Genome-wide transcriptomic responses of a human isolate of Lactobacillus plantarum exposed to p-coumaric acid stress

Honey Varietals Differentially Impact Bifidobacterium animalis ssp. lactis Survivability in Yogurt through Simulated In Vitro Digestion

BACKGROUND

Bifidobacterium animalis ssp. lactis DN-173 010/CNCM I-2494 (B. animalis) is a probiotic strain commonly added to yogurt. Yogurt and honey are a popular culinary pairing. Honey improves bifidobacteria survival in vitro. However, probiotic survival in yogurt with honey during in vitro digestion has not been investigated.

OBJECTIVES

The study aimed to evaluate the effects of different honey varietals and concentrations on B. animalis survivability in yogurt through in vitro digestion.

METHODS

Yogurt with honey or control-treated samples underwent in vitro simulated oral, gastric, and intestinal digestion. B. animalis cells were enumerated on de Man Rogosa and Sharpe (MRS) medium followed by an overlay with a modified selective MRS medium; all underwent anaerobic incubation. B. animalis were enumerated predigestion and after oral, gastric, and intestinal digestion. There were 2 study phases: Phase 1 tested 4 honey varietals at 20% wt/wt per 170 g yogurt, and Phase 2 tested 7 dosages of clover honey (20, 14, 10, 9, 8, 6, and 4% wt/wt) per 170 g yogurt.

RESULTS

Similar B. animalis counts were observed between all treatments after oral and gastric digestion (<1 Log colony forming units (CFU)/g probiotic reduction). Higher B. animalis survivability was observed in yogurt with clover honey after exposure to simulated intestinal fluids (∼3.5 Log CFU/g reduction; P < 0.05) compared to all control treatments (∼5.5 Log CFU/g reduction; P < 0.05). Yogurt with 10-20% wt/wt clover honey increased B. animalis survivability after simulated in vitro digestion (≤ ∼4.7 Log CFU/g survival; P < 0.05).

CONCLUSIONS

Yogurt with added honey improves probiotic survivability during in vitro digestion. The effective dose of clover honey in yogurt was 10-20% wt/wt per serving (1-2 tablespoons per 170 g yogurt) for increased probiotic survivability during in vitro digestion.

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.

Impact of Lactic Acid Bacteria Fermentation on Phenolic Compounds and Antioxidant Activity of Avocado Leaf Extracts

The growing global consumption of avocados, associated with contents including bioactive compounds with numerous health-promoting properties, is producing a large amount of agro wastes around the world. Different management approaches are available for the recovery of bioactive compounds from wastes as potential ingredients for use in the production of functional foods and nutraceuticals. Lactic acid fermentation can be used to exploit nutritional potential and add value to agro wastes. In this study, fermentations with lactic acid bacteria were carried out in avocado leaves, and the total phenolic content and the antioxidant activity were determined by DPPH and FRAP assays from hydroalcoholic extracts obtained from fermented avocado leaves. Fifteen new phenolic compounds were identified for the first time in avocado leaves by HPLC-ESI-TOF-MS. L. plantarum CECT 748T and P. pentosaceus CECT 4695T showed the highest antioxidant activity. The sum of phenolic compounds was increased by 71, 62, 55 and 21% in fermentations with P. pentosaceus CECT 4695T, L. brevis CECT 5354, P. acidilactici CECT 5765T and L. plantarum CECT 9567, respectively, while it was reduced in the fermentation with L. plantarum 748T by 21% as demonstrated by HPLC-ESI-TOF-MS. Biotransformations induced by bacterial metabolism modified the phenolic compound profile of avocado leaves in a strain-specific-dependent manner. P. pentosaceus CECT 4695T significantly increased kaempferol, P. pentosaceus 4695T, L. brevis 5354 and L. plantarum 9567 increased rutin, and dihydro-p-coumaric acid was increased by the five selected lactic acid bacteria. Total flavonoids were highly increased after fermentations with the five selected lactic acid bacteria but flavonoid glucosides were decreased by L. plantarum 748T, which was related to its higher antioxidant activity. Our results suggest that lactic acid bacteria led the hydrolysis of compounds by enzymatic activity such as glycosidases or decarboxylase and the release of phenolics bound to the plant cell wall, thus improving their bioavailability.

Global transcriptomic response of Escherichia coli to p-coumaric acid

The aromatic compound p-coumaric acid (p-CA) is a secondary metabolite produced by plants. This aromatic acid and derived compounds have positive effects on human health, so there is interest in producing them in biotechnological processes with recombinant Escherichia coli strains. To determine the physiologic response of E. coli W3110 to p-CA, dynamic expression analysis of selected genes fused to a fluorescent protein reporter as well as RNA-seq and RT-qPCR were performed. The observed transcriptional profile revealed the induction of genes involved in functions related to p-CA active export, synthesis of cell wall and membrane components, synthesis of amino acids, detoxification of formaldehyde, phosphate limitation, acid stress, protein folding and degradation. Downregulation of genes encoding proteins involved in energy production, carbohydrate import and metabolism, as well as several outer and plasma membrane proteins was detected. This response is indicative of cell envelope damage causing the leakage of intracellular components including amino acids and phosphate-containing compounds. The cellular functions responding to p-CA that were identified in this study will help in defining targets for production strains improvement.

Molecular Responses of Lactobacilli to Plant Phenolic Compounds: A Comparative Review of the Mechanisms Involved

Lactobacilli are well-studied bacteria that can undergo oxidative selective pressures by plant phenolic compounds (PPCs) in plants, during some food fermentations or in the gastrointestinal tract of animals via dietary inputs. Lactobacilli are known to be more tolerant to PPCs than other bacterial groups and, therefore, must have mechanisms to cope with the effects of these metabolites. In this review, we intend to present what is currently known about the basics beyond the responses of Lactobacillus spp. to individual PPCs. We review the molecular mechanisms that are engaged in the PPC-modulated responses studied to date in these bacteria that have been mainly characterized by system-based strategies, and we discuss their differences and similarities. A wide variety of mechanisms are induced to increase the oxidative stress response highlighting the antimicrobial nature of PPCs. However other uncovered mechanisms that are involved in the response to these compounds are reviewed, including the capacity of PPCs to modulate the expression of molecular functions used by lactobacilli to adapt to host environments. This shows that these phytochemicals can act as more than just antimicrobial agents in the dual interaction with lactobacilli.

Lactiplantibacillus plantarum-Nomad and Ideal Probiotic

Probiotics are increasingly recognized as capable of positively modulating several aspects of human health. There are numerous attributes that make an ideal probiotic. Lactiplantibacillus plantarum (Lp) exhibits an ecological and metabolic flexibility that allows it to thrive in a variety of environments. The present review will highlight the genetic and functional characteristics of Lp that make it an ideal probiotic and summarizes the current knowledge about its potential application as a prophylactic or therapeutic intervention.

Controlled fermentation of curly kale juice with the use of autochthonous starter cultures

The aim of this paper was to evaluate the influence of different indigenous lactic acid bacteria isolates - as a single culture or bacterial consortium - on the functional and physicochemical properties of fermented curly kale juice. All tested variants exhibited good growth parameters, manifested by efficient pH lowering, increases in acidity, and fructose and glucose metabolism, as well as a significant inhibition of pathogens. A slight increase in total phenolic content was observed, while antioxidant activity remained unchanged. L. sakei and MIX A were associated with an increase in riboflavin and pyridoxine content, while L. plantarum only contributed to an increase in vitamin B₆ content. Bioconversion of individual phenolic compounds, carotenoids, and glucosinolates strongly depended on the strain-specific metabolism. In the process, the levels of ferulic acid and other hydroxycinnamic acids were maintained, while the content of 9-cis lutein increased. Considering presented results and our previous research regarding probiotic features of LAB strains, among tested starter cultures - L. plantarum seemed to possess the best characteristics as a potential starter culture for controlled fermentation of curly kale juice.

Utilization of Oenococcus oeni strains to ferment grape juice: Metabolic activities and beneficial health potential

This study aimed to investigate the behavior of Oenococcus oeni MS9 and MS46 strains in sterile grape juice (SGJ, pH 4.0) incubated at 30 °C, in terms of growth and glucose, organic acids and total phenolic compounds utilization. In addition, their antimicrobial activity and the changes in antioxidant properties of fermented juice with selected strain were evaluated. Both strains grew without lag period by ~1.40 log CFU/mL at 12 days with maximum growth rates of about 0.019 h^-1. After this time the MS9 and MS46 strains counts declined by 0.6 log units and remained unchanged respectively. O. oeni MS46 was evaluated in SGJ for low inoculum size (~10⁴ CFU/mL). In this condition it also grew without lag period by 3.11 ± 0.01 log CFU/mL with a μmax of 0.05 h^-1. Glucose and L-malic and citric acids were simultaneously utilized but at different rates and extents, yielding mainly lactic acid with concomitant pH reduction. Acetic acid ranged between 11 and 19 mmol/L. Total phenolic compounds significantly decreased in fermented SGJ with strain MS9 but not MS46. In this last condition, the antioxidant activity increased by 21%. In addition, both O. oeni strains showed antibacterial properties against Escherichia coli 700, Salmonella Typhimurium and Listeria monocytogenes. O. oeni strains, especially MS46, with the ability to growth in SGJ, high malolactic potential and adequate sugars and organic acids profiles from the sensorial viewpoint may be used to ferment grape juice with safer and healthier properties than fresh juice.

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.

Buckwheat Secondary Metabolites: Potential Antifungal Agents

Research groups have put significant emphasis on the evaluation of nutritional, health-promoting, and other biological activities of secondary metabolites from buckwheat. Among these phytochemicals, phenolic and lipophilic antioxidants, particularly, phenolic acids, flavonoids, and tocopherols, have been the focus of the latest studies since antioxidant activity has recently been associated with the possibility of inhibiting fungal growth and mycotoxin biosynthesis. The mycotoxin contamination of cereal and pseudocereal grains caused primarily by Fusarium, Penicillium, and Aspergillus species poses a significant hazard to human health. Therefore, efforts to examine the involvement of plant antioxidants in the biosynthesis of mycotoxins at the transcriptional level have emerged. In addition, hydrophobic interactions of buckwheat phenolics with cell membranes could also explain their capacity to reduce fungal development. Eventually, possibilities of enhancing the biological activity of cereal and pseudocereal phytochemicals have been studied, and sourdough fermentation has been proposed as an efficient method to increase antioxidant activities. This effect could result in an increased antifungal effects of sourdough and bakery products. This review reports the main advances in research on buckwheat phenolics and other antioxidant phytochemicals, highlighting possible mechanisms of action and processes that could improve their biological activities.

The role of microorganisms on biotransformation of brewers' spent grain

Brewers' spent grain (BSG) is the most abundant by-product of brewing. Due to its microbiological instability and high perishability, fresh BSG is currently disposed of as low-cost cattle feed. However, BSG is an appealing source of nutrients to obtain products with high added value through microbial-based transformation. As such, BSG could become a potential source of income for the brewery itself. While recent studies have covered the relevance of BSG chemical composition in detail, this review aims to underline the importance of microorganisms from the stabilization/contamination of fresh BSG to its biotechnological exploitation. Indeed, the evaluation of BSG-associated microorganisms, which include yeast, fungi, and bacteria, can allow their safe use and the best methods for their exploitation. This bibliographical examination is particularly focused on the role of microorganisms in BSG exploitation to (1) produce enzymes and metabolites of industrial interest, (2) supplement human and animal diets, and (3) improve soil fertility. Emerging safety issues in the use of BSG as a food and feed additive is also considered, particularly considering the presence of mycotoxins.Key points• Microorganisms are used to enhance brewers' spent grain nutritional value.• Knowledge of brewers' spent grain microbiota allows the reduction of health risks. Graphical abstract.

Mutual influence of polyphenols and Lactobacillus spp. bacteria in food: a review

This paper presents the effect of polyphenols on microorganisms inhabiting the human gastrointestinal tract (mainly bacteria belonging to the Lactobacillus genus) and pathogenic microorganisms classified as the most common food contaminants. Plant secondary metabolites have the ability to modulate the growth of many microorganisms. Due to the metabolic changes induced by their presence in the environment, many pathogenic microorganisms are unable to grow, which in turn cause a significant reduction in their pathogenic potential. These processes include primarily the induction of ruptures in the cell membrane and disturbance of cell respiration. Often, the lack of integrity of cell membranes also leads to the disturbance of intracellular homeostasis and leakage of cellular components, such as proteins, ATP molecules or intracellular ions. Autoxidizing polyphenols also act as pro-oxidative substances. Hydrogen peroxide formed in the process of oxidation of polyphenolic compounds acts as a bactericidal substance (by induction of DNA breaks). With regard to intestinal microbiota, polyphenols are considered prebiotic substances that increase the number of commensal bacteria. They can positively influence the growth of Lactobacillus bacteria, which have the ability to metabolize undigested antioxidants in the digestive tract of humans and animals. Depending on the pH of the environment and the presence of ions, plant polyphenols in the human digestive tract can act as substances with antioxidant potential or become pro-oxidants. Thus, combining functional food with polyphenols and Lactobacillus bacteria not only protects food products against the development of undesirable and pathogenic microbiota, but also has a positive effect on human health. The paper also describes the possibility of changes in the genome of Lactobacillus bacteria (under the influence of polyphenols) and the influence of Lactobacillus spp. bacteria on the antimicrobial properties of polyphenols. The enzymatic abilities of bacteria of the genus Lactobacillus, which influence the transformation of polyphenolic compounds, were also described.

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.

Genetic Determinants of Hydroxycinnamic Acid Metabolism in Heterofermentative Lactobacilli

Phenolic acids are among the most abundant phenolic compounds in edible parts of plants. Lactic acid bacteria (LAB) metabolize phenolic acids, but the enzyme responsible for reducing hydroxycinnamic acids to phenylpropionic acids (HcrB) was only recently characterized in Lactobacillus plantarum In this study, heterofermentative LAB species were screened for their hydroxycinnamic acid metabolism. Data on strain-specific metabolism in combination with comparative genomic analyses identified homologs of HcrB as putative phenolic acid reductases. Par1 and HcrF both encode putative multidomain proteins with 25% and 63% amino acid identity to HcrB, respectively. Of these genes, par1 in L. rossiae and hcrF in L. fermentum were overexpressed in response to hydroxycinnamic acids. The deletion of par1 in L. rossiae led to the loss of phenolic acid metabolism. The strain-specific metabolism of phenolic acids was congruent with the genotype of lactobacilli; however, phenolic acid reductases were not identified in strains of Weissella cibaria that reduced hydroxycinnamic acids to phenylpropionic acids. Phylogenetic analysis of major genes involved in hydroxycinnamic acid metabolism in strains of the genus Lactobacillus revealed that Par1 was found to be the most widely distributed phenolic acid reductase, while HcrB was the least abundant, present in less than 9% of Lactobacillus spp. In conclusion, this study increased the knowledge on the genetic determinants of hydroxycinnamic acid metabolism, explaining the species- and strain-specific metabolic variations in lactobacilli and providing evidence of additional enzymes involved in hydroxycinnamic acid metabolism of lactobacilli.IMPORTANCE The metabolism of secondary plant metabolites, including phenolic compounds, by food-fermenting lactobacilli is a significant contributor to the safety, quality, and nutritional quality of fermented foods. The enzymes mediating hydrolysis, reduction, and decarboxylation of phenolic acid esters and phenolic acids in lactobacilli, however, are not fully characterized. The genomic analyses presented here provide evidence for three novel putative phenolic acid reductases. Matching comparative genomic analyses with phenotypic analysis and quantification of gene expression indicates that two of the three putative phenolic acid reductases, Par1 and HcrF, are involved in reduction of hydroxycinnamic acids to phenylpropionic acids; however, the activity of Par2 may be unrelated to phenolic acids and recognizes other secondary plant metabolites. These findings expand our knowledge on the metabolic potential of lactobacilli and facilitate future studies on activity and substrate specificity of enzymes involved in metabolism of phenolic compounds.

Oleuropein Transcriptionally Primes Lactobacillus plantarum to Interact With Plant Hosts

Oleuropein (OLE) is a secoiridoid unique to Oleaceae known to play a role in the plant–herbivore interaction. However, it is not clear how this molecule is induced to mediate plant responses to microbes and how microbes, in turn, withstand with OLE. To better understand how OLE affects the plant–microbe interaction, the contribution of differential gene expression in the adaptation to OLE was characterized by whole genome transcriptional profiling in Lactobacillus plantarum, a bacterium associated to the olive. OLE downregulated functions associated to rapid growth, remodeled membrane phospholipid biosynthesis pathways and markedly repressed the expression of several ABC transporters from L. plantarum. Genes encoding the plantaricin and lamABDCA quorum-sensing (QS) systems were down-regulated indicating the potential of OLE as a QS-antagonist. Notably, OLE diminished the expression of a set of genes encoding inmunomodulatory components and reoriented metabolic pathways to increase protein acetylation, probably to attenuate plant immunity. Responses were also triggered to repress the transport of acetoin and to buffer reactive oxygen species accumulation, two signals involved in plant development. The results suggest that OLE could act as a signaling molecule in the plant–microbe interaction and facilitate the accommodation of beneficial microbes such as L. plantarum by the plant host, via controlled expression of bacterial molecular players involved in this reciprocal interplay.

Ethylphenol Formation by Lactobacillus plantarum: Identification of the Enzyme Involved in the Reduction of Vinylphenols

Ethylphenols are strong odorants produced by microbial activity that are described as off flavors in several foods. Lactobacillus plantarum is a lactic acid bacterial species able to produce ethylphenols by the reduction of vinylphenols during the metabolism of hydroxycinnamic acids. However, the reductase involved has not been yet uncovered. In this study, the involvement in vinylphenol reduction of a gene encoding a putative reductase (lp_3125) was confirmed by the absence of reduction activity in the Δlp_3125 knockout mutant. The protein encoded by lp_3125, VprA, was recombinantly produced in Escherichia coli VprA was assayed against vinylphenols (4-vinylphenol, 4-vinylcatechol, and 4-vinylguaiacol), and all were reduced to their corresponding ethylphenols (4-ethylphenol, 4-ethylcatechol, and 4-ethylguaiacol). PCR and high-performance liquid chromatography (HPLC) detection methods revealed that the VprA reductase is not widely distributed among the lactic acid bacteria studied and that only the bacteria possessing the vprA gene were able to produce ethylphenol from vinylphenol. However, all the species belonging to the L. plantarum group were ethylphenol producers. The identification of the L. plantarum VprA protein involved in hydroxycinnamate degradation completes the route of degradation of these compounds in lactic acid bacteria.IMPORTANCE The presence of volatile phenols is considered a major organoleptic defect of several fermented alcoholic beverages. The biosynthesis of these compounds has been mainly associated with Brettanomyces/Dekkera yeasts. However, the potential importance of lactic acid bacteria in volatile phenol spoilage is emphasized by reports describing a faster ethylphenol production by these bacteria than by yeasts. The genetic identification of the bacterial vinylphenol reductase involved in volatile phenol production provides new insights into the role of lactic acid bacteria in the production of these off flavors. The development of a molecular method for the detection of ethylphenol-producing bacteria could be helpful to design strategies to reduce the bacterial production of vinylphenols in fermented foods.

Unravelling the Reduction Pathway as an Alternative Metabolic Route to Hydroxycinnamate Decarboxylation in Lactobacillus plantarum

Lactobacillus plantarum is the lactic acid bacterial species most frequently found in plant-food fermentations where hydroxycinnamic acids are abundant. L. plantarum efficiently decarboxylates these compounds and also reduces them, yielding substituted phenylpropionic acids. Although the reduction step is known to be induced by a hydroxycinnamic acid, the enzymatic machinery responsible for this reduction pathway has not been yet identified and characterized. A previous study on the transcriptomic response of L. plantarum to p-coumaric acid revealed a marked induction of two contiguous genes, lp_1424 and lp_1425, encoding putative reductases. In this work, the disruption of these genes abolished the hydroxycinnamate reductase activity of L. plantarum, supporting their involvement in such chemical activity. Functional in vitro studies revealed that Lp_1425 (HcrB) exhibits hydroxycinnamate reductase activity but was unstable in solution. In contrast, Lp_1424 (HcrA) was inactive but showed high stability. When the hcrAB genes were co-overexpressed, the formation of an active heterodimer (HcrAB) was observed. Since L. plantarum reductase activity was only observed on hydroxycinnamic acids (o-coumaric, m-coumaric, p-coumaric, caffeic, ferulic, and sinapic acids), the presence of a hydroxyl group substituent on the benzene ring appears to be required for activity. In addition, hydroxycinnamate reductase activity was not widely present among lactic acid bacteria, and it was associated with the presence of hcrAB genes. This study revealed that L. plantarum hydroxycinnamate reductase is a heterodimeric NADH-dependent coumarate reductase acting on a carbon-carbon double bond.IMPORTANCELactobacillus plantarum is a bacterial species frequently found in the fermentation of vegetables where hydroxycinnamic acids are present. The bacterial metabolism on these compounds during fermentation plays a fundamental role in the biological activity of hydroxycinnamates. L. plantarum strains exhibit an as yet unknown reducing activity, transforming hydroxycinnamates to substituted phenylpropionic acids, which possess higher antioxidant activity than their precursors. The protein machinery involved in hydroxycinnamate reduction, HcrAB, was genetically identified and characterized. The heterodimeric NADH-dependent coumarate reductase HcrAB described in this work provides new insights on the L. plantarum metabolic response to counteract the stressful conditions generated by food phenolics.

Transcriptome-Based Analysis in Lactobacillus plantarum WCFS1 Reveals New Insights into Resveratrol Effects at System Level

SCOPE

This study was undertaken to expand our insights into the mechanisms involved in the tolerance to resveratrol (RSV) that operate at system-level in gut microorganisms and advance knowledge on new RSV-responsive gene circuits.

METHODS AND RESULTS

Whole genome transcriptional profiling was used to characterize the molecular response of Lactobacillus plantarum WCFS1 to RSV. DNA repair mechanisms were induced by RSV and responses were triggered to decrease the load of copper, a metal required for RSV-mediated DNA cleavage, and H₂ S, a genotoxic gas. To counter the effects of RSV, L. plantarum strongly up- or downregulated efflux systems and ABC transporters pointing to transport control of RSV across the membrane as a key mechanism for RSV tolerance. L. plantarum also downregulated tRNAs, induced chaperones, and reprogrammed its transcriptome to tightly control ammonia levels. RSV induced a probiotic effector gene and a likely deoxycholate transporter, two functions that improve the host health status.

CONCLUSION

Our data identify novel protective mechanisms involved in RSV tolerance operating at system level in a gut microbe. These insights could influence the way RSV is used for a better management of gut microbial ecosystems to obtain associated health benefits.

Barleria cristata: perspective towards phytopharmacological aspects

OBJECTIVES

Barleria cristata (Family: Acanthaceae), commonly known as Philippine violet, is used in different ethnomedical systems for the treatment of a wide range of ailments. This review aimed to provide a scientific overview of B. cristata with reference to its ethnobotanical aspects, geographical distribution, medicinal uses, phytochemistry and pharmacological activity, and critical analyses research gaps and future research opportunities for investigations on this plant.

KEY FINDINGS

Ethnomedical uses of the plant have been observed in lungs disorders, inflammatory conditions, toothache, anaemia, snake bite, diabetes and tuberculosis. The exhaustive bibliographic research carried out on this plant revealed that the plant parts are rich in various phytochemical constituents including triterpenes, phenolic compounds, glycosides and flavonoids type phenolic compounds. Furthermore, the plant was also investigated in terms of its anti-inflammatory, antibacterial, antidiabetic, antifungal, hepatoprotective and antioxidant activity.

CONCLUSIONS

This review confirms that B. cristata is a potential herb for the treatment of a wide range of diseases especially lung disorders and inflammatory conditions. Modern pharmacological studies have also validated many ethnobotanical uses of B. cristata, though data regarding many aspects of this plant such as mechanism of action, adverse effects of extracts and active compounds are still limited which call for additional studies.

Early Transcriptome Response of Lactococcus lactis to Environmental Stresses Reveals Differentially Expressed Small Regulatory RNAs and tRNAs

Bacteria can deploy various mechanisms to combat environmental stresses. Many genes have previously been identified in Lactococcus lactis that are involved in sensing the stressors and those that are involved in regulating and mounting a defense against the stressful conditions. However, the expression of small regulatory RNAs (sRNAs) during industrially relevant stress conditions has not been assessed yet in L. lactis, while sRNAs have been shown to be involved in many stress responses in other bacteria. We have previously reported the presence of hundreds of putative regulatory RNAs in L. lactis, and have used high-throughput RNA sequencing (RNA-seq) in this study to assess their expression under six different stress conditions. The uniformly designed experimental set-up enabled a highly reliable comparison between the different stress responses and revealed that many sRNAs are differentially expressed under the conditions applied. The primary stress responses of L. lactis NCDO712 was benchmarked to earlier work and, for the first time, the differential expression was assessed of transfer RNAs (tRNAs) and the genes from the six recently sequenced plasmids of NCDO712. Although, we only applied stresses for 5 min, the majority of the well-known specific stress-induced genes are already differentially expressed. We find that most tRNAs decrease after all stresses applied, except for a small number, which are increased upon cold stress. Starvation was shown to induce the highest differential response, both in terms of number and expression level of genes. Our data pinpoints many novel stress-related uncharacterized genes and sRNAs, which calls for further assessment of their molecular and cellular function. These insights furthermore could impact the way parameters are designed for bacterial culture production and milk fermentation, as we find that very short stress conditions already greatly alter gene expression.

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.

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

Lactobacillus plantarum has been isolated from a large variety of ecological niches, thus highlighting its remarkable environmental adaptability as a generalist. Plant fermentation conditions markedly affect the functional features of L. plantarum strains. We investigated the plant niche-specific traits of L. plantarum through whole-transcriptome and phenotypic microarray profiles. Carrot (CJ) and pineapple (PJ) juices were chosen as model systems, and MRS broth was used as a control. A set of 3,122 genes was expressed, and 21 to 31% of genes were differentially expressed depending on the plant niche and cell physiological state. L. plantarum C2 seemed to specifically respond to plant media conditions. When L. plantarum was cultured in CJ, useful pathways were activated, which were aimed to sense the environment, save energy and adopt alternative routes for NAD⁺ regeneration. In PJ the acidic environment caused a transcriptional switching, which was network-linked to an acid tolerance response involving carbohydrate flow, amino acid and protein metabolism, pH homeostasis and membrane fluidity. The most prominent phenotypic dissimilarities observed in cells grown in CJ and PJ were related to carbon and nitrogen metabolism, respectively. Summarising, a snapshot of a carrot and pineapple sensing and adaptive regulation model for L. plantarum C2 was proposed.

Molecular adaptation of Lactobacillus plantarum WCFS1 to gallic acid revealed by genome-scale transcriptomic signature and physiological analysis

Background

Gallic acid (GA) is a model hydroxybenzoic acid that occurs esterified in the lignocellulosic biomass of higher plants. GA displays relevant biological activities including anticancer properties. Owing to its antimicrobial and cellulase-inhibiting activities, GA also imposes constraints to the fermentability of lignocellulosic hydrolysates. In depth-knowledge of the mechanisms used by tolerant microorganisms to adapt to hydroxybenzoic acids would be a step forward to improve the bioavailability of GA or select/engineer production hosts with improved metabolic traits for the bioconversion of pretreated lignocellulosic biomass.

Results

Whole genome transcriptional profiling using DNA microarrays was used to characterize the molecular response of Lactobacillus plantarum WCFS1 to GA. Expression levels of 14 and 40 genes were differentially regulated at 1.5 and 15 mM GA, respectively. The transcriptomic analysis identified a marked induction of genes with confirmed or related roles to gastrointestinal survival, the repression of genes coding for certain ABC-type transporters and modulation of genes involved in the control of intracellular ammonia levels, among other responses. Most notably, a core set of genes dedicated to produce GA from polyphenols (tanB_Lp), decarboxylate GA to pyrogallol (lpdB, lpdC and lpdD) and transport functions (lp_2943) was highly overexpressed at both GA concentrations. Correspondingly, resting cells of strain WCFS1 induced by GA, but not their non-induced controls, produced pyrogallol. Gene expression and organization of genes involved in GA metabolism suggested a chemiosmotic mechanism of energy generation. Resting cells of L. plantarum induced by GA generated a membrane potential and a pH gradient across the membrane immediately upon addition of GA. Altogether, transcriptome profiling correlated with physiological observations indicating that a proton motive force could be generated during GA metabolism as a result of electrogenic GA uptake coupled with proton consumption by the intracellular gallate decarboxylase.

Conclusions

The combination of transcriptome and physiological analyses revealed versatile molecular mechanisms involved in the adaptation of L. plantarum to GA. These data provide a platform to improve the survival of Lactobacillus in the gut. Our data may also guide the selection/engineering of microorganisms that better tolerate phenolic inhibitors present in pretreated lignocellulosic feedstocks.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0345-y) contains supplementary material, which is available to authorized users.

Analysis of Clostridium beijerinckii NCIMB 8052's transcriptional response to ferulic acid and its application to enhance the strain tolerance

BACKGROUND

Plant-based cellulose presents the best source of renewable sugars for biofuel production. However, the lignin associated with plant cellulose presents a hurdle as hydrolysis of this component leads to the production of inhibitory compounds, such as ferulic acid.

RESULTS

The impacts of ferulic acid, a phenolic compound commonly found in lignin hydrolysates, on the growth, solvent production, and transcriptional responses of Clostridium beijerinckii NCIMB 8052 were determined. Addition of ferulic acid to growing cultures resulted in a decrease in the growth and solvent production by 30% and 25%, respectively, when compared to the control cultures. To better understand the toxicity of this compound, microarray analyses were performed using samples taken from these cultures at three different growth states. Several gene ontology terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified showing significant change at each status, including ATP-binding cassette (ABC) transporters, two component system, and oxidoreductase activity. Moreover, genes related with efflux systems and heat shock proteins were also strongly up-regulated. Among these, expression of the groESL operon was induced by more than fourfold and was consequently selected to improve C. beijerinckii tolerance to ferulic acid. Real-time quantitative PCR (RT-qPCR) analysis confirmed that C. beijerinckii harboring the plasmid, pSAAT-ptb_Gro, had a two- to fivefold increased groESL operon expression during growth of these cultures. Moreover, this strain was more tolerant to ferulic acid as the growth of this recombinant strain and its bioconversion of glucose into solvents were both improved.

CONCLUSIONS

Using transcriptomics, we identified numerous genes that are differentially expressed when C. beijerinckii cultures were exposed to ferulic acid for varying amounts of time. The operon expressing groESL was consistently up-regulated, suggesting that this gene cluster may contribute to strain tolerance. This was confirmed as recombinant cultures showed both an enhanced growth and solvent yield in the presence of 0.5 g/L ferulic acid.

Functional genomics of lactic acid bacteria: from food to health

Genome analysis using next generation sequencing technologies has revolutionized the characterization of lactic acid bacteria and complete genomes of all major groups are now available. Comparative genomics has provided new insights into the natural and laboratory evolution of lactic acid bacteria and their environmental interactions. Moreover, functional genomics approaches have been used to understand the response of lactic acid bacteria to their environment. The results have been instrumental in understanding the adaptation of lactic acid bacteria in artisanal and industrial food fermentations as well as their interactions with the human host. Collectively, this has led to a detailed analysis of genes involved in colonization, persistence, interaction and signaling towards to the human host and its health. Finally, massive parallel genome re-sequencing has provided new opportunities in applied genomics, specifically in the characterization of novel non-GMO strains that have potential to be used in the food industry. Here, we provide an overview of the state of the art of these functional genomics approaches and their impact in understanding, applying and designing lactic acid bacteria for food and health.

Polyphenols from olive mill waste affect biofilm formation and motility in Escherichia coli K-12

Olive mill wastes are sources of phenolic compounds with a wide array of biological activities, including antimicrobial effects. A potential option for bioremediation to overcome ecological problems is the reutilization of these natural compounds in food production. The aim of this work was to gain a better understanding of the antimicrobial mode of action of a phenols extract from olive vegetation water (PEOVW) at molecular level by studying Escherichia coli as a model microorganism. Genome-wide transcriptional analysis was performed on E. coli K-12 exposed to PEOVW. The repression of genes for flagellar synthesis and the involvement of genes linked to biofilm formation and stress response were observed. Sub-inhibitory concentrations of PEOVW significantly decreased biofilm formation, swarming and swimming motility, thus confirming the gene expression data. This study provides interesting insights on the molecular action of PEOVW on E. coli K-12. Given these anti-biofilm properties and considering that biofilm formation is a serious problem for the food industry and human health, PEOVW has proved to be a high-value natural product.

Tannic acid-dependent modulation of selected Lactobacillus plantarum traits linked to gastrointestinal survival

BACKGROUND

Owing to its antimicrobial properties dietary tannins may alter the functional efficacy of probiotic lactobacilli in the gastrointestinal (GI)-tract influencing their growth, viability and molecular adaptation to the intestinal environment.

METHODS AND FINDINGS

The effects of tannic acid on Lactobacillus plantarum WCFS1 were studied by in vitro growth monitoring and visualizing the morphological alteration on the cell wall using transmission electron microscopy. Growth upon tannic acid was characterized by dose-dependent reductions of initial viable counts and extended lag phases. Lag phase-cells growing upon 0.5 mM tannic acid were abnormally shaped and experienced disturbance on the cell wall such as roughness, occasional leakage and release of cell debris, but resumed growth later at tannic acid concentrations high as 2.5 mM. To gain insight on how the response to tannic acid influenced the molecular adaptation of L. plantarum to the GI-tract conditions, gene expression of selected biomarkers for GI-survival was assessed by RT-qPCR on cDNA templates synthetized from mRNA samples obtained from cells treated with 0.5 or 2 mM tannic acid. Tannic acid-dependent gene induction was confirmed for selected genes highly expressed in the gut or with confirmed roles in GI-survival. No differential expression was observed for the pbp2A gene, a biomarker negatively related with GI-survival. However PBP2A was not labeled by Bocillin FL, a fluorescent dye-labeled penicillin V derivative, in the presence of tannic acid which suggests for enhanced GI-survival reportedly associated with the inactivation of this function.

CONCLUSIONS

Probiotic L. plantarum WCFS1 is able to overcome the toxic effects of tannic acid. This dietary constituent modulates molecular traits linked to the adaptation to intestinal environment in ways previously shown to enhance GI-survival.