Genomics-based analysis of four porcine-derived lactic acid bacteria strains and their evaluation as potential probiotics

The search for probiotics and exploration of their functions are crucial for livestock farming. Recently, porcine-derived lactic acid bacteria (LAB) have shown great potential as probiotics. However, research on the evaluation of porcine-derived LAB as potential probiotics through genomics-based analysis is relatively limited. The present study analyzed four porcine-derived LAB strains (Lactobacillus johnsonii L16, Latilactobacillus curvatus ZHA1, Ligilactobacillus salivarius ZSA5 and Ligilactobacillus animalis ZSB1) using genomic techniques and combined with in vitro tests to evaluate their potential as probiotics. The genome sizes of the four strains ranged from 1,897,301 bp to 2,318,470 bp with the GC contents from 33.03 to 41.97%. Pan-genomic analysis and collinearity analysis indicated differences among the genomes of four strains. Carbohydrate active enzymes analysis revealed that L. johnsonii L16 encoded more carbohydrate active enzymes than other strains. KEGG pathway analysis and in vitro tests confirmed that L. johnsonii L16 could utilize a wide range of carbohydrates and had good utilization capacity for each carbohydrate. The four strains had genes related to acid tolerance and were tolerant to low pH, with L. johnsonii L16 showing the greatest tolerance. The four strains contained genes related to bile salt tolerance and were able to tolerate 0.1% bile salt. Four strains had antioxidant related genes and exhibited antioxidant activity in in vitro tests. They contained the genes linked with organic acid biosynthesis and exhibited antibacterial activity against enterotoxigenic Escherichia coli K88 (ETEC K88) and Salmonella 6,7:c:1,5, wherein, L. johnsonii L16 and L. salivarius ZSA5 had gene clusters encoding bacteriocin. Results suggest that genome analysis combined with in vitro tests is an effective approach for evaluating different strains as probiotics. The findings of this study indicate that L. johnsonii L16 has the potential as a probiotic strain among the four strains and provide theoretical basis for the development of probiotics in swine production.

Effect of LuxS/AI-2-mediated quorum sensing system on bacteriocin production of Lactobacillus plantarum NMD-17

Lactobacillus plantarum NMD-17 separated from koumiss could produce a bacteriocin named plantaricin MX against Gram-positive bacteria and Gram-negative bacteria. The bacteriocin synthesis of L. plantarum NMD-17 was remarkably induced in co-cultivation with Lactobacillus reuteri NMD-86 as the increase of cell numbers and AI-2 activity, and the expressions of luxS encoding signal AI-2 synthetase, plnB encoding histidine protein kinase, plnD encoding response regulator, and plnE and plnF encoding structural genes of bacteriocin were significantly upregulated in co-cultivation, showing that the bacteriocin synthesis of L. plantarum NMD-17 in co-cultivation may be regulated by LuxS/AI-2-mediated quorum sensing system. In order to further demonstrate the role of LuxS/AI-2-mediated quorum sensing system in the bacteriocin synthesis of L. plantarum NMD-17, plasmids pUC18 and pMD18-T simple were used as the skeleton to construct the suicide plasmids pUC18-UF-tet-DF and pMD18-T simple-plnB-tet-plnD for luxS and plnB-plnD gene deletion, respectively. luxS and plnB-plnD gene knockout mutants were successfully obtained by homologous recombination. luxS gene knockout mutant lost its AI-2 synthesis ability, suggesting that LuxS protein encoded by luxS gene is key enzyme for AI-2 synthesis. plnB-plnD gene knockout mutant lost the ability to synthesize bacteriocin against Salmonella typhimurium ATCC14028, indicating that plnB-plnD gene was a necessary gene for bacteriocin synthesis of L. plantarum NMD-17. Bacteriocin synthesis, cell numbers, and AI-2 activity of luxS or plnB-plnD gene knockout mutants in co-cultivation with L. reuteri NMD-86 were obviously lower than those of wild-type strain in co-cultivation at 6-9 h (P < 0.01). The results showed that LuxS/AI-2-mediated quorum sensing system played an important role in the bacteriocin synthesis of L. plantarum NMD-17 in co-cultivation.

Lactiplantibacillus plantarum ZJ316-fermented milk ameliorates dextran sulfate sodium-induced chronic colitis by improving the inflammatory response and regulating intestinal microbiota

The pathogenesis of inflammatory bowel disease may be related to local inflammatory damage and disturbances in intestinal microecology. Probiotic therapy is a safe and effective therapeutic approach. Considering that fermented milk is accepted and enjoyed by many people as a daily dietary intervention strategy, its potential to alleviate dextran sulfate sodium (DSS)-induced chronic colitis in mice needs to be explored. In this study, we evaluated the therapeutic effects of Lactiplantibacillus plantarum ZJ316-fermented milk by establishing a mouse model of DSS-induced chronic colitis. The results showed that the disease severity and colonic lesions of inflammatory bowel disease were effectively alleviated by ingestion of fermented milk. At the same time, the expression of proinflammatory cytokines (TNF-α, IL-1β, and IL-6) effectively decreased, and the expression of antiinflammatory cytokines (IL-10) increased. Results based on 16S rRNA gene sequencing indicated that the structure and diversity of intestinal microorganisms changed markedly by intake of L. plantarum ZJ316-fermented milk, and fermented milk reduced the abundance of harmful bacteria (Helicobacter) while promoting the growth of beneficial bacteria (Faecalibacterium, Lactiplantibacillus, and Bifidobacterium). Additionally, the levels of short-chain fatty acids (acetic acid, propionic acid, butyric acid, pentanoic acid, and isobutyric acid) were also increased. In conclusion, the intake of L. plantarum ZJ316-fermented milk can alleviate chronic colitis by suppressing the inflammatory response and regulating intestinal microbiota.

Probiotic characteristics of Lactobacillus gasseri TF08-1: A cholesterol-lowering bacterium, isolated from human gut

Lactobacillus contribute to maintain the human healthy and use for nutritional additives as probiotics. In this study, a cholesterol-lowering bacterium, Lactobacillus gasseri TF08-1, was isolated from the feces of a healthy adolescent, and its probiotic potentials were evaluated through genomic mining and in vitro test. The assembled draft genome comprised of 1,974,590 bp and was predicted total of 1,940 CDSs. The annotation of the genome revealed that L. gasseri TF08-1 harbored abundant categories of functional genes in metabolic and information processing. Moreover, strain TF08-1 has capacity to utilize D-Glucose, Sucrose, D-Maltose, Salicin, D-Xylose, D-Cellobiose, D-Mannose, and D-Trehalose, as the carbon source. The safety assessment showed strain TF08-1 contained few antibiotic resistance genes and virulence factors and was only resistant to 2 antibiotics detected by antimicrobial susceptibility test. A high bile salt hydrolase activity was found and a cholesterol-reducing effect was determined in vitro, which the result showed a remarkable cholesterol removal capability of L. gasseri TF08-1 with an efficiency of 84.40 %. This study demonstrated that the strain showed great capability of exopolysaccharide production, and tolerance to acid and bile salt. Therefore, these results indicate that L. gasseri TF08-1 can be considered as a safe candidate for probiotic, especially its potential in biotherapeutic for metabolic diseases.

Effects of Probiotic Supplementation on Exercise and the Underlying Mechanisms

Long-term, high-intensity exercise can trigger stress response pathways in multiple organs, including the heart and lungs, gastrointestinal tract, skeletal muscle, and neuroendocrine system, thus affecting their material and energy metabolism, immunity, oxidative stress, and endocrine function, and reducing exercise function. As a natural, safe, and convenient nutritional supplement, probiotics have been a hot research topic in the field of biomedical health in recent years. Numerous studies have shown that probiotic supplementation improves the health of the body through the gut-brain axis and the gut-muscle axis, and probiotic supplementation may also improve the stress response and motor function of the body. This paper reviews the progress of research on the role of probiotic supplementation in material and energy metabolism, intestinal barrier function, immunity, oxidative stress, neuroendocrine function, and the health status of the body, as well as the underlying mechanisms.

Subspecies Classification and Comparative Genomic Analysis of Lactobacillus kefiranofaciens HL1 and M1 for Potential Niche-Specific Genes and Pathways

(1) Background: Strains HL1 and M1, isolated from kefir grains, have been tentatively identified, based on their partial 16S rRNA gene sequences, as Lactobacillus kefiranofaciens. The two strains demonstrated different health benefits. Therefore, not only the genetic factors exerting diverse functionalities in different L. kefiranofaciens strains, but also the potential niche-specific genes and pathways among the L. kefiranofaciens strains, should be identified. (2) Methods: Phenotypic and genotypic approaches were employed to identify strains HL1 and M1 at the subspecies level. For the further characterization of the probiotic properties of both strains, comparative genomic analyses were used. (3) Results: Both strains were identified as L. kefiranofaciens subsp. kefirgranum. According to the COG function category, dTDP-rhamnose and rhamnose-containing glycans were specifically detected in the L. kefiranofaciens subsp. Kefirgranum genomes. Three unique genes (epsI, epsJ, and epsK) encoding glycosyltransferase in the EPS gene cluster, and the ImpB/MucB/SamB family protein encoding gene were found in HL1 and M1. The specific ability to degrade arginine via the ADI pathway was found in HL1. The presence of the complete glycogen metabolism (glg) operon in the L. kefiranofaciens strains suggested the importance of glycogen synthesis to enable colonization in kefir grains and extend survival under environmental stresses. (4) Conclusions: The obtained novel information on the potential genes and pathways for polysaccharide synthesis and other functionalities in our HL1 and M1 strains could be applied for further functionality predictions for potential probiotic screening.

Mechanism of gastrointestinal adaptability and antioxidant function of infant-derived Lactobacillus plantarum BF_15 through genomics

Lactobacillus plantarum is an essential probiotic in the human gastrointestinal tract. L. plantarum BF_15, a functional probiotic isolated from the feces of breast-fed infants, has been reported in many in vitro and in vivo studies with strong gastrointestinal adaptability and outstanding anti-oxidative activities. Therefore, the whole genome of L. plantarum BF_15 was sequenced. Several genes, encoding the gastrointestinal adaptability-related proteins, were identified, including genes related to gastrointestinal environment-induced stress resistance, adhesive performance, and ability to transport and metabolize resistant starch and oligosaccharides. Genes related to alleviating oxidative stress were also found. Further functional verification was carried out by RT-qPCR on the 10 and 12 key adhesion and antioxidant genes. Overall, this study might provide a critical basis for L. plantarum BF_15 as a potential candidate for probiotics.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01132-w.

Comparative genomics-based probiotic relevance of Limosilactobacillus fermentum KUB-D18

Limosilactobacillus fermentum KUB-D18 is a heterofermentative lactic acid bacterium that its potential probiotic relevance originally isolated from the chicken intestine. This study sequenced a whole-genome of L. fermentum KUB-D18 and annotated its genes and functions in relation to probiotic properties. As a result, the genome sequence of L. fermentum KUB-D18 approximately contained 2.02 Mbps with GC content of51.7%. After annotating the genome by integrated protein and pathway databases, 2,158 protein-encoding genes were majorly annotated for metabolisms of amino acids, carbohydrates and cofactors as well as vitamins which showed a versatile metabolic capability to gastrointestinal microhabitats. According to the comparative genome analysis of L. fermentum KUB-D18 and the other related strains, L. fermentum KUB-D18 showed common characteristics e.g., folate biosynthesis and bile salt hydrolase enzymes-related cholesterol lowering effect as well as a unique gene cluster involved in metabolism of L-ascorbic acid of L. fermentum KUB-D18. Taken together, L. fermentum KUB-D18 genome provides the genetic basis towards cellular capability for further elucidating the functional mechanisms of its probiotic properties. This study serves for designing desirable targets for the development of probiotic foods and feeds.

Assessments of Probiotic Potentials of Lactiplantibacillus plantarum Strains Isolated From Chinese Traditional Fermented Food: Phenotypic and Genomic Analysis

The lack of rapid and effective approaches to determine the health benefits of strains is one of the main challenges affecting the selection of probiotics from large numbers of candidates. In this study, the probiotic potential of 44 Lactiplantibacillus plantarum strains isolated from different Chinese traditional fermented foods was evaluated, including acid and bile salt resistance, adhesion ability, survival in simulated human gastrointestinal transit, antioxidant activity, bile salt hydrolase (BSH) activity, and antibacterial activity. All tested L. plantarum strains showed high antioxidant capacity, BSH activity, and antibacterial activity. Among the strains, B652, C232, D444, and E932 were identified as the best comprehensive performed strains, which were selected for whole-genome sequencing, in order to provide clear information and identify key genes responsible for functional characteristics in vitro. It demonstrated that the antioxidant activity, adhesion activity, and ability to survive in the simulated gastric environment were found to be closely correlated with antioxidant enzyme encoding genes, cell-surface protein-encoding genes, and stress response genes, respectively. The numbers of functional genes present in strains might decide their performance in probiotic profile evaluation. The outcome of the study could support the development of a novel approach for the screening and identification of probiotics.

Antibacterial Effects of Bacteriocin PLNC8 against Helicobacter pylori and Its Potential Mechanism of Action

Helicobacter pylori (H. pylori) is a bacterium that can cause a variety of gastric diseases. Most bacteriocins have gained popularity due to their non-toxic effects on cells and antibacterial effects against a wide range of pathogenic bacteria. In this study, the chemical synthesis of the bipeptide bacteriocin PLNC8 was used to investigate its possible action mechanism against H. pylori ZJC03 in vitro. Results showed that PLNC8 had significant anti-H. pylori ZJC03 potential, which resulted in a significant reduction in urease activity and a minimum inhibitory concentration (MIC) of 80 μM. PLNC8 inhibited the growth of H. pylori ZJC03, disrupting its structure as observed by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). In addition, PLNC8 decreased the ATP level and hydrogen peroxide sensitivity of H. pylori ZJC03. In conclusion, PLNC8 disrupts the ability of H. pylori ZJC03 to alter the host environment, providing a new avenue for the prevention and control of H. pylori infection, providing a theoretical foundation for further elucidation of its regulatory mechanism.

Decoding the Gene Variants of Two Native Probiotic Lactiplantibacillus plantarum Strains through Whole-Genome Resequencing: Insights into Bacterial Adaptability to Stressors and Antimicrobial Strength

In this study, whole-genome resequencing of two native probiotic Lactiplantibacillus plantarum strains—UTNGt21A and UTNGt2—was assessed in order to identify variants and perform annotation of genes involved in bacterial adaptability to different stressors, as well as their antimicrobial strength. A total of 21,906 single-nucleotide polymorphisms (SNPs) were detected in UTNGt21A, while 17,610 were disclosed in the UTNGt2 genome. The comparative genomic analysis revealed a greater number of deletions, transversions, and transitions within the UTNGt21A genome, while a small difference in the number of insertions was detected between the strains. A divergent number of types of variant annotations were detected in both strains, and categorized in terms of low, moderate, and high modifier impact on the protein effectiveness. Although both native strains shared common specific genes involved in the stress response to the gastrointestinal environment, which may qualify as a putative probiotic (bile salt, acid, temperature, osmotic stress), they were different in their antimicrobial gene cluster organization, with UTNGt21A displaying a complex bacteriocin gene arrangement and dissimilar gene variants that might alter their defense mechanisms and overall inhibitory capacity. The genome comparison revealed 34 and 9 genomic islands (GIs) in the UTNGt21A and UTNGt2 genomes, respectively, with the overrepresentation of genes involved in defense mechanisms and carbohydrate utilization. In addition, pan-genome analysis disclosed the presence of various strain-specific genes (shell genes), suggesting a high genome variation between strains. This genome analysis illustrates that the bacteriocin signature and gene variants reflect a niche-inherent pattern. These extensive genomic datasets will guide us to understand the potential benefits of the native strains and their utility in the food or pharmaceutical sectors.

A Comparative Genomic and Safety Assessment of Six Lactiplantibacillus plantarum subsp. argentoratensis Strains Isolated from Spontaneously Fermented Greek Wheat Sourdoughs for Potential Biotechnological Application

The comparative genome analysis of six Lactiplantibacillus plantarum subsp. argentoratensis strains previously isolated from spontaneously fermented Greek wheat sourdoughs is presented. Genomic attributes related to food safety have been studied according to the European Food Safety Authority (EFSA) suggestions for the use of lactic acid bacteria (LAB) in the production of foods. Bioinformatic analysis revealed a complete set of genes for maltose, sucrose, glucose, and fructose fermentation; conversion of fructose to mannitol; folate and riboflavin biosynthesis; acetoin production; conversion of citrate to oxaloacetate; and the ability to produce antimicrobial compounds (plantaricins). Pathogenic factors were absent but some antibiotic resistance genes were detected. CRISPR and cas genes were present as well as various mobile genetic elements (MGEs) such as plasmids, prophages, and insertion sequences. The production of biogenic amines by these strains was not possible due to the absence of key genes in their genome except lysine decarboxylase associated with cadaverine; however, potential degradation of these substances was identified due to the presence of a blue copper oxidase precursor and a multicopper oxidase protein family. Finally, comparative genomics and pan-genome analysis showed genetic differences between the strains (e.g., variable pln locus), and it facilitated the identification of various phenotypic and probiotic-related properties.

Genome Sequence and Assessment of Safety and Potential Probiotic Traits of Lactobacillus johnsonii CNCM I-4884

The probiotic strain Lactobacillus johnsonii CNCM I-4884 exhibits anti-Giardia activity in vitro and in vivo in a murine model of giardiasis. The aim of this study was the identification and characterization of the probiotic potential of L. johnsonii CNCM I-4884, as well as its safety assessment. This strain was originally classified as Lactobacillus gasseri based on 16S gene sequence analysis. Whole genome sequencing led to a reclassification as L. johnsonii. A genome-wide search for biosynthetic pathways revealed a high degree of auxotrophy, balanced by large transport and catabolic systems. The strain also exhibits tolerance to low pH and bile salts and shows strong bile salt hydrolase (BSH) activity. Sequencing results revealed the absence of antimicrobial resistance genes and other virulence factors. Phenotypic tests confirm that the strain is susceptible to a panel of 8 antibiotics of both human and animal relevance. Altogether, the in silico and in vitro results confirm that L. johnsonii CNCM I-4884 is well adapted to the gastrointestinal environment and could be safely used in probiotic formulations.

Immunomodulatory potential of four candidate probiotic Lactobacillus strains from plant and animal origin using comparative genomic analysis

Probiotic strains from different origins have shown promise in recent decades for their health benefits, for example in promoting and regulating the immune system. The immunomodulatory potential of four Lactobacillus strains from animal and plant origins was evaluated in this paper based on their genomic information. Comparative genomic analysis was performed through genome alignment, average nucleotide identity (ANI) analysis and gene mining for putative immunomodulatory genes. The genomes of the four Lactobacillus strains show relative similarities in multiple regions, as observed in the genome alignment. However, ANI analysis showed that L. mucosae LM1 and L. fermentum SK152 are the most similar when considering their nucleotide sequences alone. Gene mining of putative immunomodulatory genes studied from L. plantarum WCFS1 yielded multiple results in the four potential probiotic strains, with L. plantarum SK151 showing the largest number of genes at around 74 hits, followed by L. johnsonii PF01 at 41 genes when adjusted for matches with at least 30 % identity. Looking at the immunomodulatory genes in each strain, L. plantarum SK151 and L. johnsonii PF01 may have wider activity, covering both immune activation and immune suppression, as compared to L. mucosae LM1 and L. fermentum SK152, which could be more effective in activating immune cells and the pro-inflammatory cascade rather than suppressing it. The similarities and differences between the four Lactobacillus species showed that there is no definitive trend based on the origin of isolation alone. Moreover, higher percentage identities between genomes do not directly correlate with higher similarities in potential activity, such as in immunomodulation. The immunomodulatory function of each of the four Lactobacillus strains should be observed and verified experimentally in the future, since some the activity of some genes may be strain-specific, which would not be identified through comparative genomics alone.

Lactobacillus plantarum ZJ316 improves the quality of Stachys sieboldii Miq. pickle by inhibiting harmful bacteria growth and degrading nitrite, promoting the gut microbiota health in vitro

Microbial contamination and nitrite accumulation are two major concerns on the quality control of fermented vegetables. In the present study, a lactic acid bacteria strain Lactobacillus plantarum ZJ316 (ZJ316) was...

Advancements in the Use of Fermented Fruit Juices by Lactic Acid Bacteria as Functional Foods: Prospects and Challenges of Lactiplantibacillus (Lpb.) plantarum subsp. plantarum Application

Lactic acid fermentation of fresh fruit juices is a low-cost and sustainable process, that aims to preserve and even enhance the organoleptic and nutritional features of the raw matrices and extend their shelf life. Selected Lactic Acid Bacteria (LAB) were evaluated in the fermentation of various fruit juices, leading in some cases to fruit beverages, with enhanced nutritional and sensorial characteristics. Among LAB, Lactiplantibacillus (Lpb.) plantarum subsp. plantarum strains are quite interesting, regarding their application in the fermentation of a broad range of plant-derived substrates, such as vegetables and fruit juices, since they have genome plasticity and high versatility and flexibility. L. plantarum exhibits a remarkable portfolio of enzymes that make it very important and multi-functional in fruit juice fermentations. Therefore, L. plantarum has the potential for the production of various bioactive compounds, which enhance the nutritional value and the shelf life of the final product. In addition, L. plantarum can positively modify the flavor of fruit juices, leading to higher content of desirable volatile compounds. All these features are sought in the frame of this review, aiming at the potential and challenges of L. plantarum applications in the fermentation of fruit juices.

Comparative Whole Genome Sequence Analysis and Biological Features of Clostridioides difficile Sequence Type 2‡

Clostridioides difficile sequence type 2 (ST2) has been increasingly recognized as one of the major genotypes in China, while the genomic characteristics and biological phenotypes of Chinese ST2 strains remain to be determined. We used whole-genome sequencing and phylogenetic analysis to investigate the genomic features of 182 ST2 strains, isolated between 2011 and 2017. PCR ribotyping (RT) was performed, and antibiotic resistance, toxin concentration, and sporulation capacity were measured. The core genome Maximum-likelihood phylogenetic analysis showed that ST2 strains were distinctly segregated into two genetically diverse lineages [L1 (67.0% from Northern America) and L2], while L2 further divided into two sub-lineages, SL2a and SL2b (73.5% from China). The 36 virulence-related genes were widely distributed in ST2 genomes, but in which only 11 antibiotic resistance-associated genes were dispersedly found. Among the 25 SL2b sequenced isolates, RT014 (40.0%, n = 10) and RT020 (28.0%, n = 7) were two main genotypes with no significant difference on antibiotic resistance (χ² = 0.024-2.667, P > 0.05). A non-synonymous amino acid substitution was found in tcdB (Y1975D) which was specific to SL2b. Although there was no significant difference in sporulation capacity between the two lineages, the average toxin B concentration (5.11 ± 3.20 ng/μL) in SL2b was significantly lower in comparison to those in L1 (10.49 ± 15.82 ng/μL) and SL2a (13.92 ± 2.39 ng/μL) (χ² = 12.30, P < 0.05). This study described the genomic characteristics of C. difficile ST2, with many virulence loci and few antibiotic resistance elements. The Chinese ST2 strains with the mutation in codon 1975 of the tcdB gene clustering in SL2b circulating in China express low toxin B, which may be associated with mild or moderate C. difficile infection.

LuxS-mediated quorum sensing system in Lactobacillus plantarum NMD-17 from koumiss: induction of plantaricin MX in co-cultivation with certain lactic acid bacteria

A bacteriocin termed plantaricin MX with a broad antimicrobial spectrum was produced by Lactobacillus plantarum NMD-17, which was isolated from Inner Mongolia traditional koumiss of china. Among 300 strains of lactic acid bacteria (LAB) belonging to the genera Lactococcus, Lactobacillus, Streptococcus, Leuconostoc, and Enterococcus, five strains including Lactobacillus reuteri NMD-86, Lactobacillus helveticus NMD-137, Lactococcus lactis NMD-152, Enterococcus faecalis NMD-178, and Enterococcus faecium NMD-219 were revealed to significantly induce the bacteriocin synthesis and greatly increase the cell numbers of Lactobacillus plantarum NMD-17 and activity of AI-2 signaling molecule. Bacteriocin synthesis was not increased by cell-free supernatants and autoclaved cultures of inducing strains, demonstrating that intact cells of inducing strains were essential to the induction of bacteriocin synthesis. The existence of bacteriocin structural plnEF genes and the plnD and luxS genes involved in quorum sensing was confirmed by PCR, and the presence of plnB gene encoding histidine protein kinase was determined by single oligonucleotide nested PCR (Son-PCR). Quantitative real-time PCR demonstrated that plnB, plnD, luxS, plnE, and plnF genes of L. plantarum NMD-17 were upregulated significantly (P < 0.01) in co-cultivation with L. reuteri NMD-86. The results showed that the bacteriocin synthesis of L. plantarum NMD-17 in co-cultivation might have a close relationship with LuxS-mediated quorum sensing system.

Nutrient consumption patterns of Lactobacillus plantarum and their application in suancai

The purpose of the present study was to control the fermentation time and nitrite content of suancai prepared with Lactobacillus plantarum. According to analyses of the consumption amount and rate of nutrients, growth-stimulating nutrients, essential nutrients and nutrients accelerating the fermentation process of suancai, Asp, Thr, Glu, Cys, Tyr, Mg²⁺, Mn²⁺ and inosine were selected as additions to suancai prepared with L. plantarum. The fermentation time and nitrite content of suancai supplemented with nutrients and prepared with L. plantarum were shortened by 2 days and 5 days and reduced by approximately 0.1-fold and 0.7-fold, respectively, compared with unsupplemented suancai prepared with L. plantarum at 25 °C and 10 °C. The fermentation time and nitrite content of suancai supplemented with nutrients and prepared with L. plantarum were shortened by 6 days and 15 days and reduced by approximately 0.17-fold and 0.8-fold, respectively, compared with suancai undergoing spontaneous fermentation at 25 °C and 10 °C. Furthermore, no significant differences were observed in sensory properties in suancai. The results of this study indicated that certain nutrients accelerated the growth of L. plantarum and reduced the fermentation time and nitrite content of suancai prepared with L. plantarum. These findings help to establish a foundation for the practical use of nutrients to control the fermentation of suancai.

Lactobacillus plantarum ZJ316 Attenuates Helicobacter pylori-Induced Gastritis in C57BL/6 Mice

Helicobacter pylori is a highly prevalent human-specific pathogen that causes various gastric diseases. In the present study, Lactobacillus plantarum ZJ316, which could survive well in simulated gastrointestinal conditions, was found to have significant anti-H. pylori ability. Animal assays revealed that L. plantarum ZJ316 had preventive and therapeutic effects on H. pylori-induced gastritis. L. plantarum ZJ316 significantly decreased interferon γ (IFN-γ) and interleukin 6 (IL-6) levels, increased the IL-10 level, and repaired mucosal damage. Moreover, 16S rRNA gene sequencing revealed that the relative abundance of H. pylori could be significantly reduced by L. plantarum ZJ316 administration. Members of the families Dehalobacteriaceae and Geodermatophilaceae were more prevalent in the prevention group, while Lactobacillaceae and Actinomycetaceae were more prevalent in the treatment group. These results indicate that L. plantarum ZJ316 serves as a potential candidate for the prevention and treatment of H. pylori-induced gastritis by regulating the gastric microbiota and reducing mucosal inflammation.

Whole genome and acid stress comparative transcriptome analysis of Lactiplantibacillus plantarum ZDY2013

Previous study has reported that Lactiplantibacillus plantarum ZDY2013 which was screened from traditional Chinese fermented soybeans has a strong acid resistance. The purpose of this study was to uncover the genes potentially related to its genetic adaptation and probiotic profiles, based on comparative genomic and comparative transcriptome analysis. We got the basic information about L. plantarum ZDY2013 and identified genes which are related to genetic adaptation and probiotic profiles, including carbohydrate transport and metabolism, cell wall/membrane/envelope biogenesis, proteolytic enzyme systems and amino acid biosynthesis, CRISPR adaptive immunity, stress responses, ability to adhere to the host intestinal wall, exopolysaccharide (EPS) biosynthesis, and bacteriocin biosynthesis. Comparative transcriptome showed CK group (normal MRS culture L. plantarum ZDY2013) and SCL group (pH 3.0 MRS culture L. plantarum ZDY2013) had 652 significant differentially expressed genes including 310 up-regulated genes and 342 down-regulated genes. Besides that, these genes had been classified through KEGG and GO functional annotation. In addition, we also found top 20 KEGG pathways adjusted to acid stress. Then, some genes were selected to verify the transcriptome analysis and explore the mechanism of how L. plantarum ZDY2013 tolerate acid stress. We found that some genes of ABC transporter, phosphotransferase system, oxidation reduction process, membrane transporter and phosphorylation metabolism process had a significant change. These results suggested that comparative characterization of the L. plantarum ZDY2013 genome and transcriptome provided the genetic basis for further elucidating the functional mechanisms of it.

Health-Promoting Role of Lactiplantibacillus plantarum Isolated from Fermented Foods

Fermentation processes have been used for centuries for food production and preservation. Besides the contribution of fermentation to food quality, recently, scientific interest in the beneficial nature of fermented foods as a reservoir of probiotic candidates is increasing. Fermented food microbes are gaining attention for their health-promoting potential and for being genetically related to human probiotic bacteria. Among them, Lactiplantibacillus (Lpb.) plantarum strains, with a long history in the food industry as starter cultures in the production of a wide variety of fermented foods, are being investigated for their beneficial properties which are similar to those of probiotic strains, and they are also applied in clinical interventions. Food-associated Lpb. plantarum showed a good adaptation and adhesion ability in the gastro-intestinal tract and the potential to affect host health through various beneficial activities, e.g., antimicrobial, antioxidative, antigenotoxic, anti-inflammatory and immunomodulatory, in several in vitro and in vivo studies. This review provides an overview of fermented-associated Lpb. plantarum health benefits with evidence from clinical studies. Probiotic criteria that fermented-associated microbes need to fulfil are also reported.

Cyclic peptide production from lactic acid bacteria (LAB) and their diverse applications

In recent years, cyclic peptides gave gained increasing attention owing to their pH tolerance, heat stability and resistance to enzymatic actions. The increasing outbreaks of antibiotic resistant pathogens and food spoilage have prompted researchers to search for new approaches to combat them. The increasing number of reports on novel cyclic peptides from lactic acid bacteria (LAB) is considered as a breakthrough due to their potential applications. Although an extensive investigation is required to understand the mechanism of action and range of applications, LAB cyclic peptides can be considered as potential substitutes for commercially available antibiotics and bio preservatives. This review summarizes the current updates of LAB cyclic peptides with emphasis on their structure, mode of action and applications. Recent trends in cyclic peptide applications are also discussed.

Physiological function analysis of Lactobacillus plantarum Y44 based on genotypic and phenotypic characteristics

In our previous studies, Lactobacillus plantarum Y44 showed antioxidant activity and favorable gastric and intestinal transit tolerance. In the current study, we investigated the physiological function of L. plantarum Y44 based on an analysis of its genotype and phenotype. The complete genome of L. plantarum Y44 contained a single circular chromosome of 3,255,555 bp, with a GC content of 44.6%, and a single circular plasmid of 51,167 bp, with a GC content of 38.8%. The L. plantarum Y44 genome contained 3,293 genes including 3,112 protein coding sequences, 16 rRNAs, 66 tRNAs, 4 small (s)RNAs, and 95 pseudo genes. Lactobacillus plantarum Y44 could metabolize 24 different carbohydrate sources. Nineteen complete phosphoenolpyruvate-dependent sugar phosphotransferase system complex genes and intact Embden-Meyerhof-Parnas pathway and hexose monophosphate pathway enzyme genes, as well as abundant carbohydrate active enzyme genes, were identified in the L. plantarum Y44 genome. We also identified genes related to the biosynthesis of exopolysaccharide and surface proteins. Surface proteins played an important role in the L. plantarum Y44 adhesion to HT-29 cell monolayers, as evidenced by the removal of cell surface proteins leading to decreased adhesion capacity. The L. plantarum Y44 genome contained genes encoding chaperones, intracellular proteases, and 2-component systems, which were associated with the general stress response. Genes encoding bile salt hydrolase, F₀F₁-ATPase, Na⁺/H⁺-antiporter, H⁺/Cl^- exchange transporter, cyclopropane-fatty acyl-phospholipid synthase, and alkaline shock protein were identified in the L. plantarum Y44 genome, which might explain the strain's favorable gastric and intestinal transit tolerance. Some genes associated with encoding the NADH system, glutathione system, and thioredoxin system were predicted via in silico analysis and might account for the strain's ability to scavenge reactive oxygen species. Lactobacillus plantarum Y44 was susceptive to 7 antibiotics and did not produce biogenic amines, likely due to the absence of acquired antibiotic resistance genes and amino acid decarboxylase genes. The phenotype profile of L. plantarum Y44 was associated with its genetic characteristics, indicating that strains with certain physiological functions can be screened by analyzing their phenotypic and genotypic characteristics. Lactobacillus plantarum Y44 has the potential to be used as a starter culture in fermented dairy products.

Genomic Insights Into Five Strains of Lactobacillus plantarum With Biotechnological Potential Isolated From chicha, a Traditional Maize-Based Fermented Beverage From Northwestern Argentina

Lactic acid bacteria (LAB) are indigenous microorganisms that have been involved in food fermentations throughout history to preserve food and also to give special characteristics to them. The traditional fermented foods that are still being elaborated in indigenous populations around the world are a potential source of LAB with important biotechnological properties and/or beneficial to health. In a previous work, LAB biodiversity associated with chicha, a traditional maize-based fermented beverage from Northwestern Argentina, was studied, both by culture dependent and independent methods. From that study, 392 isolates were recovered, mostly members of Lactobacillus and Leuconostoc. Biotechnological characterization of representative isolates led to the selection of five strains belonging to the species Lactobacillus plantarum for their ability to produce vitamin B2 (riboflavin) and vitamin B9 (folates), their antimicrobial properties and antibiotics susceptibility. In this work, we present the Whole Genome Sequences (WGS) of these five strains that have been deposited in the Spanish Type Culture Collection: M5MA1 (= CECT 8962), M9MM1 (= CECT 8963), M9MM4 (= CECT 8964), M9MG6 (= CECT 8965), and M9Y2 (= CECT 8966), and a detailed description of their characterization, through a genomic approach, analyzing the genes responsible for these biotechnological properties, making a comparative study of the five genomes and reporting the aspects related to food safety, in accordance with the recommendations of the European Food Safety Authority (EFSA FEEDAP Panel, 2018) aiming at their use in the design of functional foods. The analysis unveiled, for the five strains, the complete set of genes for folate and riboflavin biosynthesis, the absence of pathogenic factors, the presence of CRISPR and cas genes, phage sequences, insertion elements and an aminoglycosides resistance gene, aadA, whose resistance could not be proved phenotypically in any strain. Genomic comparisons showed that strain CECT 8962 was significantly different in terms of genetic content and allowed the identification of carbohydrates metabolism and membrane transport related genes as the main components of the unique and accessory genome.

Purification and Characterization of Plantaricin ZJ316, a Novel Bacteriocin against Listeria monocytogenes from Lactobacillus plantarum ZJ316

Bacteriocins are known to be natural preservatives, which are becoming increasingly necessary in many types of food to control the proliferation of pathogenic bacteria. In this study, a novel bacteriocin produced by Lactobacillus plantarum ZJ316, called plantaricin ZJ316, was purified by ammonium sulfate precipitation, gel chromatography, and high-performance liquid chromatography. By mass spectrometry, the molecular mass of plantaricin ZJ316 was determined to be 2,366.06 Da. No homologous sequences were found in databases based on comparisons with the N-terminal amino acid sequencing. The bacteriocin was heat resistant and stable after incubation at pH 2.0 to 10.0. It was sensitive to α-chymotrypsin, trypsin, and proteinase K. Plantaricin ZJ316 had a broad inhibitory activity against gram-negative and gram-positive bacteria, especially Listeria monocytogenes. Our results suggested that this bacteriocin has the potential to inhibit pathogenic bacteria in food products.

Complete genome sequencing of exopolysaccharide-producing Lactobacillus plantarum K25 provides genetic evidence for the probiotic functionality and cold endurance capacity of the strain

Lactobacillus plantarum (L. plantarum) K25 is a probiotic strain isolated from Tibetan kefir. Previous studies showed that this exopolysaccharide (EPS)-producing strain was antimicrobial active and cold tolerant. These functional traits were evidenced by complete genome sequencing of strain K25 with a circular 3,175,846-bp chromosome and six circular plasmids, encoding 3365 CDSs, 16 rRNA genes and 70 tRNA genes. Genomic analysis of L. plantarum K25 illustrates that this strain contains the previous reported mechanisms of probiotic functionality and cold tolerance, involving plantaricins, lysozyme, bile salt hydrolase, chaperone proteins, osmoprotectant, oxidoreductase, EPSs and terpenes. Interestingly, strain K25 harbors more genes that function in defense mechanisms, and lipid transport and metabolism, in comparison with other L. plantarum strains reported. The present study demonstrates the comprehensive analysis of genes related to probiotic functionalities of an EPS-producing L. plantarum strain based on whole genome sequencing.

Genomic resequencing combined with quantitative proteomic analyses elucidate the survival mechanisms of Lactobacillus plantarum P-8 in a long-term glucose-limited experiment

Lactobacillus plantarum, commonly isolated from plant material, is widely used to produce various types of fermented foods. However, nutrient-limiting conditions are often encountered during industrial applications. The present study aimed to investigate the response of L. plantarum P-8 to glucose-limited conditions in a long-term experiment. Genotypic and proteomic changes in L. plantarum P-8 were monitored over 3 years in glucose-limited and glucose-normal media using whole-genome resequencing and tandem mass tag-based quantitative proteomic analysis. Results showed that L. plantarum employed numerous survival mechanisms, including alteration of the cell envelope, activation of the PTS system, accumulation and consumption of amino acids, increase in the metabolism of carbohydrates (via glycolysis, citric acid cycle, and pyruvate metabolism), and increase in the production of ATP in response to glucose starvation. This study demonstrates the feasibility of experimental evolution of L. plantarum P-8, while whole-genome resequencing of adapted isolates provided clues toward bacterial functions involved and a deeper mechanistic understanding of the adaptive response of L. plantarum to glucose-limited conditions.

SIGNIFICANCE

We have conducted a 3-year experiment monitoring genotypic and proteomic changes in Lactobacillus plantarum P-8 in glucose-limited and glucose-normal media. Whole-genome resequencing and tandem mass tag-based quantitative proteomics were performed for analyzing genomic evolution of L. plantarum P-8 in glucose-limited and glucose-normal conditions. In addition, differential expressed proteins in all generations between these two conditions were identified and functions of these proteins specific to L group were predicted. L. plantarum employed numerous survival mechanisms, including alteration of the cell envelope, activation of the PTS system, accumulation and consumption of amino acids, increase in the metabolism of carbohydrates (glycolysis, citric acid cycle, and pyruvate metabolism), and increase in the production of ATP in response to glucose starvation.