Strain diversity of plant-associated Lactiplantibacillus plantarum

Genetic specialization of key bifidobacterial phylotypes in multiple mother-infant dyad cohorts from geographically isolated populations

Little has been known about symbiotic relationships and host specificity for symbionts in the human gut microbiome so far. Bifidobacteria are a paragon of the symbiotic bacteria biota in the human gut. In this study, we characterized the population genetic structure of three bifidobacteria species from 58 healthy mother-infant pairs of three ethnic groups in China, geographically isolated, by Rep-PCR, multi-locus sequence analysis (MLSA), and in vitro carbohydrate utilization. One hundred strains tested were incorporated into 50 sequence types (STs), of which 29 STs, 17 STs, and 4 STs belong to B. longum subsp. longum, B. breve, and B. animalis subsp. lactis, respectively. The conspecific strains from the same mother-child pair were genetically very similar, supporting the vertical transmission of Bifidobacterium phylotypes from mother to offspring. In particular, results based on allele profiles and phylogeny showed that B. longum subsp. longum and B. breve exhibited considerable intraspecies genetic heterogeneity across three ethnic groups, and strains were clustered into ethnicity-specific lineages. Yet almost all strains of B. animalis subsp. lactis were incorporated into the same phylogenetic clade, regardless of ethnic origin. Our findings support the hypothesis of co-evolution between human gut symbionts and their respective populations, which is closely linked to the lifestyle of specific bacterial lineages. Hence, the natural and evolutionary history of Bifidobacterium species would be an additional consideration when selecting bifidobacterial strains for industrial and therapeutic applications.

Pangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family

Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.

Applicable Strains, Processing Techniques and Health Benefits of Fermented Oat Beverages: A Review

Based on the high nutrients of oat and the demand of health-conscious consumers for value-added and functional foods, fermented oat beverages have great market prospects. This review summarizes the applicable strains, processing techniques and health benefits of fermented oat beverages. Firstly, the fermentation characteristics and conditions of the applicable strains are systematically described. Secondly, the advantages of pre-treatment processes such as enzymatic hydrolysis, germination, milling and drying are summarized. Furthermore, fermented oat beverages can increase the nutrient content and reduce the content of anti-nutritional factors, thereby reducing some risk factors related to many diseases such as diabetes, high cholesterol and high blood pressure. This paper discusses the current research status of fermented oat beverages, which has academic significance for researchers interested in the application potential of oat. Future studies on fermenting oat beverages can focus on the development of special compound fermentation agents and the richness of their taste.

Molecular Detection and Identification of Plant-Associated Lactiplantibacillus plantarum

Lactiplantibacillus plantarum is a lactic acid bacterium often isolated from a wide variety of niches. Its ubiquity can be explained by a large, flexible genome that helps it adapt to different habitats. The consequence of this is great strain diversity, which may make their identification difficult. Accordingly, this review provides an overview of molecular techniques, both culture-dependent, and culture-independent, currently used to detect and identify L. plantarum. Some of the techniques described can also be applied to the analysis of other lactic acid bacteria.

In-process real-time probiotic phenotypic strain identity tracking: The use of Fourier transform infrared spectroscopy

Probiotic bacteria, capable of conferring benefits to the host, can present challenges in design, development, scale-up, manufacturing, commercialization, and life cycle management. Strain identification is one of the main quality parameters; nevertheless, this task can be challenging since established methodologies can lack resolution at the strain level for some microorganisms and\or are labor-intensive and time-consuming. Fourier transform infrared spectroscopy (FTIRS) has been largely used for the investigation of pathogenic species in the clinical field, whereas only recently has been proposed for the identification of probiotic strains. Within the probiotic industrial production, bacterial strains can be subjected to stressful conditions that may affect genomic and phenotypic characteristics; therefore, real-time monitoring of all the sequential growth steps is requested. Considering the fast, low-cost, and high-throughput features, FTIRS is an innovative and functional technology for typing probiotic strains from bench-top experiments to large-scale industrial production, allowing the monitoring of stability and identity of probiotic strains. In this study, the discriminatory power of FTIRS was assessed for four Lactiplantibacillus plantarum probiotic strains grown under different conditions, including temperatures (30 and 37°C) and medium (broth and agar), after consecutive sub-culturing steps. A comparison between the generated spectra with pulsed-field gel electrophoresis (PFGE) profiles was also performed. FTIRS was not only able to distinguish the strains of L. plantarum under different growth conditions but also to prove the phenotypic stability of L. plantarum type strain LP-CT after six growing steps. Regardless of the growth conditions, FTIRS spectra related to LP-CT constituted a unique hierarchical cluster, separated from the other L. plantarum strains. These results were confirmed by a PFGE analysis. In addition, based on FTIRS data, broth cultures demonstrated a higher reproducibility and discriminatory power with respect to agar ones. These results support the introduction of FTIRS in the probiotic industry, allowing for the step-by-step monitoring of massive microbial production while also guaranteeing the stability and purity of the probiotic strain. The proposed novel approach can constitute an impressive improvement in the probiotic manufacturing process.

Evaluation of the Volatile Composition and Sensory Behavior of Habanero Pepper during Lactic Acid Fermentation by L. plantarum

Habanero pepper is recognized for its appealing aroma and flavor. Lactic acid fermentation can improve these sensory properties, especially aroma, by the synthesis of volatile compounds, which might also increase the consumer preference. Thus, the aim of this research was to compare the volatile composition as well as different sensory parameters such as preference and emotions related to the lactic acid fermentation of Habanero pepper by two strains (wild and commercial) of Lactiplantibacillus plantarum. A multiple factor ANOVA was used to compare the volatile composition with different fermentation times and strains. The results demonstrated that the interaction between the strain and fermentation time had significant effects on the volatile compound production that includes 1-hexanol, cis-3-hexenyl hexanoate, linalool, and 3,3 dimethyl-1-hexanol while only time influenced the production of trans-2-hexen-1-al. The wild strain (WIL) at 48 h of fermentation produced the highest concentration of 3,3 dimethyl-1-hexanol and trans-2-hexen-1-al. On the other hand, the commercial strain (COM) presented the highest concentration of 1-hexanol and cis-3-hexenyl hexanoate with a 72 h fermentation. The most preferred sample was that fermented by WIL for 48 h for the attribute of odor, while for taste, the most preferred sample was that fermented for 72 h with COM.

Screening of Lactiplantibacillus plantarum Strains from Sourdoughs for Biosuppression of Pseudomonas syringae pv. syringae and Botrytis cinerea in Table Grapes

Grapes (Vitis vinifera L.) are an essential crop for fresh consumption and wine production. Vineyards are attacked by several economically important bacterial and fungal diseases that require regular pesticide treatment. Among them, Pseudomonas syringae pv. syringae (Ps. syringae) and Botrytis cinerea (B. cinerea) infections cause huge economic losses. The fresh fruit market has shifted to functional natural foodstuffs with clear health benefits and a reduced use of chemicals along the production chain. Lactic acid bacteria (LAB) have a biopreservative effect and are applied to ensure food safety in response to consumers' demands. In the present study, the possibilities of using microorganisms with a potential antimicrobial effect against Ps. syringae and B. cinerea in the production of table grapes were investigated. LAB of the genus Lactiplantibacillus can be a natural antagonist of pathogenic bacteria and fungi by releasing lactic acid, acetic acid, ethanol, carbon dioxide and bacteriocins in the medium. The present study focuses on the characterization of nine Lactiplantibacillus plantarum (Lp. plantarum) strains isolated from spontaneously fermented sourdoughs. Species-specific PCR identified the isolated LAB for partial recA gene amplification with an amplicon size of 318 bp. RAPD-PCR analysis showed the intraspecific diversity of the individual strains. Thirteen plantaricin-like peptides (PlnA, PlnB, PlnC, PlnD, PlnEF, PlnG, PlnI, PlnJ, PlnK, PlnN, PlnNC8, PlnS, and PlnW) produced by isolated Lp. plantarum strains were detected by PCR with gene-specific primers. The key features for future industrial applications were their antimicrobial properties. The culture medium and cell-free supernatant (CFS) were used to establish in vitro antimicrobial activities of Lp. plantarum strains against Ps. syringae and B. cinerea, and inhibition of phytopathogen development was observed. The inhibitory effect of the CFS (cell-free supernatant) of all strains was assessed by infecting table grapes with these pathogens in in vivo experiments. Lp. plantarum Q4 showed the most effective suppression of the pathogens both in vitro and in vivo, which indicates its potential use as a biocontrol agent against berry rot and grey rot on grapes, caused by Ps. syringae and B. cinerea.

Lactiplantibacillus plantarum LOC1 Isolated from Fresh Tea Leaves Modulates Macrophage Response to TLR4 Activation

Previously, we demonstrated that Lactiplantibacillus plantarum LOC1, originally isolated from fresh tea leaves, was able to improve epithelial barrier integrity in in vitro models, suggesting that this strain is an interesting probiotic candidate. In this work, we aimed to continue characterizing the potential probiotic properties of the LOC1 strain, focusing on its immunomodulatory properties in the context of innate immunity triggered by Toll-like receptor 4 (TLR4) activation. These studies were complemented by comparative and functional genomics analysis to characterize the bacterial genes involved in the immunomodulatory capacity. We carried out a transcriptomic study to evaluate the effect of L. plantarum LOC1 on the response of murine macrophages (RAW264.7 cells) to the activation of TLR4. We demonstrated that L. plantarum LOC1 exerts a modulatory effect on lipopolysaccharide (LPS)-induced inflammation, resulting in a differential regulation of immune factor expression in macrophages. The LOC1 strain markedly reduced the LPS-induced expression of some inflammatory cytokines (IL-1β, IL-12, and CSF2) and chemokines (CCL17, CCL28, CXCL3, CXCL13, CXCL1, and CX3CL1), while it significantly increased the expression of other cytokines (TNF-α, IL-6, IL-18, IFN-β, IFN-γ, and CSF3), chemokines (IL-15 and CXCL9), and activation markers (H2-k1, H2-M3, CD80, and CD86) in RAW macrophages. Our results show that L. plantarum LOC1 would enhance the intrinsic functions of macrophages, promoting their protective effects mediated by the stimulation of the Th1 response without affecting the regulatory mechanisms that help control inflammation. In addition, we sequenced the LOC1 genome and performed a genomic characterization. Genomic comparative analysis with the well-known immunomodulatory strains WCSF1 and CRL1506 demonstrated that L. plantarum LOC1 possess a set of adhesion factors and genes involved in the biosynthesis of teichoic acids and lipoproteins that could be involved in its immunomodulatory capacity. The results of this work can contribute to the development of immune-related functional foods containing L. plantarum LOC1.

Calcium Determines Lactiplantibacillus plantarum Intraspecies Competitive Fitness

The importance of individual nutrients for microbial strain robustness and coexistence in habitats containing different members of the same species is not well understood. To address this for Lactiplantibacillus plantarum in food fermentations, we performed comparative genomics and examined the nutritive requirements and competitive fitness for L. plantarum strains B1.1 and B1.3 isolated from a single sample of teff injera fermentation batter. Compared to B1.1 and other L. plantarum strains, B1.3 has a smaller genome, limited biosynthetic capacities, and large mobilome. Despite these differences, B1.3 was equally competitive with B1.1 in a suspension of teff flour. In commercially sourced, nutrient-replete MRS (cMRS) medium, strain B1.3 reached 3-fold-higher numbers than B1.1 within 2 days of passage. Because B1.3 growth and competitive fitness were poor in mMRS medium (here called mMRS), a modified MRS medium lacking beef extract, we used mMRS to identify nutrients needed for robust B1.3 growth. No improvement was observed when mMRS was supplemented with nucleotides, amino acids, vitamins, or monovalent metals. Remarkably, the addition of divalent metal salts increased the growth rate and cell yields of B1.3 in mMRS. Metal requirements were confirmed by inductively coupled plasma mass spectrometry, showing that total B1.3 intracellular metal concentrations were significantly (up to 2.7-fold) reduced compared to B1.1. Supplemental CaCl₂ conferred the greatest effect, resulting in equal growth between B1.1 and B1.3 over five successive passages in mMRS. Moreover, calcium supplementation reversed a B1.3 strain-specific, stationary-phase, flocculation phenotype. These findings show how L. plantarum calcium requirements affect competitive fitness at the strain level.

IMPORTANCE Ecological theory states that the struggle for existence is stronger between closely related species. Contrary to this assertion, fermented foods frequently sustain conspecific individuals, in spite of their high levels of phylogenetic relatedness. Therefore, we investigated two isolates of Lactiplantibacillus plantarum, B1.1 and B1.3, randomly selected from a single batch of teff injera batter. These strains spanned the known genomic and phenotypic range of the L. plantarum species, and in laboratory culture medium used for strain screening, B1.3 exhibited poor growth and was outcompeted by the more robust strain B1.1. Nonetheless, B1.1 and B1.3 were equally competitive in teff flour. This result shows how L. plantarum has adapted for coexistence in that environment. The capacity for the single macronutrient calcium to restore B1.3 competitive fitness in laboratory culture medium suggests that L. plantarum intraspecies diversity found in food systems is fine-tuned to nutrient requirements at the strain level.

Going wild: ecology and genomics are crucial to understand yeast evolution

Improved and more accessible genome-sequencing approaches have allowed the analysis of large sets of natural yeast isolates. As a consequence, this unprecedented level of description of yeast-genome characteristics and variations in natural environments has provided crucial insights on yeast ecology and evolution. Here, we review some of the most relevant and intriguing aspects of yeast evolution pointed out, thanks to the combination of yeast ecology and genomics, and critically examine the resulting improvement of our knowledge on this field. Only integrated approaches, taking into consideration not only the characteristics of the microbe but also those of the hosting environment, will significantly move forward the exploration of yeast diversity, ecology, and evolution.

Evaluation of IR Biotyper for Lactiplantibacillus plantarum Typing and Its Application Potential in Probiotic Preliminary Screening

IR Biotyper (IRBT), which is a spectroscopic system for microorganism typing based on Fourier transform infrared (FTIR) technology, has been used to detect the spread of clones in clinical microbiology laboratories. However, the use of IRBT to detect probiotics has rarely been reported. Herein, we evaluated the discriminatory power of IRBT to type Lactiplantibacillus plantarum isolates at the strain level and explored its application potential in probiotic preliminary selection. Twenty Lactiplantibacillus isolates collected from pickled radishes during successive fermentation were used to test the robustness of IRBT at the strain level. IRBT was then compared with genotyping methods such as whole-genome sequencing (WGS), pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST) to evaluate its discrimination power. IRBT distributed the 20 isolates into five clusters, with L. argentoratensis isolate C7-83 being the most distant from the other isolates, which belonged to L. plantarum. IRBT showed good reproducibility, although deviation in the discriminative power of IRBT was found at the strain level across laboratories, probably due to technical variance. All examined methods allowed bacterial identification at the strain level, but IRBT had higher discriminatory power than MLST and was comparable to the WGS and PFGE. In the phenotypic comparison study, we observed that the clustering results of probiotic physiological attributes (e.g., sensitivity to acid and bile salts, hydrophobicity of the cell surface, and resistance to antibiotics) were consistent with the typing results of IRBT. Our results indicated that IRBT is a robust tool for L. plantarum strain typing that could improve the efficiency of probiotic identification and preliminary screening, and can potentially be applied in probiotic traceability and quality control.

Extracellular electron transfer increases fermentation in lactic acid bacteria via a hybrid metabolism

Energy conservation in microorganisms is classically categorized into respiration and fermentation; however, recent work shows some species can use mixed or alternative bioenergetic strategies. We explored the use of extracellular electron transfer for energy conservation in diverse lactic acid bacteria (LAB), microorganisms that mainly rely on fermentative metabolism and are important in food fermentations. The LAB Lactiplantibacillus plantarum uses extracellular electron transfer to increase its NAD+/NADH ratio, generate more ATP through substrate-level phosphorylation, and accumulate biomass more rapidly. This novel, hybrid metabolism is dependent on a type-II NADH dehydrogenase (Ndh2) and conditionally requires a flavin-binding extracellular lipoprotein (PplA) under laboratory conditions. It confers increased fermentation product yield, metabolic flux, and environmental acidification in laboratory media and during kale juice fermentation. The discovery of a single pathway that simultaneously blends features of fermentation and respiration in a primarily fermentative microorganism expands our knowledge of energy conservation and provides immediate biotechnology applications.

The Interactions among Isolates of Lactiplantibacillus plantarum and Dairy Yeast Contaminants: Towards Biocontrol Applications

Yeast diversity in the cheese manufacturing process and in the cheeses themselves includes indispensable species for the production of specific cheeses and undesired species that cause cheese defects and spoilage. The control of yeast contaminants is problematic due to limitations in sanitation methods and chemicals used in the food industry. The utilisation of lactic acid bacteria and their antifungal products is intensively studied. Lactiplantibacillus plantarum is one of the most frequently studied species producing a wide spectrum of bioactive by-products. In the present study, twenty strains of L. plantarum from four sources were tested against 25 species of yeast isolated from cheeses, brines, and dairy environments. The functional traits of L. plantarum strains, such as the presence of class 2a bacteriocin and chitinase genes and in vitro production of organic acids, were evaluated. The extracellular production of bioactive peptides and proteins was tested using proteomic methods. Antifungal activity against yeast was screened using in vitro tests. Testing of antifungal activity on artificial media and reconstituted milk showed significant variability within the strains of L. plantarum and its group of origin. Strains from sourdoughs (CCDM 3018, K19-3) and raw cheese (L12, L24, L32) strongly inhibited the highest number of yeast strains on medium with reconstituted milk. These strains showed a consistent spectrum of genes belonging to class 2a bacteriocins, the gene of chitinase and its extracellular product 9 LACO Chitin-binding protein. Strain CCDM 3018 with the spectrum of class 2a bacteriocin gene, chitinase and significant production of lactic acid in all media performed significant antifungal effects in artificial and reconstituted milk-based media.