Transcriptional reprogramming and phenotypic switching associated with the adaptation of Lactobacillus plantarum C2 to plant niches

Antioxidant properties and changes in vitro digestion of the fermented kiwifruit extract prepared by lactic acid bacteria and yeasts

The health benefits of fermented fruits have attracted consumers' attention. High levels of antioxidant ability in the fermented kiwifruit extract were found at the early stage of fermentation. The co-fermention with Lactobacillus paracasei LG0260 and Kluyveromyces marxianus J2853 showed the highest ABTS radical scavenging ability (ABTS⋅+-SA) and superoxide dismutase (SOD) activity. Also, the typical antioxidant components of SOD activity, vitamin C concentration and total phenol content were highly correlated with ABTS⋅+-SA. Obviously, polyphenols in the fermented kiwifruit extract evolved into monophenols during fermentation. Compared to undigested samples, the activity of ABTS⋅+-SA and reducing power capacity (RP-CA) after the final intestinal digestion decreased and ranged 387.44-531.89 VCμg/mL, 650.95-981.63 VCμg/mL, respectively (P < 0.05). Meanwhile, SOD activity on the 10th day of fermentation were still remained 222.82 U/mL, 206.98 U/mL and 217.23 U/mL, respectively. These results suggested that the fermented kiwifruit extract could exhibit antioxidant activity through tolerance to the digestive environment.

Selection of a galactose-positive mutant strain of Streptococcus thermophilus and its optimized production as a high-vitality starter culture

Streptococcus thermophilus (S. thermophilus) is a common starter in yogurt production and plays an important role in the dairy industry. In this study, a galactose-positive (Gal+) mutant strain, IMAU20246Y, was produced using the chemical mutagen N-methyl-N'-nitro-N-nitrosoguanidine (NTG) from wild type S. thermophilus IMAU20246 which was known to have good fermentation characteristics. The sugar content of milk fermented by either the mutant or the wild type was determined using high performance liquid chromatography (HPLC); metabolism of lactose and galactose was significantly increased in the mutant strain. In addition, we used the response surface methodology to optimize components of the basic medium M17 for survival ratio of the mutant strain. Under these optimal conditions, the viable counts of mutant S. thermophilus IMAU20246Y reached 4.15 × 108 cfu/mL and following freeze drying in the medium retained cell viability of up to 67.42%. The above results are conducive to production of a high vitality starter culture and development of 'low sugar, high sweetness' dairy products.

Fermented foods, their microbiome and its potential in boosting human health

Fermented foods (FFs) are part of the cultural heritage of several populations, and their production dates back 8000 years. Over the last ~150 years, the microbial consortia of many of the most widespread FFs have been characterised, leading in some instances to the standardisation of their production. Nevertheless, limited knowledge exists about the microbial communities of local and traditional FFs and their possible effects on human health. Recent findings suggest they might be a valuable source of novel probiotic strains, enriched in nutrients and highly sustainable for the environment. Despite the increasing number of observational studies and randomised controlled trials, it still remains unclear whether and how regular FF consumption is linked with health outcomes and enrichment of the gut microbiome in health-associated species. This review aims to sum up the knowledge about traditional FFs and their associated microbiomes, outlining the role of fermentation with respect to boosting nutritional profiles and attempting to establish a link between FF consumption and health-beneficial outcomes.

Lentils protein isolate as a fermenting substrate for the production of bioactive peptides by lactic acid bacteria and neglected yeast species

In the current trend where plant-based foods are preferred over animal-based foods, pulses represent an alternative source of protein but also of bioactive peptides (BPs). We investigated the pattern of protein hydrolysis during fermentation of red lentils protein isolate (RLPI) with various lactic acid bacteria and yeast strains. Hanseniaspora uvarum SY1 and Fructilactobacillus sanfranciscensis E10 were the most proteolytic microorganisms. H. uvarum SY1 led to the highest antiradical, angiotensin-converting enzyme-inhibitory and antifungal activities, as found in low molecular weight water soluble extracts (LMW-WSE). The 2039 peptide sequences identified by LMW-WSE were screened using BIOPEP UWM database, and 36 sequences matched with known BPs. Fermentation of RLPI by lactic acid bacteria and yeasts generated 12 peptides undetected in raw RLPI. Besides, H. uvarum SY1 led to the highest abundance (peak areas) of BPs, in particular with antioxidant and ACE-inhibitory activities. The amino acid sequences LVR and LVL, identified in the fermented RLPI, represent novel findings, as they were detected for the first time in substrates subjected to microbial fermentation. KVI, another BP highly characteristic of RLPI-SY1, was previously observed only in dried bonito. 44 novel potential BPs, worthy of further characterization, were correlated with antifungal activity.

Impacts of Ultrasonic Treatment for Black Soybean Okara Culture Medium Containing Choline Chloride on the β-Glucosidase Activity of Lactiplantibacillus plantarum BCRC 10357

The effects of ultrasonic treatment for the culture medium of solid black soybean okara with choline chloride (ChCl) on the survival and β-glucosidase activity of Lactiplantibacillus plantarum BCRC 10357 (Lp-BCRC10357) were investigated. A mixture of 3% dried black soybean okara in de Man-Rogosa-Sharpe (w/v) was used as the Oka medium. With ultrasonic treatment (40 kHz/300 W) of the Oka medium at 60 °C for 3 h before inoculation, the β-glucosidase activity of Lp-BCRC10357 at 12 h and 24 h of incubation amounted to 13.35 and 15.50 U/mL, respectively, which was significantly larger than that (12.58 U/mL at 12 h and 2.86 U/mL at 24 h) without ultrasonic treatment of the medium. This indicated that ultrasonic treatment could cause the microstructure of the solid black soybean okara to be broken, facilitating the transport of ingredients and Lp-BCRC10357 into the internal structure of the okara for utilization. For the effect of ChCl (1, 3, or 5%) added to the Oka medium (w/v) with ultrasonic treatment before inoculation, using 1% ChCl in the Oka medium could stimulate the best response of Lp-BCRC10357 with the highest β-glucosidase activity of 19.47 U/mL in 12 h of incubation, showing that Lp-BCRC10357 had a positive response when confronting the extra ChCl that acted as an osmoprotectant and nano-crowder in the extracellular environment. Furthermore, the Oka medium containing 1% ChCl with ultrasonic treatment led to higher β-glucosidase activity of Lp-BCRC10357 than that without ultrasonic treatment, demonstrating that the ultrasonic treatment could enhance the contact of ChCl and Lp-BCRC10357 to regulate the physiological behavior for the release of enzymes. In addition, the analysis of the isoflavone content and antioxidant activity of the fermented product revealed that the addition of 1% ChCl in the Oka medium with ultrasonic treatment before inoculation allowed a higher enhancement ratio for the biotransformation of isoflavone glycosides to their aglycones, with a slight enhancement in the antioxidant activity at 24 h of fermentation. This study developed a methodology by combining ultrasonic treatment with a limited amount of ChCl to allow the culture medium to acclimate Lp-BCRC10357 and release high levels of β-glucosidase, and this approach has the potential to be used in the fermentation of okara-related products as nutritional supplements in foods.

An integrated transcriptomic and metabolic phenotype analysis to uncover the metabolic characteristics of a genetically engineered Candida utilis strain expressing δ-zein gene

Introduction

Candida utilis (C. utilis) has been extensively utilized as human food or animal feed additives. With its ability to support heterologous gene expression, C. utilis proves to be a valuable platform for the synthesis of proteins and metabolites that possess both high nutritional and economic value. However, there remains a dearth of research focused on the characteristics of C. utilis through genomic, transcriptomic and metabolic approaches.

Methods

With the aim of unraveling the molecular mechanism and genetic basis governing the biological process of C. utilis, we embarked on a de novo sequencing endeavor to acquire comprehensive sequence data. In addition, an integrated transcriptomic and metabolic phenotype analysis was performed to compare the wild-type C. utilis (WT) with a genetically engineered strain of C. utilis that harbors the heterologous δ-zein gene (RCT).

Results

δ-zein is a protein rich in methionine found in the endosperm of maize. The integrated analysis of transcriptomic and metabolic phenotypes uncovered significant metabolic diversity between the WT and RCT C. utilis. A total of 252 differentially expressed genes were identified, primarily associated with ribosome function, peroxisome activity, arginine and proline metabolism, carbon metabolism, and fatty acid degradation. In the experimental setup using PM1, PM2, and PM4 plates, a total of 284 growth conditions were tested. A comparison between the WT and RCT C. utilis demonstrated significant increases in the utilization of certain carbon source substrates by RCT. Gelatin and glycogen were found to be significantly utilized to a greater extent by RCT compared to WT. Additionally, in terms of sulfur source substrates, RCT exhibited significantly increased utilization of O-Phospho-L-Tyrosine and L-Methionine Sulfone when compared to WT.

Discussion

The introduction of δ-zein gene into C. utilis may lead to significant changes in the metabolic substrates and metabolic pathways, but does not weaken the activity of the strain. Our study provides new insights into the transcriptomic and metabolic characteristics of the genetically engineered C. utilis strain harboring δ-zein gene, which has the potential to advance the utilization of C. utilis as an efficient protein feed in agricultural applications.

Revised Aspects into the Molecular Bases of Hydroxycinnamic Acid Metabolism in Lactobacilli

Hydroxycinnamic acids (HCAs) are phenolic compounds produced by the secondary metabolism of edible plants and are the most abundant phenolic acids in our diet. The antimicrobial capacity of HCAs is an important function attributed to these phenolic acids in the defense of plants against microbiological threats, and bacteria have developed diverse mechanisms to counter the antimicrobial stress imposed by these compounds, including their metabolism into different microbial derivatives. The metabolism of HCAs has been intensively studied in Lactobacillus spp., as the metabolic transformation of HCAs by these bacteria contributes to the biological activity of these acids in plant and human habitats or to improve the nutritional quality of fermented foods. The main mechanisms known to date used by Lactobacillus spp. to metabolize HCAs are enzymatic decarboxylation and/or reduction. Here, recent advances in the knowledge regarding the enzymes that contribute to these two enzymatic conversions, the genes involved, their regulation and the physiological significance to lactobacilli are reviewed and critically discussed.

Assessment of Ultrasonic Stress on Survival and β-Glucosidase Activity of Encapsulated Lactiplantibacillus plantarum BCRC 10357 in Fermentation of Black Soymilk

The enhanced β-glucosidase activity of encapsulated Lactiplantibacillus plantarum BCRC 10357 within calcium alginate capsules was investigated by ultrasonic stimulation to induce the stress response of the bacteria for the biotransformation of isoflavones in black soymilk. The effects of various ultrasound durations, sodium alginate concentrations (% ALG), and cell suspensions on the β-glucosidase activity of encapsulated bacteria were explored. The β-glucosidase activity of encapsulated L. plantarum BCRC 10357 with ultrasonic stimulation (40 kHz/300 W) was greater than that without ultrasound. With 20 min of ultrasonic treatment, the β-glucosidase activity of encapsulated L. plantarum BCRC 10357 from 2% ALG/0.85% NaCl cell suspension was 11.47 U/mL at 12 h, then increased to 27.43 U/mL at 36 h and to 26.25 U/mL at 48 h in black soymilk at 37 °C, showing the high adaptation of encapsulated L. plantarum BCRC 10357 encountering ultrasonic stress to release high β-glucosidase until 48 h, at which point the ratio of isoflavone aglycones (daidzein and genistein) in total isoflavones (daidzin, genistin, daidzein, and genistein) was 98.65%, reflecting the effective biotransformation of isoflavone glycosides into aglycones by β-glucosidase. In this study, the survivability and β-glucosidase activity of encapsulated L. plantarum BCRC 10357 were enhanced under ultrasonic stimulation, and were favorably used in the fermentation of black soymilk.

Date Seeds Flour Used as Value-Added Ingredient for Wheat Sourdough Bread: An Example of Sustainable Bio-Recycling

Our study proposed date seeds flour (DSF) as an innovative ingredient for sourdough bread production through sustainable bio-recycling. We isolated autochthonous lactic acid bacteria and yeasts from DSF and DSF-derived doughs to build up a reservoir of strains from which to select starters ensuring rapid adaptation and high ecological fitness. The screening based on pro-technological criteria led to the formulation of a mixed starter consisting of Leuconostoc mesenteroides, Lactiplantibacillus plantarum, and Saccharomyces cerevisiae strains, which allowed obtaining a mature type I sourdough after consecutive refreshments, in which an aliquot of the durum wheat flour (DWF) was replaced by DSF. The resulting DSF sourdough and bread underwent an integrated characterization. Sourdough biotechnology was confirmed as a suitable procedure to improve some functional and sensory properties of DWF/DSF mixture formulation. The radical scavenging activity increased due to the consistent release of free phenolics. Perceived bitterness and astringency were considerably diminished, likely because of tannin degradation.

NMR-based metabolomics approach on optimization of malolactic fermentation of sea buckthorn juice with Lactiplantibacillus plantarum

This work investigated the impact of malolactic fermentation on the metabolomic profile of sea buckthorn juice to optimize the fermentation process for flavor modification. Six strains of L. plantarum were used with varied pH of the juice, cell acclimation, and fermentation time. ¹H-NOESY spectra were acquired from fresh and fermented juices with a total of 46 metabolites identified. Less sugars and quinic acid were metabolized at pH 2.7 while oxidation of ascorbic acid was reduced at pH 3.5. l-Malic acid, essential amino acids, and nucleosides were consumed early during fermentation while sugars in general were consumed later in the fermentation. If deacidification is the main target of fermentation, strains that produce less acids and ferment less sugars, shorter fermentation time, and lower starter pH should be used. Higher starter pH and longer fermentation time promote formation of antimicrobial compounds and potentially increase antioxidant stability.

Polyphenol-Mediated Gut Microbiota Modulation: Toward Prebiotics and Further

The genome of gut microbes encodes a collection of enzymes whose metabolic functions contribute to the bioavailability and bioactivity of unabsorbed (poly)phenols. Datasets from high throughput sequencing, metabolome measurements, and other omics have expanded the understanding of the different modes of actions by which (poly)phenols modulate the microbiome conferring health benefits to the host. Progress have been made to identify direct prebiotic effects of (poly)phenols; albeit up to date, these compounds are not recognized as prebiotics sensu stricto. Interestingly, certain probiotics strains have an enzymatic repertoire, such as tannase, α-L-rhamnosidase, and phenolic acid reductase, involved in the transformation of different (poly)phenols into bioactive phenolic metabolites. In vivo studies have demonstrated that these (poly)phenol-transforming bacteria thrive when provided with phenolic substrates. However, other taxonomically distinct gut symbionts of which a phenolic-metabolizing activity has not been demonstrated are still significantly promoted by (poly)phenols. This is the case of Akkermansia muciniphila, a so-called antiobesity bacterium, which responds positively to (poly)phenols and may be partially responsible for the health benefits formerly attributed to these molecules. We surmise that (poly)phenols broad antimicrobial action free ecological niches occupied by competing bacteria, thereby allowing the bloom of beneficial gut bacteria. This review explores the capacity of (poly)phenols to promote beneficial gut bacteria through their direct and collaborative bacterial utilization and their inhibitory action on potential pathogenic species. We propose the term duplibiotic, to describe an unabsorbed substrate modulating the gut microbiota by both antimicrobial and prebiotic modes of action. (Poly)phenol duplibiotic effect could participate in blunting metabolic disturbance and gut dysbiosis, positioning these compounds as dietary strategies with therapeutic potential.

Application of ultrasonication at different microbial growth stages during apple juice fermentation by Lactobacillus plantarum: Investigation on the metabolic response

In this work, low-intensity ultrasonication (58.3 and 93.6 W/L) was performed at lag, logarithmic and stationary growth phases of Lactobacillus plantarum in apple juice fermentation, separately. Microbial responses to sonication, including microbial growth, profiles of organic acids profile, amino acids, phenolics, and antioxidant capacity, were examined. The results revealed that obvious responses were made by Lactobacillus plantarum to ultrasonication at lag and logarithmic phases, whereas sonication at stationary phase had a negligible impact. Sonication at lag and logarithmic phases promoted microbial growth and intensified biotransformation of malic acid to lactic acid. For example, after sonication at lag phase for 0.5 h, microbial count and lactic acid content in the ultrasound-treated samples at 58.3 W/L reached 7.91 ± 0.01 Log CFU/mL and 133.70 ± 7.39 mg/L, which were significantly higher than that in the non-sonicated samples. However, the ultrasonic effect on microbial growth and metabolism of organic acids attenuated with fermentation. Moreover, ultrasonication at lag and logarithmic phases had complex influences on the metabolism of apple phenolics such as chlorogenic acid, caffeic acid, procyanidin B2, catechin and gallic acid. Ultrasound could positively affect the hydrolysis of chlorogenic acid to caffeic acid, the transformation of procyanidin B2 and decarboxylation of gallic acid. The metabolism of organic acids and free amino acids in the sonicated samples was statistically correlated with phenolic metabolism, implying that ultrasound may benefit phenolic derivation by improving the microbial metabolism of organic acids and amino acids.

Evaluation of Semi-Solid-State Fermentation of Elaeocarpus serratus L. Leaves and Black Soymilk by Lactobacillus plantarum on Bioactive Compounds and Antioxidant Capacity

Elaeocarpus serratus L. leaves (EL) containing phenolic compounds and flavonoids, including myricitrin with pharmacological properties, could be valorized as nutritional additive in foods. In this study, the semi-solid-state fermentation of EL and black soymilk (BS) by Lactobacillus plantarum BCRC 10357 was investigated. Without adding EL in MRS medium, the β-glucosidase activity of L. plantarum quickly reduced to 2.33 ± 0.15 U/mL in 36 h of fermentation; by using 3% EL, the stability period of β-glucosidase activity was prolonged as 12.94 ± 0.69 U/mL in 12 h to 13.71 ± 0.94 in 36 h, showing positive response of the bacteria encountering EL. Using L. plantarum to ferment BS with 3% EL, the β-glucosidase activity increased to 23.78 ± 1.34 U/mL in 24 h, and in the fermented product extract (FPE), the content of myricitrin (2297.06 μg/g-FPE) and isoflavone aglycones (daidzein and genistein, 474.47 μg/g-FPE) at 48 h of fermentation were 1.61-fold and 1.95-fold of that before fermentation (at 0 h), respectively. Total flavonoid content, myricitrin, and ferric reducing antioxidant power in FPE using BS and EL were higher than that using EL alone. This study developed the potential fermented product of black soymilk using EL as a nutritional supplement with probiotics.

Role of Lactic Acid Bacteria Phospho-β-Glucosidases during the Fermentation of Cereal by-Products

Bioprocessing using lactic acid bacteria (LAB) is a powerful means to exploit plant-derived by-products as a food ingredient. LAB have the capability to metabolize a large variety of carbohydrates, but such metabolism only relies on few metabolic routes, conferring on them a high fermentation potential. One example of these pathways is that involving phospho-β-glucosidase genes, which are present in high redundancy within LAB genomes. This enzymatic activity undertakes an ambivalent role during fermentation of plant-based foods related to the release of a wide range of phenolic compounds, from their β-D-glycosylated precursors and the degradation of β-glucopyranosyl derived carbohydrates. We proposed a novel phenomic approach to characterize the metabolism drift of Lactiplantibacillus plantarum and Leuconostoc pseudomesenteroides caused by a lignocellulosic by-product, such as the brewers’ spent grain (BSG), in contrast to Rich De Man, Rogosa and Sharpe (MRS) broth. We observed an increased metabolic activity for gentiobiose, cellobiose and β-glucoside conjugates of phenolic compounds during BSG fermentation. Gene expression analysis confirmed the importance of cellobiose metabolism while a release of lignin-derived aglycones was found during BSG fermentation. We provided a comprehensive view of the important role exerted by LAB 6-phospho-β-glucosidases as well the major metabolic routes undertaken during plant-based fermentations. Further challenges will consider a controlled characterization of pbg gene expression correlated to the metabolism of β-glucosides with different aglycone moieties.

Characterization of transcriptional response of Lactobacillus plantarum under acidic conditions provides insight into bacterial adaptation in fermentative environments

Lactic acid bacteria (LAB) play an important role in kimchi fermentation by metabolizing raw materials into diverse metabolites. Bacterial adaptation is therefore a crucial element of fermentation. In this study, we investigated the transcriptional changes of Lactobacillus plantarum under acidic conditions to evaluate the elements of bacterial adaptation critical for fermentation. Differentially expressed genes (DEGs) have shown that transport function is primarily affected by acidic conditions. Five of the 13 significantly down-regulated genes and 7 of the 25 significantly up-regulated genes were found to have transport-related functions. We quantified the intracellular leucine content of bacteria grown at different pH ranges, determining that optimal bacterial leucine transport could be controlled by acidity during fermentation. Inhibition of L. plantarum growth was investigated and compared with other LAB at a pH range of 6.2–5.0. Interestingly, valinomycin inhibited L. plantarum growth from pH 6.2 to 5.0. This showed that L. plantarum had a wider range of transport functions than other LAB. These results suggested that L. plantarum had robust transport functions, and that this was the crucial factor for bacterial adaptation during fermentation.

Probiotic potential of lactic acid bacteria obtained from fermented curly kale juice

The aim of the paper was to analyse changes in lactic acid bacteria (LAB) populations during spontaneous fermentation of green curly kale juice (Brasicca oleracea L. var. acephala L.) and to determine the probiotic potential of LAB isolates. The analyses revealed that changes in LAB populations were specific for spontaneously fermented vegetable juices. The initial microbiota, composed mostly of Leuconostoc mesenteroides bacteria, was gradually replaced by Lactobacillus species, mainly Lactobacillus plantarum, Lactobacillus sakei, and Lactobacillus coryniformis. Screening tests for the antimicrobial properties and antibiotic susceptibility of isolates allowed for the selection of 12 strains with desirable characteristics. L. plantarum isolates were characterized by the widest spectrum of antimicrobial interactions, both towards Gram-positive and Gram-negative bacteria. Also, L. plantarum strains exhibited the best growth abilities under low pH conditions, and at different NaCl and bile salt concentrations. All strains showed different levels of antibiotic sensitivity, although they were resistant to vancomycin and kanamycin. The present study has shown that bacterial isolates obtained from spontaneously fermented kale juice could constitute valuable probiotic starter cultures, which may be used in fermentation industry.

Microbial high throughput phenomics: The potential of an irreplaceable omics

The phenotype-genotype landscape is a projection coming from detailed phenotypic and genotypic data under environmental pressure. Although phenome of microbes or microbial consortia mirrors the functional expression of a genome or set of genomes, metabolic traits rely on the phenotype. Phenomics has the potential to revolution functional genomics. In this review, we discuss why and how phenomics was developed. We described how phenomics may extend our understanding of the assembly of microbial consortia and their functionality, and then we outlined the novel applications within the study of phenomes using Omnilog platform together with a revision of its current application to study lactic acid bacteria (LAB) metabolic traits during food processing. LAB were proposed as a suitable model system to analyze and discuss the implementation and exploitation of this emerging omics approach. We introduced the 'phenotype switching', as a new phenotype microarray approach to get insights in bacterial physiology. An overview of methodologies and tools to manage and analyze the generated data was provided. Finally, pro and cons of pipelines developed so far, including the most innovative ones were critically analyzed. We propose an R pipeline, recently deposited, which allows to automatically analyze Omnilog data integrating the latest approaches and implementing the new concepts described here.

Biotechnological re-cycling of apple by-products: A reservoir model to produce a dietary supplement fortified with biogenic phenolic compounds

This study is an example of apple by-products (AP) recycling through a designed fermentation by selected autochthonous Lactobacillus plantarum AFI5 and Lactobacillus fabifermentans ALI6 used singly or as binary cultures with the selected Saccharomyces cerevisiae AYI7. Compared to Raw-, Unstarted- and Chemically Acidified-AP, Fermented-AP promoted the highest levels of total and insoluble dietary fibers, DPPH scavenging capacity, and free phenolics. The binary culture of L. plantarum AFI5 and S. cerevisiae AYI7 had the best effect on the bioavailability phenolic compounds as resulted by the LC-MS/MS validated method. The accumulation of phenolic acids derivatives highlighted the microbial metabolism during AP fermentation. Bio-converted phenolics were likely responsible for the increased DPPH scavenging capacity. The potential health-promoting effects of Fermented-AP were highlighted using Caco-2 cells. With variations among single and binary cultures, fermented-AP counteracted the inflammatory processes and the effects of oxidative stress in Caco-2 cells, and preserved the integrity of tight junctions.

Transcriptomic Evidence of Molecular Mechanisms Underlying the Response of Lactobacillus Plantarum WCFS1 to Hydroxytyrosol

This study was aimed to gain new insights into the molecular mechanisms used by Lactobacillus plantarum WCFS1 to respond to hydroxytyrosol (HXT), one of the main and health-relevant plant phenolics present in olive oil. To this goal, whole genome transcriptomic profiling was used to better understand the contribution of differential gene expression in the adaptation to HXT by this microorganism. The transcriptomic profile reveals an HXT-triggered antioxidant response involving genes from the ROS (reactive oxygen species) resistome of L. plantarum, genes coding for H₂S-producing enzymes and genes involved in the response to thiol-specific oxidative stress. The expression of a set of genes involved in cell wall biogenesis was also upregulated, indicating that this subcellular compartment was a target of HXT. The expression of several MFS (major facilitator superfamily) efflux systems and ABC-transporters was differentially affected by HXT, probably to control its transport across the membrane. L. plantarum transcriptionally reprogrammed nitrogen metabolism and involved the stringent response (SR) to adapt to HXT, as indicated by the reduced expression of genes involved in cell proliferation or related to the metabolism of (p)ppGpp, the molecule that triggers the SR. Our data have identified, at genome scale, the antimicrobial mechanisms of HXT action as well as molecular mechanisms that potentially enable L. plantarum to cope with the effects of this phenolic compound.

Abundance, diversity and plant-specific adaptations of plant-associated lactic acid bacteria

Lactic acid bacteria (LAB) are essential for many fruit, vegetable and grain food and beverage fermentations. However, the numbers, diversity and plant-specific adaptions of LAB found on plant tissues prior to the start of those fermentations are not well understood. When measured, these bacteria have been recovered from the aerial surfaces of plants in a range from <10 CFU g^-1 to over 10^8.5 CFU g^-1 of plant tissue and in lower quantities from the soil and rhizosphere. Plant-associated LAB include well-known generalist taxa such as Lactobacillus plantarum and Leuconostoc mesenteroides, which are essential for numerous food and beverage fermentations. Other plant-associated LAB encompass specialist taxa such as Lactobacillus florum and Fructobacillus, many of which were discovered relatively recently and their significance on plants and in foods is not yet recognized. LAB recovered from plants possess the capacity to consume plant sugars, detoxify phenolic compounds and tolerate the numerous biotic and abiotic stresses common to plant surfaces. Although most generalist and some specialist LAB grow rapidly in food and beverages fermentations and can cause spoilage of fresh and fermented fruits and vegetables, the importance of living plants as habitats for these bacteria and LAB contributions to plant microbiomes remain to be shown.

Lactic Fermentation as a Strategy to Improve the Nutritional and Functional Values of Pseudocereals

One of the greatest challenges is to reduce malnutrition worldwide while promoting sustainable agricultural and food systems. This is a daunting task due to the constant growth of the population and the increasing demands by consumers for functional foods with higher nutritional values. Cereal grains are the most important dietary energy source globally; wheat, rice, and maize currently provide about half of the dietary energy source of humankind. In addition, the increase of celiac patients worldwide has motivated the development of gluten-free foods using alternative flour types to wheat such as rice, corn, cassava, soybean, and pseudocereals (amaranth, quinoa, and buckwheat). Amaranth and quinoa have been cultivated since ancient times and were two of the major crops of the Pre-Colombian cultures in Latin- America. In recent years and due to their well-known high nutritional value and potential health benefits, these pseudocereals have received much attention as ideal candidates for gluten-free products. The importance of exploiting these grains for the elaboration of healthy and nutritious foods has forced food producers to develop novel adequate strategies for their processing. Fermentation is one of the most antique and economical methods of producing and preserving foods and can be easily employed for cereal processing. The nutritional and functional quality of pseudocereals can be improved by fermentation using Lactic Acid Bacteria (LAB). This review provides an overview on pseudocereal fermentation by LAB emphasizing the capacity of these bacteria to decrease antinutritional factors such as phytic acid, increase the functional value of phytochemicals such as phenolic compounds, and produce nutritional ingredients such as B-group vitamins. The numerous beneficial effects of lactic fermentation of pseudocereals can be exploited to design novel and healthier foods or grain ingredients destined to general population and especially to patients with coeliac disease.

Transcriptomic approach and membrane fatty acid analysis to study the response mechanisms of Escherichia coli to thyme essential oil, carvacrol, 2-(E)-hexanal and citral exposure

AIMS

The application of essential oils (EOs) and their components as food preservatives is promising but requires a deeper understanding of their mechanisms of action. This study aims to evaluate the effects of thyme EO, carvacrol, citral and 2-(E)-hexenal, on whole-genome gene expression (the transcriptome), as well as the fatty acid (FA) composition of the cell membranes of Escherichia coli K12.

METHODS AND RESULTS

Therefore, we studied the response against 1 h of exposure to sublethal concentrations of natural antimicrobials, of exponentially growing E. coli K12, using DNA microarray technology and a gas chromatographic method. The results show that treatment with a sublethal concentration of the antimicrobials strongly affects global gene expression in E. coli for all antimicrobials used. Major changes in the expression of genes involved in metabolic pathways as well as in FA biosynthesis and protection against oxidative stress were evidenced. Moreover, the sublethal treatments resulted in increased levels of unsaturated and cyclic FAs as well as an increase in the chain length compared to the controls.

CONCLUSIONS

The down-regulation of genes involved in aerobic metabolism indicates a shift from respiration to fermentative growth. Moreover, the results obtained suggest that the cytoplasmic membrane of E. coli is the major cellular target of EOs and their components. In addition, the key role of membrane unsaturated FAs in the response mechanisms of E. coli to natural antimicrobials has been confirmed in this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

The transcriptomic data obtained signify a further step to understand the mechanisms of action of natural antimicrobials also when sublethal concentrations and short-term exposure. In addition, this research goes in deep correlating the transcriptomic modification with the changes in E. coli FA composition of cell membrane identified as the main target of the natural antimicrobials.

Carrot Juice Fermentations as Man-Made Microbial Ecosystems Dominated by Lactic Acid Bacteria

Spontaneous vegetable fermentations, with their rich flavors and postulated health benefits, are regaining popularity. However, their microbiology is still poorly understood, therefore raising concerns about food safety. In addition, such spontaneous fermentations form interesting cases of man-made microbial ecosystems. Here, samples from 38 carrot juice fermentations were collected through a citizen science initiative, in addition to three laboratory fermentations. Culturing showed that Enterobacteriaceae were outcompeted by lactic acid bacteria (LAB) between 3 and 13 days of fermentation. Metabolite-target analysis showed that lactic acid and mannitol were highly produced, as well as the biogenic amine cadaverine. High-throughput 16S rRNA gene sequencing revealed that mainly species of Leuconostoc and Lactobacillus (as identified by 8 and 20 amplicon sequence variants [ASVs], respectively) mediated the fermentations in subsequent order. The analyses at the DNA level still detected a high number of Enterobacteriaceae, but their relative abundance was low when RNA-based sequencing was performed to detect presumptive metabolically active bacterial cells. In addition, this method greatly reduced host read contamination. Phylogenetic placement indicated a high LAB diversity, with ASVs from nine different phylogenetic groups of the Lactobacillus genus complex. However, fermentation experiments with isolates showed that only strains belonging to the most prevalent phylogenetic groups preserved the fermentation dynamics. The carrot juice fermentation thus forms a robust man-made microbial ecosystem suitable for studies on LAB diversity and niche specificity.

IMPORTANCE The usage of fermented food products by professional chefs is steadily growing worldwide. Meanwhile, this interest has also increased at the household level. However, many of these artisanal food products remain understudied. Here, an extensive microbial analysis was performed of spontaneous fermented carrot juices which are used as nonalcoholic alternatives for wine in a Belgian Michelin star restaurant. Samples were collected through an active citizen science approach with 38 participants, in addition to three laboratory fermentations. Identification of the main microbial players revealed that mainly species of Leuconostoc and Lactobacillus mediated the fermentations in subsequent order. In addition, a high diversity of lactic acid bacteria was found; however, fermentation experiments with isolates showed that only strains belonging to the most prevalent lactic acid bacteria preserved the fermentation dynamics. Finally, this study showed that the usage of RNA-based 16S rRNA amplicon sequencing greatly reduces host read contamination.

Transcriptional Reprogramming at Genome-Scale of Lactobacillus plantarum WCFS1 in Response to Olive Oil Challenge

Dietary fats may exert selective pressures on Lactobacillus species, however, knowledge on the mechanisms of adaptation to fat stress in these organisms is still fragmentary. This study was undertaken to gain insight into the mechanisms of adaptation of Lactobacillus plantarum WCFS1 to olive oil challenge by whole genome transcriptional profiling using DNA microarrays. A set of 230 genes were differentially expressed by L. plantarum WCFS1 to respond to this vegetable oil. This response involved elements typical of the stringent response, as indicated by the induction of genes involved in stress-related pathways and downregulation of genes related to processes associated with rapid growth. A set of genes involved in the transport and metabolism of compatible solutes were downregulated, indicating that this organism does not require osmoprotective mechanisms in presence of olive oil. The fatty acid biosynthetic pathway was thoroughly downregulated at the transcriptional level, which coincided with a diminished expression of genes controlled by this pathway in other organisms and that are required for the respiratory function, pyruvate dehydrogenase activity, RNA processing and cell size setting. Finally, a set of genes involved in host-cell signaling by L. plantarum were differentially regulated indicating that olive oil can influence the expression of metabolic traits involved in the crosstalk between this bacterium and the host.

Next-generation sequencing approaches for improvement of lactic acid bacteria-fermented plant-based beverages

Plant-based beverages and milk alternatives produced from cereals and legumes have grown in popularity in recent years due to a range of consumer concerns over dairy products. These plant-based products can often have undesirable physiochemical properties related to flavour, texture, and nutrient availability and/or deficiencies. Lactic acid bacteria (LAB) fermentation offers potential remediation for many of these issues, and allows consumers to retain their perception of the resultant products as natural and additive-free. Using next-generation sequencing (NGS) or omics approaches to characterize LAB isolates to find those that will improve properties of plant-based beverages is the most direct way to product improvement. Although NGS/omics approaches have been extensively used for selection of LAB for use in the dairy industry, a comparable effort has not occurred for selecting LAB for fermenting plant raw substrates, save those used in producing wine and certain types of beer. Here we review the few and recent applications of NGS/omics to profile and improve LAB fermentation of various plant-based substrates for beverage production. We also identify specific issues in the production of various LAB fermented plant-based beverages that such NGS/omics applications have the power to resolve.