Functional Annotation of Lactiplantibacillus plantarum 13-3 as a Potential Starter Probiotic Involved in the Food Safety of Fermented Products

Probiotic Potential of Lactobacillus and Enterococcus Strains Isolated From the Faecal Microbiota of Critically Endangered Hangul Deer (Cervus hanglu hanglu): Implications for Conservation Management

The mammalian gut microbiota plays a crucial role in promoting host health, and lactic acid bacteria (LAB) are commonly employed as probiotics for their beneficial effects. The Hangul deer (Cervus hanglu hanglu), a critically endangered red deer subspecies found in the Indian subcontinent, requires meticulous health management for its conservation. This pioneering study aimed to isolate, identify, and evaluate the in-vitro probiotic functional properties of LAB strains from the faeces of Hangul deer. A total of 27 LAB strains were isolated and identified using 16S rDNA gene sequencing, followed by comprehensive probiotic characterization and safety assessment. Remarkably, four species exhibited robust resistance and survivability against varying pH levels and bile salts, along with high aggregation and co-aggregation capacities. Notably, Lactobacillus acidophilus and Enterococcus mundtii strains displayed antibacterial activities. Safety assessment revealed the absence of hemolytic activity and virulence genes in all four strains. Antibiotic susceptibility testing showed that Lactobacillus acidophilus and Enterococcus casseliflavus were susceptible to all tested antibiotics, while Enterococcus mundtii exhibited resistance to clindamycin, and Enterococcus gallinarum exhibited resistance to erythromycin. These findings suggest that the isolated LAB strains possess advantageous probiotic characteristics and hold potential as dietary supplements for promoting the health and disease management of Hangul deer.

Hypocholesterolemic potential of Bacillus amyloliquefaciens KAVK1 modulates lipid accumulation on 3T3-L1 adipose cells and high fat diet-induced obese rat model

The significance of microorganisms occurring in foods is predominantly targeted due to their application for identifying a novel range of the bacterial spectrum. Diverse microbial species are capable of exhibiting potential pharmacological activities like antimicrobial and anticancer. Microbial strains capable of reducing obesity-related syndromes have also been reported. In the present study, the hypocholesterolemic efficacy of Bacillus amyloliquefaciens isolated from dairy products was scrutinised by in vitro (3T3-L1 adipose cells) and in vivo (high-fat diet-induced obese Wistar albino rats) methods. Potential cholesterol-lowering isolates were screened using a plate assay method and optimised by physical parameters. Molecular identification of the topmost five cholesterol-lowering isolates was acquired by amplification of the 16 S rRNA gene region. Bacillus amyloliquefaciens strain KAVK1, followed by strains KAVK2, KAVK3, KAVK4, and KAVK5 were molecularly determined. Further, cholesterol-lowering strains degraded the spectral patterns determined by the side chain of a cholesterol molecule. The anti-lipase activity was demonstrated using the porcine pancreatic lipase inhibitory method and compared with the reference compound Atorvastatin. Lyophilised strain KAVK1 revealed maximum pancreatic lipase inhibition. Strain KAVK1 attenuated lipid accumulation in 3T3-L1 adipose cell line predicted by Oil Red O staining method. Significant reduction of body weight and change in lipid profile was recognised after the supplement of KAVK1 to obese rats. Histopathological changes in organs were predominantly marked. The result of this study implies that the cholesterol-lowering B. amyloliquefaciens KAVK1 strain was used to treat hypercholesterolemia.

The Networked Interaction between Probiotics and Intestine in Health and Disease: A Promising Success Story

Probiotics are known to promote human health either precautionary in healthy individuals or therapeutically in patients suffering from certain ailments. Although this knowledge was empirical in past tomes, modern science has already verified it and expanded it to new limits. These microorganisms can be found in nature in various foods such as dairy products or in supplements formulated for clinical or preventive use. The current review examines the different mechanisms of action of the probiotic strains and how they interact with the organism of the host. Emphasis is put on the clinical therapeutic use of these beneficial microorganisms in various clinical conditions of the human gastrointestinal tract. Diseases of the gastrointestinal tract and particularly any malfunction and inflammation of the intestines seriously compromise the health of the whole organism. The interaction between the probiotic strains and the host's microbiota can alleviate the clinical signs and symptoms while in some cases, in due course, it can intervene in the underlying pathology. Various safety issues of the use of probiotics are also discussed.

Elucidating the role of diet in maintaining gut health to reduce the risk of obesity, cardiovascular and other age-related inflammatory diseases: recent challenges and future recommendations

A healthy balanced diet is crucial in protecting the immune system against infections and diseases. Poor diets, such as the Western diet, contribute to the development of metabolic diseases, hypertension, and obesity. Microbiota, primarily composed of different microorganisms and residing in the gastrointestinal tract (GIT), also play a significant role in maintaining gut health. Polyphenols and probiotics found in fruits, vegetables, whole grains, legumes, nuts, and seeds promote gut health and support the growth of beneficial bacteria. Different types of diets, their categories, and their impact on health are also mentioned. The relationship between diet, gut health, and the risk of developing obesity, cardiovascular diseases, and inflammatory diseases is discussed in this review article. The rationale behind the review concludes future recommendations for maintaining gut health and reducing the occurrence of obesity, cardiometabolic diseases, and other inflammatory diseases. There is also the need for standardized research methods, long-term studies, and translating scientific knowledge into practical dietary recommendations.

Carbohydrate-active enzyme profiles of Lactiplantibacillus plantarum strain 84-3 contribute to flavor formation in fermented dairy and vegetable products

Microbes are critical for flavor formation in fermented foods; however, their mechanisms of action are not fully understood. The microbial composition of 51 dairy and 47 vegetable products was functionally annotated and the carbohydrate-active enzyme (CAZyme) profiles of Lactiplantibacillus plantarum 84-3 (Lp84-3), isolated from dairy samples, can promote resistant starch (RS) degradation, were analyzed. Lactobacillus, Streptococcus, and Lactococcus were the predominant genera in dairy products, whereas the major genera in vegetables were Lactobacillus, Weissella, and Carnimonas. Phages from Siphoviridae, Myoviridae, and Herelleviridae were also present in dairy products. Additionally, the glycosyl hydrolase (GHs) family members GH1 and GH13 and the glycosyltransferase (GTs) family members GT2 and GT4 were abundant in Lp84-3. Moreover, Lp84-3 was enriched in butanoate metabolism enzymes and butanoate metabolite compounds. Therefore, fermented food microbes, especially Lp84-3, have an abundant repertoire of enzymes that promote flavor production, as starter improving the flavor of fermented dairy and vegetable products.

Probiotic Potential and Safety Assessment of Lactiplantibacillus plantarum cqf-43 and Whole-Genome Sequence Analysis

This study reports the whole-genome sequence of Lactiplantibacillus plantarum cqf-43 isolated from healthy sow feces. Based on genomic analysis, we performed a comprehensive safety assessment of strain cqf-43, using both in vitro and in vivo experiments, and explored its probiotic potential. The total genome length measures 3,169,201 bp, boasting a GC content of 44.59%. Through phylogenetic analyses, leveraging both 16S rRNA gene and whole-genome sequences, we confidently categorize strain cqf-43 as a member of Lactiplantibacillus. Genome annotation using Prokka unveiled a total of 3141 genes, encompassing 2990 protein-coding sequences, 71 tRNAs, 16 rRNAs, and 1 tmRNA. Functional annotations derived from COG and KEGG databases highlighted a significant abundance of genes related to metabolism, with a notable emphasis on carbohydrate utilization. The genome also revealed the presence of prophage regions and CRISPR-Cas regions while lacking virulence and toxin genes. Screening for antibiotic resistance genes via the CARD database yielded no detectable transferable resistance genes, effectively eliminating the potential for harmful gene transfer. It is worth highlighting that the virulence factors identified via the VFDB database primarily contribute to bolstering pathogen resilience in hostile environments. This characteristic is particularly advantageous for probiotics. Furthermore, the genome is devoid of menacing genes such as hemolysin, gelatinase, and biogenic amine-producing genes. Our investigation also unveiled the presence of three unannotated secondary metabolite biosynthetic gene clusters, as detected by the online tool antiSMASH, suggesting a great deal of unknown potential for this strain. Rigorous in vitro experiments confirmed tolerance of strain cqf-43 in the intestinal environment, its antimicrobial efficacy, sensitivity to antibiotics, absence of hemolysis and gelatinase activity, and its inability to produce biogenic amines. In addition, a 28-day oral toxicity test showed that the strain cqf-43 did not pose a health hazard in mice, further establishing it as a safe strain.

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.

Draft genome sequence of Lactiplantibacillus plantarum subsp. plantarum strain HF43, a human gut-associated potential probiotic

Lactiplantibacillus plantarum adapts to a wide range of ecological niches, including the human gut. Numerous health-promoting benefits have been associated with L. plantarum strains. Motivated for the development of human-origin target-based probiotics with known genetic markers, we report the draft genome sequence of human gut-associated Lactiplantibacillus plantarum subsp. plantarum HF43.

Structural and biosynthetic diversity of plantaricins from Lactiplantibacillus

Lactiplantibacillus plantarum (L. plantarum) produces an antimicrobial peptide known as plantaricin. Plantaricin-producing L. plantarum is of interest for its gut-friendly nature, wide range of sugar utilization, palatability, and probiotic attributes, making it a better candidate for the food industry. Numerous strains of plantaricin-producing L. plantarum have been isolated from different ecological niches and found to follow different mechanisms for plantaricin production. The mechanism of plantaricin production is sensitive to environmental factors; therefore, any alteration in the optimum conditions can inhibit/halt bacteriocin production. To regain the lost or hidden plantaricin-producing character of the L. plantarum strains under ideal laboratory conditions, it is essential to understand the mechanism of plantaricin production. Previously, discrete information on various mechanisms of plantaricin production has been elaborated. However, based on the literature analysis, we observed that a systematic classification of plantaricins produced by L. plantarum is not explored. Hence, we aim to collect information about rapidly emerging plantaricins and distribute them among the different classes of bacteriocin, followed by classifying them based on different mechanisms of plantaricin production. This may help scaleup the bacteriocin production at industrial levels, which is otherwise challenging to achieve. This will also help the reader understand plantaricins and their mechanism of plantaricin production to a deeper extent and to characterize/reproduce the peptide where plantaricin production is a hidden character. KEY POINTS: • L. plantarum produces the antimicrobial compound plantaricin. • L. plantarum has different regulatory operons which control plantaricin production. • Based on the regulatory operon, the mechanism of plantaricin production is different.

Integrated metabolomics and peptidomics to delineate characteristic metabolites in milk fermented with novel Lactiplantibacillus plantarum L3

A novel wild-type Lactiplantibacillus plantarum (L. plantarum) L3 with good fermentation characteristics and protein degradation capacity was isolated from raw milk samples. In this study, the metabolites in milk fermented with L. plantarum L3 were investigated by metabolomic and peptidomics analyses. The metabolomics results revealed that the metabolites in milk fermented with L. plantarum L3 were Thr-Pro, Val-Lys, l-creatine, pyridoxine, and muramic acid, which improved the taste and nutritional qualities of the milk. Moreover, the water-soluble peptides derived from L3 fermented milk exhibited high antioxidant properties and angiotensin I-converting enzyme inhibitory (ACEI) activities. Additionally, 152 peptides were found using liquid chromatography-mass spectrometry (LC-MS/MS). Furthermore, endogenous enzymes secreted by L. plantarum L3 cleaved β- and α-casein to release six ACEI peptides (ACEIPs), nineteen antioxidant peptides (AOPs), and five antimicrobial peptides (AMPS). Overall, these findings could be valuable in improving the quality of fermented milk.

Comparative genomics of food-derived probiotic Lactiplantibacillus plantarum K25 reveals its hidden potential, compactness, and efficiency

This study aimed to investigate the intricate genetic makeup of the Lactiplantibacillus plantarum K25 strain by conducting a comprehensive analysis of comparative genomics. The results of our study demonstrate that the genome exhibits a high-level efficiency and compactness, comprising a total of 3,199 genes that encode proteins and a GC content of 43.38%. The present study elucidates the evolutionary lineage of Lactiplantibacillus plantarum strains through an analysis of the degree of gene order conservation and synteny across a range of strains, thereby underscoring their closely interrelated evolutionary trajectories. The identification of various genetic components in the K25 strain, such as bacteriocin gene clusters and prophage regions, highlights its potential utility in diverse domains, such as biotechnology and medicine. The distinctive genetic elements possess the potential to unveil innovative therapeutic and biotechnological remedies in future. This study provides a comprehensive analysis of the L. plantarum K25 strain, revealing its remarkable genomic potential and presenting novel prospects for utilizing its unique genetic features in diverse scientific fields. The present study contributes to the existing literature on Lactiplantibacillus plantarum and sets the stage for prospective investigations and practical implementations that leverage the exceptional genetic characteristics of this adap organism.

Effects of the Exopolysaccharide from Lactiplantibacillus plantarum HMX2 on the Growth Performance, Immune Response, and Intestinal Microbiota of Juvenile Turbot, Scophthalmus maximus

In this study, the exopolysaccharide (EPS) from Lactiplantibacillus plantarum (HMX2) was isolated from Chinese Northeast Sauerkraut. Its effects on juvenile turbot were investigated by adding different concentrations of HMX2-EPS (C: 0 mg/kg, H1: 100 mg/kg, H2: 500 mg/kg) to the feed. Compared with the control group, HMX2-EPS significantly improved the growth performance of juvenile turbot. The activities of antioxidant enzymes, digestive enzymes, and immune-related enzymes were significantly increased. HMX2-EPS could also increase the secretion of inflammatory factors and enhance the immune response of turbot by regulating the IFN signal transduction pathway and exhibit stronger survival rates after the A. hydrophila challenge. Moreover, HMX2-EPS could improve the diversity of intestinal microbiota in juvenile fish, increase the abundance of potential probiotics, and reduce the abundance of pathogenic bacteria. The function of gut microbes in metabolism and the immune system could also be improved. All results showed better effects with high concentrations of HMX2-EPS. These results indicated that HMX2-EPS supplementation in the diet could promote growth, improve antioxidant activity, digestive capacity, and immunity capacity, and actively regulate the intestinal microbiota of juvenile turbot. In conclusion, this study might provide basic technical and scientific support for the application of L. plantarum in aquatic feed.

Draft Genome Sequence of Lactiplantibacillus plantarum Strain ISO1, a Potential Probiotic Bacterium Isolated from the Milk of South African Saanen Goats

Lactiplantibacillus plantarum strain ISO1, a potential probiotic with wide food and biotechnological applications, was isolated from the raw milk of South African Saanen goats. Here, we report the draft genome sequence of this bacterium. Sequencing yielded a 3.23-Mb genome and 2,967 protein-coding sequences.

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.

Investigating the effect on biogenic amines, nitrite, and N-nitrosamine degradation in cultured sausage ripening through inoculation of Staphylococcus xylosus and lactic acid bacteria

Introduction

Microbial inoculants can reinvent the value and edible security of cultured sausages. Various studies have demonstrated that starter cultures made up of Lactic acid bacteria (LAB) and Staphylococcus xylosus (known as L-S) isolated from traditional fermented foods were used in fermented sausage manufacturing.

Methods

This study evaluated the impact of the mixed inoculation cultures on limiting biogenic amines, nitrite depletion, N-nitrosamine reduction, and quality metrics. Inoculation of sausages with the commercial starter culture (SBM-52) was evaluated for comparison.

Results and discussion

Results showed that the L-S strains could rapidly decrease the water activity (Aw) and pH of fermented sausages. The ability of the L-S strains to delay lipid oxidation was equivalent to the SBM-52 strains. The non-protein nitrogen (NPN) contents of L-S-inoculated sausages (0.31%) were higher than that of SBM-52-inoculated sausages (0.28%). After the ripening process, the nitrite residues in the L-S sausages were 1.47 mg/kg lower than in the SBM-52 sausages. Compared to the SBM-52 sausages, there was a 4.88 mg/kg reduction in the biogenic amines' concentrations in L-S sausage, especially for histamine and phenylethylamine concentrations. The N-nitrosamine accumulations of the L-S sausages (3.40 ug/kg) were lower than that of the SBM-52 sausages (3.70 ug/kg), and the NDPhA accumulations of the L-S sausages were 0.64 ug/kg lower than that of the SBM-52 sausages. Due to their significant contributions to nitrite depletion, biogenic amine reduction, and N-nitrosamine depletion in fermented sausages, the L-S strains have the potential to serve as an initial inoculant in the process of manufacturing fermented sausages.

Development of a whey-based beverage with enhanced levels of conjugated linoleic acid (CLA) as facilitated by endogenous walnut lipase

In this study, optimization of fermentation conditions, and applying endogenous walnut lipase were investigated for the manufacture of a fermented, whey-based beverage containing conjugated linoleic acid (CLA). Among different commercial starter and probiotic cultures, the culture containing Lactobacillus delbrueckii subsp. bulgaricus and Streptococcus thermophilus showed high potency for CLA synthesis. The fermentation time and the type of walnut oil (lipolyzed or non-lipolyzed) had significant effects on CLA production, as the highest CLA content (36 mg/g fat) was synthesized in the sample containing 1 % lipolyzed walnut oil fermented at 42 °C for 24 h. Moreover, fermentation time had the highest contribution on viable cell counts, proteolysis, DPPH scavenging activity, and final pH. A significant and positive correlation between cell counts and CLA content was also observed (r = +0.823, p < 0.05). This study establishes a cost effective approach for converting cheese whey to a value added beverage enriched with CLA.