac1109 and Bac2485, were predicted from scratch by limiting open reading frames. Furthermore, during refrigerated storage of snakehead fish, PCZ4 crude extract reduced the total bacterial count, slowed the increase in TVB-N and pH values, improved the sensory quality of the snakehead, and extended its shelf life by 2 days. Meanwhile, PCZ4 effectively inhibited the growth of artificially contaminated Aeromonas hydrophila in snakehead fish. These findings indicate that Lp. pentosus PCZ4 can produce multiple antibacterial substances with strong potential for food preservation applications.

Dual effects of a bacteriocin-producing Lactiplantibacillus pentosus CF-6HA, isolated from fermented aloreña table olives, as potential probiotic and antimicrobial agent

The probiotic potential of Lactiplantibacillus pentosus CF-6HA isolated from traditionally fermented Aloreña table olives was analyzed in vitro and in silico. Results obtained suggested that this strain can be catalogued as "talented" bacterium exhibiting bacteriocin production with antimicrobial activity against human/animal and plant pathogens, such as Pseudomonas syringae and Verticillium dahliae. The robustness, safety and probiotic potential of L. pentosus CF-6HA was confirmed by in silico analysis. In addition, a plethora of coding genes for defense and adaptability to different life styles besides functional properties were identified. In this sense, defense mechanisms of L. pentosus CF-6HA consist of 17 ISI elements, 98 transposases and 13 temperate phage regions as well as a CRISPR (clustered regularly interspaced short palindromic repeats)/cas system. Moreover, the functionality of this strain was confirmed by the presence of genes coding for secondary metabolites, exopolysaccharides and other bioactive molecules. Finally, we demonstrated the ability of L. pentosus CF-6HA to biotransform selenite to nanoparticles (SeNPs) highlighting its potential role in selenium bioremediation to be exploited in foods, agriculture and the environment; but also for the bio-enrichment of fermented foods with selenium.

Antigen surface display in two novel whole genome sequenced food grade strains, Lactiplantibacillus pentosus KW1 and KW2

BACKGROUND

Utilization of commensal bacteria for delivery of medicinal proteins, such as vaccine antigens, is an emerging strategy. Here, we describe two novel food-grade strains of lactic acid bacteria, Lactiplantibacillus pentosus KW1 and KW2, as well as newly developed tools for using this relatively unexplored but promising bacterial species for production and surface-display of heterologous proteins.

RESULTS

Whole genome sequencing was performed to investigate genomic features of both strains and to identify native proteins enabling surface display of heterologous proteins. Basic characterization of the strains revealed the optimum growth temperatures for both strains to be 35-37 °C, with peak heterologous protein production at 33 °C (KW1) and 37 °C (KW2). Negative staining revealed that only KW1 produces closely bound exopolysaccharides. Production of heterologous proteins with the inducible pSIP-expression system enabled high expression in both strains. Exposure to KW1 and KW2 skewed macrophages toward the antigen presenting state, indicating potential adjuvant properties. To develop these strains as delivery vehicles, expression of the mycobacterial H56 antigen was fused to four different strain-specific surface-anchoring sequences.

CONCLUSION

All experiments that enabled comparison of heterologous protein production revealed KW1 to be the better recombinant protein production host. Use of the pSIP expression system enabled successful construction of L. pentosus strains for production and surface display of an antigen, underpinning the potential of these strains as novel delivery vehicles.

Advancing Insights into Probiotics during Vegetable Fermentation

Fermented vegetables have a long history and are enjoyed worldwide for their unique flavors and health benefits. The process of fermentation improves the nutritional value, taste, and shelf life of foods. Microorganisms play a crucial role in this process through the production of metabolites. The flavors of fermented vegetables are closely related to the evaluation and succession of microbiota. Lactic acid bacteria (LABs) are typically the dominant bacteria in fermented vegetables, and they help inhibit the growth of spoilage bacteria and maintain a healthy gut microbiota in humans. However, homemade and small-scale artisanal products rely on spontaneous fermentation using bacteria naturally present on fresh vegetables or from aged brine, which may introduce external microorganisms and lead to spoilage and substandard products. Hence, understanding the role of LABs and other probiotics in maintaining the quality and safety of fermented vegetables is essential. Additionally, selecting probiotic fermentation microbiota and isolating beneficial probiotics from fermented vegetables can facilitate the use of safe and healthy starter cultures for large-scale industrial production. This review provides insights into the traditional fermentation process of making fermented vegetables, explains the mechanisms involved, and discusses the use of modern microbiome technologies to regulate fermentation microorganisms and create probiotic fermentation microbiota for the production of highly effective, wholesome, safe, and healthy fermented vegetable foods.

The Rising Role of Omics and Meta-Omics in Table Olive Research

Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives' intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives' microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology.

Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages

The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.

In Silico Evidence of the Multifunctional Features of Lactiplantibacillus pentosus LPG1, a Natural Fermenting Agent Isolated from Table Olive Biofilms

In recent years, there has been a growing interest in obtaining probiotic bacteria from plant origins. This is the case of Lactiplantibacillus pentosus LPG1, a lactic acid bacterial strain isolated from table olive biofilms with proven multifunctional features. In this work, we have sequenced and closed the complete genome of L. pentosus LPG1 using both Illumina and PacBio technologies. Our intention is to carry out a comprehensive bioinformatics analysis and whole-genome annotation for a further complete evaluation of the safety and functionality of this microorganism. The chromosomic genome had a size of 3,619,252 bp, with a GC (Guanine-Citosine) content of 46.34%. L. pentosus LPG1 also had two plasmids, designated as pl1LPG1 and pl2LPG1, with lengths of 72,578 and 8713 bp (base pair), respectively. Genome annotation revealed that the sequenced genome consisted of 3345 coding genes and 89 non-coding sequences (73 tRNA and 16 rRNA genes). Taxonomy was confirmed by Average Nucleotide Identity analysis, which grouped L. pentosus LPG1 with other sequenced L. pentosus genomes. Moreover, the pan-genome analysis showed that L. pentosus LPG1 was closely related to the L. pentosus strains IG8, IG9, IG11, and IG12, all of which were isolated from table olive biofilms. Resistome analysis reported the absence of antibiotic resistance genes, whilst PathogenFinder tool classified the strain as a non-human pathogen. Finally, in silico analysis of L. pentosus LPG1 showed that many of its previously reported technological and probiotic phenotypes corresponded with the presence of functional genes. In light of these results, we can conclude that L. pentosus LPG1 is a safe microorganism and a potential human probiotic with a plant origin and application as a starter culture for vegetable fermentations.