Differential Gene Expression by Lactobacillus plantarum WCFS1 in Response to Phenolic Compounds Reveals New Genes Involved in Tannin Degradation

Microbiota, natural products, and human health: exploring interactions for therapeutic insights

The symbiotic relationship between the human digestive system and its intricate microbiota is a captivating field of study that continues to unfold. Comprising predominantly anaerobic bacteria, this complex microbial ecosystem, teeming with trillions of organisms, plays a crucial role in various physiological processes. Beyond its primary function in breaking down indigestible dietary components, this microbial community significantly influences immune system modulation, central nervous system function, and disease prevention. Despite the strides made in microbiome research, the precise mechanisms underlying how bacterial effector functions impact mammalian and microbiome physiology remain elusive. Unlike the traditional DNA-RNA-protein paradigm, bacteria often communicate through small molecules, underscoring the imperative to identify compounds produced by human-associated bacteria. The gut microbiome emerges as a linchpin in the transformation of natural products, generating metabolites with distinct physiological functions. Unraveling these microbial transformations holds the key to understanding the pharmacological activities and metabolic mechanisms of natural products. Notably, the potential to leverage gut microorganisms for large-scale synthesis of bioactive compounds remains an underexplored frontier with promising implications. This review serves as a synthesis of current knowledge, shedding light on the dynamic interplay between natural products, bacteria, and human health. In doing so, it contributes to our evolving comprehension of microbiome dynamics, opening avenues for innovative applications in medicine and therapeutics. As we delve deeper into this intricate web of interactions, the prospect of harnessing the power of the gut microbiome for transformative medical interventions becomes increasingly tantalizing.

Genomic Modifications of Lactic Acid Bacteria and Their Applications in Dairy Fermentation

Lactic Acid Bacteria (LAB) have a long history of safe use in milk fermentation and are generally recognized as health-promoting microorganisms when present in fermented foods. LAB are also important components of the human intestinal microbiota and are widely used as probiotics. Considering their safe and health-beneficial properties, LAB are considered appropriate vehicles that can be genetically modified for food, industrial and pharmaceutical applications. Here, this review describes (1) the potential opportunities for application of genetically modified LAB strains in dairy fermentation and (2) the various genomic modification tools for LAB strains, such as random mutagenesis, adaptive laboratory evolution, conjugation, homologous recombination, recombineering, and CRISPR (clustered regularly interspaced short palindromic repeat)- Cas (CRISPR-associated protein) based genome engineering. Lastly, this review also discusses the potential future developments of these genomic modification technologies and their applications in dairy fermentations.

Food phenolics and Lactiplantibacillus plantarum

Phenolic compounds are important constituents of plant food products. These compounds play a key role in food characteristics such as flavor, astringency and color. Lactic acid bacteria are naturally found in raw vegetables, being Lactiplantibacillus plantarum the most commonly used commercial starter for the fermentation of plant foods. Hence, the metabolism of phenolic compounds of L. plantarum has been a subject of study in recent decades. Such studies confirm that L. plantarum, in addition to presenting catalytic capacity to transform aromatic alcohols and phenolic glycosides, exhibits two main differentiated metabolic routes that allow the biotransformation of dietary hydroxybenzoic and hydroxycinnamic acid-derived compounds. These metabolic pathways lead to the production of new compounds with new biological and organoleptic properties. The described metabolic pathways involve the action of specialized esterases, decarboxylases and reductases that have been identified through genetic analysis and biochemically characterized. The purpose of this review is to provide a comprehensive and up-to-date summary of the current knowledge of the metabolism of food phenolics in L. plantarum.

The prFMNH2-binding chaperone LpdD assists UbiD decarboxylase activation

The UbiD enzyme family of prenylated flavin (prFMN)-dependent reversible decarboxylases is near ubiquitously present in microbes. For some UbiD family members, enzyme activation through prFMNH2 binding and subsequent oxidative maturation of the cofactor readily occurs, both in vivo in a heterologous host and through in vitro reconstitution. However, isolation of the active holo-enzyme has proven intractable for others, notably the canonical Escherichia coli UbiD. We show that E. coli heterologous expression of the small protein LpdD-associated with the UbiD-like gallate decarboxylase LpdC from Lactobacillus plantarum-unexpectedly leads to 3,4-dihydroxybenzoic acid decarboxylation whole-cell activity. This activity was shown to be linked to endogenous E. coli ubiD expression levels. The crystal structure of the purified LpdD reveals a dimeric protein with structural similarity to the eukaryotic heterodimeric proteasome assembly chaperone Pba3/4. Solution studies demonstrate that LpdD protein specifically binds to reduced prFMN species only. The addition of the LpdD-prFMNH2 complex supports reconstitution and activation of the purified E. coli apo-UbiD in vitro, leading to modest 3,4-dihydroxybenzoic acid decarboxylation. These observations suggest that LpdD acts as a prFMNH2-binding chaperone, enabling apo-UbiD activation through enhanced prFMNH2 incorporation and subsequent oxidative maturation. Hence, while a single highly conserved flavin prenyltransferase UbiX is found associated with UbiD enzymes, our observations suggest considerable diversity in UbiD maturation, ranging from robust autocatalytic to chaperone-mediated processes. Unlocking the full (de)carboxylation scope of the UbiD-enzyme family will thus require more than UbiX coexpression.

Sustainable extraction of bioactive compound from apple pomace through lactic acid bacteria (LAB) fermentation

Apple pomace (AP), a by-product of the juice industry, is a rich and inexpensive source of natural bioactive substances, including phenolic compounds, that exhibit health-promoting effects. The recovery of these compounds from plant material using only classical extraction techniques and environmentally friendly solvents is often ineffective due to the entrapment of some compounds in the complex structures of plant cell walls. Lactic Acid Bacteria (LAB) fermentation can be a simple technology to increase the content of phenolic compounds, as well as the antioxidant activity of plant material. In this study, pomace from conventionally grown apples (Malus Domestica) of the Ligol cultivar were fermented with selected LAB strains (Lpb. plantarum KKP 3182, Lpb. plantarum KKP 1527, Lpb. plantarum ZFB 200), commercial starter cultures of Lpb. plantarum, and spontaneously. The fermented material was then subjected to ultrasound-assisted extraction, and the resulting extracts were analysed for their composition (phenolic compounds, triterpenoids, simple organic acids), and antioxidant activity. We found that: (1) the total phenolic content of AP extracts fermented with Lpb. plantarum KKP 1527 was about 30% higher than that of non-fermented AP extracts, (2) extracts of AP fermented with Lpb. plantarum KKP 1527 characterized a higher value of the antioxidant activity, (3) an increase in gallic acid procyanidin A2, protocatechuic acid, and procyanidin B2, while a decrease in rutin and quercetin was observed. The results indicated that AP fermented with Lpb. plantarum KKP 1527 may be a powerful and low-cost source of natural antioxidants which have applications in many industries.

Physiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar

AIMS

Indri indri is a lemur of Madagascar which is critically endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lactiplantibacillus plantarum isolates from indris.

METHODS AND RESULTS

Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from two individuals. The three isolates were closely related to each other, with <10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. The genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype.

CONCLUSIONS

Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.

Characterization of isogenic mutants with single or double deletions of four phenolic acid esterases in Lactiplantibacillus plantarum TMW1.460

In plants, hydroxycinnamic and hydroxybenzoic acids occur mainly as esters. This study aimed to determine the contribution of individual phenolic acid esterases in Lp. plantarum TMW1.460, which encodes for four esterases: TanA, Lp_0796, Est_1092 and a homolog of Lj0536 and Lj1228 that was termed HceP. To determine which of the phenolic acid esterases present in Lp plantarum TMW1.460 are responsible for esterase activity, mutants with deletions in lp_0796, est_1092, tanB, hceP, or hceP and est_1092 were constructed. The phenotype of wild type strain and mutants was determined with esters of hydroxycinnamic acids (chlorogenic acid and ethyl ferulate) and of hydroxybenzoic acids (methyl gallate, tannic acid and epigallocatechin-3-gallate). Lp. plantarum TMW1.460 hydrolysed chlorogenic acid, methyl ferulate and methyl gallate but not tannic acid or epigallocatechin gallate. The phenotype of mutant strains during growth in mMRS differed from the wild type as follows: Lp. plantarum TMW1.460ΔhceP did not hydrolyse esters of hydroxycinnamic acids; Lp. plantarum TMW1.460ΔtanB did not hydrolyse esters of hydroxybenzoic acids; disruption of est_1092 or Lp_0796 did not alter the phenotype. The phenotype of Lp. plantarum TMW1.460ΔΔhceP/est_1092 was identical to Lp. plantarum TMW1.460ΔhceP. The metabolism of phenolic acids during growth of the mutant strains in broccoli puree and wheat sourdough did not differ from metabolism of the wild type strain. In conclusion, esters of hydroxycinnamic and hydroxybenzoic acids each are hydrolysed by dedicated enzymes. The hydroxycinnamic acid esterase HceP is not expressed, or not active during growth of Lp. plantarum TMW1.460 in all food substrates.

Potential roles of gut microbes in biotransformation of natural products: An overview

Natural products have been extensively applied in clinical practice, characterized by multi-component and multi-target, many pharmacodynamic substances, complex action mechanisms, and various physiological activities. For the oral administration of natural products, the gut microbiota and clinical efficacy are closely related, but this relationship remains unclear. Gut microbes play an important role in the transformation and utilization of natural products caused by the diversity of enzyme systems. Effective components such as flavonoids, alkaloids, lignans, and phenols cannot be metabolized directly through human digestive enzymes but can be transformed by enzymes produced by gut microorganisms and then utilized. Therefore, the focus is paid to the metabolism of natural products through the gut microbiota. In the present study, we systematically reviewed the studies about gut microbiota and their effect on the biotransformation of various components of natural products and highlighted the involved common bacteria, reaction types, pharmacological actions, and research methods. This study aims to provide theoretical support for the clinical application in the prevention and treatment of diseases and provide new ideas for studying natural products based on gut biotransformation.

Microbial degradation and valorization of poly(ethylene terephthalate) (PET) monomers

The polyethylene terephthalate (PET) is one of the major plastics with a huge annual production. Alongside with its mass production and wide applications, PET pollution is threatening and damaging the environment and human health. Although mechanical or chemical methods can deal with PET, the process suffers from high cost and the hydrolyzed monomers will cause secondary pollution. Discovery of plastic-degrading microbes and the corresponding enzymes emerges new hope to cope with this issue. Combined with synthetic biology and metabolic engineering, microbial cell factories not only provide a promising approach to degrade PET, but also enable the conversion of its monomers, ethylene glycol (EG) and terephthalic acid (TPA), into value-added compounds. In this way, PET wastes can be handled in environment-friendly and more potentially cost-effective processes. While PET hydrolases have been extensively reviewed, this review focuses on the microbes and metabolic pathways for the degradation of PET monomers. In addition, recent advances in the biotransformation of TPA and EG into value-added compounds are discussed in detail.

Selection of Lactiplantibacillus Strains for the Production of Fermented Table Olives

Lactiplantibacillus strains (n. 77) were screened for technological properties (e.g., xylose fermentation, EPS production, antimicrobial activity, tolerance to NaCl and phenolic compounds, oleuropein degradation and hydroxytyrosol formation) relevant for the production of fermented table olives. Survival to olive mill wastewater (OMW) and to simulated gastro-intestinal tract (GIT), the capability to grow at different combinations of NaCl and pH values, radical scavenging activities and biofilm formation were further investigated in 15 selected strains. The screening step revealed high diversity among Lactiplantibacillus strains. Most of the strains were able to ferment xylose, while only a few strains produced EPS and had inhibitory activity against Y. lipolytica. Resistance to phenolic compounds (gallic, protocatechuic, hydroxybenzoic and syringic acids), as well as the ability to release hydroxytyrosol from oleuropein, was strain-specific. OMWs impaired the survival of selected strains, while combinations of NaCl ≤ 6% and pH ≥ 4.0 were well tolerated. DPPH and hydroxyl radical degradation were strain-dependent, while the capability to form biofilm was affected by incubation time. Strains were very tolerant to the GIT. The genome of Lpb. pentosus O17 was sequenced and analysed to verify the presence of genes involved in the degradation and metabolism of phenolic compounds. O17 lacks carboxylesterase and gallate decarboxylase (subunits B and D) sequences, and its gene profile differs from that of other publicly available Lpb. pentosus genomes.

Antimicrobial plant secondary metabolites, MDR transporters and antimicrobial resistance in cereal-associated lactobacilli: is there a connection?

Cereal-associated lactobacilli resist antimicrobial plant secondary metabolites. This study aimed to identify multi-drug-resistance (MDR) transporters in isolates from mahewu, a Zimbabwean fermented cereal beverage, and to determine whether these MDR-transporters relate to resistance against phenolic compounds and antibiotics. Comparative genomic analyses indicated that all seven mahewu isolates harbored multiple MATE and MFS MDR proteins. Strains of Lactiplantibacillus plantarum and Limosilactobacillus fermentum encoded for the same gene, termed mahewu phenolics resistance gene mprA, with more than 99% nucleotide identity, suggesting horizontal gene transfer. Strains of Lp. plantarum were more resistant than strains of Lm. fermentum to phenolic acids, other antimicrobials and antibiotics but the origins of strains were not related to resistance. The resistance of several strains exceeded EFSA thresholds for several antibiotics. Analysis of gene expression in one strain each of Lp. plantarum and Lm. fermentum revealed that at least one MDR gene in each strain was over-expressed during growth in wheat, sorghum and millet relative to growth in MRS5 broth. In addition, both strains over-expressed a phenolic acid reductase. The results suggest that diverse lactobacilli in mahewu share MDR transporters acquired by lateral gene transfer, and that these transporters mediate resistance to secondary plant metabolites and antibiotics.

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.

Transcriptome differences between Cupriavidus necator NH9 grown with 3-chlorobenzoate and that grown with benzoate

RNA-seq analysis of Cupriavidus necator NH9, a 3-chlorobenzoate degradative bacterium, cultured with 3-chlorobenzaote and benzoate, revealed strong induction of genes encoding enzymes in degradation pathways of the respective compound, including the genes to convert 3-chlorobenzaote and benzoate to chlorocatechol and catechol, respectively, and the genes of chlorocatechol ortho-cleavage pathway for conversion to central metabolites. The genes encoding transporters, components of the stress response, flagellar proteins, and chemotaxis proteins showed altered expression patterns between 3-chlorobenzoate and benzoate. Gene Ontology enrichment analysis revealed that chemotaxis-related terms were significantly upregulated by benzoate compared with 3-chlorobenzoate. Consistent with this, in semisolid agar plate assays, NH9 cells showed stronger chemotaxis to benzoate than to 3-chlorobenzoate. These results, combined with the absence of genes related to uptake/chemotaxis for 3-chlorobenzoate located closely to the degradation genes of 3-chlorobenzoate, suggested that NH9 has not fully adapted to the utilization of chlorinated benzoate, unlike benzoate, in nature.

Cranberry Proanthocyanidins and Dietary Oligosaccharides Synergistically Modulate Lactobacillus plantarum Physiology

Plant-based foods contain bioactive compounds such as polyphenols that resist digestion and potentially benefit the host through interactions with their resident microbiota. Based on previous observations, we hypothesized that the probiotic Lactobacillus plantarum interacts with cranberry polyphenols and dietary oligosaccharides to synergistically impact its physiology. In this study, L. plantarum ATCC BAA-793 was grown on dietary oligosaccharides, including cranberry xyloglucans, fructooligosaccharides, and human milk oligosaccharides, in conjunction with proanthocyanidins (PACs) extracted from cranberries. As a result, L. plantarum exhibits a differential physiological response to cranberry PACs dependent on the carbohydrate source and polyphenol fraction introduced. Of the two PAC extracts evaluated, the PAC1 fraction contains higher concentrations of PACs and increased growth regardless of the oligosaccharide, whereas PAC2 positively modulates its growth during xyloglucan metabolism. Interestingly, fructooligosaccharides (FOS) are efficiently utilized in the presence of PAC1, as this L. plantarum strain does not utilize this substrate typically. Relative to glucose, oligosaccharide metabolism increases the ratio of secreted acetic acid to lactic acid. The PAC2 fraction differentially increases this ratio during cranberry xyloglucan fermentation compared with PAC1. The global transcriptome links the expression of putative polyphenol degradation genes and networks and metabolic phenotypes.

Characterization of aromatic acid/proton symporters in Pseudomonas putida KT2440 toward efficient microbial conversion of lignin-related aromatics

Pseudomonas putida KT2440 (hereafter KT2440) is a well-studied platform bacterium for the production of industrially valuable chemicals from heterogeneous mixtures of aromatic compounds obtained from lignin depolymerization. KT2440 can grow on lignin-related monomers, such as ferulate (FA), 4-coumarate (4CA), vanillate (VA), 4-hydroxybenzoate (4HBA), and protocatechuate (PCA). Genes associated with their catabolism are known, but knowledge about the uptake systems remains limited. In this work, we studied the KT2440 transporters of lignin-related monomers and their substrate selectivity. Based on the inhibition by protonophores, we focused on five genes encoding aromatic acid/H⁺ symporter family transporters categorized into major facilitator superfamily that uses the proton motive force. The mutants of PP_1376 (pcaK) and PP_3349 (hcnK) exhibited significantly reduced growth on PCA/4HBA and FA/4CA, respectively, while no change was observed on VA for any of the five gene mutants. At pH 9.0, the conversion of these compounds by hcnK mutant (FA/4CA) and vanK mutant (VA) was dramatically reduced, revealing that these transporters are crucial for the uptake of the anionic substrates at high pH. Uptake assays using ¹⁴C-labeled substrates in Escherichia coli and biosensor-based assays confirmed that PcaK, HcnK, and VanK have ability to take up PCA, FA/4CA, and VA/PCA, respectively. Additionally, analyses of the predicted protein structures suggest that the size and hydropathic properties of the substrate-binding sites of these transporters determine their substrate preferences. Overall, this study reveals that at physiological pH, PcaK and HcnK have a major role in the uptake of PCA/4HBA and FA/4CA, respectively, and VanK is a VA/PCA transporter. This information can contribute to the engineering of strains for the efficient conversion of lignin-related monomers to value-added chemicals.

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.

Modifications of Phenolic Compounds, Biogenic Amines, and Volatile Compounds in Cabernet Gernishct Wine through Malolactic Fermentation by Lactobacillus plantarum and Oenococcus oeni

Malolactic fermentation is a vital red wine-making process to enhance the sensory quality. The objective of this study is to elucidate the starter cultures’ role in modifying phenolic compounds, biogenic amines, and volatile compounds after red wine malolactic fermentation. We initiated the malolactic fermentation in Cabernet Gernishct wine by using two Oenococcus oeni and two Lactobacillus plantarum strains. Results showed that after malolactic fermentation, wines experienced a content decrease of total flavanols and total flavonols, accompanied by the accumulation of phenolic acids. The Lactobacillus plantarum strains, compared to Oenococcus oeni, exhibited a prevention against the accumulation of biogenic amines. The malolactic fermentation increased the total esters and modified the aromatic features compared to the unfermented wine. The Lactobacillus plantarum strains retained more aromas than the Oenococcus oeni strains did. Principal component analysis revealed that different strains could distinctly alter the wine characteristics being investigated in this study. These indicated that Lactobacillus plantarum could serve as a better alternative starter for conducting red wine malolactic fermentation.

Passive membrane transport of lignin-related compounds

Lignin is an abundant aromatic polymer found in plant secondary cell walls. In recent years, lignin has attracted renewed interest as a feedstock for bio-based chemicals via catalytic and biological approaches and has emerged as a target for genetic engineering to improve lignocellulose digestibility by altering its composition. In lignin biosynthesis and microbial conversion, small phenolic lignin precursors or degradation products cross membrane bilayers through an unidentified translocation mechanism prior to incorporation into lignin polymers (synthesis) or catabolism (bioconversion), with both passive and transporter-assisted mechanisms postulated. To test the passive permeation potential of these phenolics, we performed molecular dynamics simulations for 69 monomeric and dimeric lignin-related phenolics with 3 model membranes to determine the membrane partitioning and permeability coefficients for each compound. The results support an accessible passive permeation mechanism for most compounds, including monolignols, dimeric phenolics, and the flavonoid, tricin. Computed lignin partition coefficients are consistent with concentration enrichment near lipid carbonyl groups, and permeability coefficients are sufficient to keep pace with cellular metabolism. Interactions between methoxy and hydroxy groups are found to reduce membrane partitioning and improve permeability. Only carboxylate-modified or glycosylated lignin phenolics are predicted to require transporters for membrane translocation. Overall, the results suggest that most lignin-related compounds can passively traverse plant and microbial membranes on timescales commensurate with required biological activities, with any potential transport regulation mechanism in lignin synthesis, catabolism, or bioconversion requiring compound functionalization.

Bioprocessing of common pulses changed seed microstructures, and improved dipeptidyl peptidase-IV and α-glucosidase inhibitory activities

Type 2 diabetes mellitus (T2DM) is a leading cause of death globally. T2DM patients experience glucose intolerance, and inhibitors of dipeptidyl peptidase IV (DPP-IV) and α-glucosidase are used as drugs for T2DM management. DPP-IV and α-glucosidase inhibitors are also naturally contained in foods, but their potency can be affected by the food matrix and processing methods. In this study, germination and solid-state fermentation (SSF) were used to alter pulse seed microstructures, to convert compounds into more bioactive forms, and to improve their bioaccessibility. Germination substantially modified the seed microstructure, protein digestibility, contents and profiles of phenolic compounds in all the pulses. It also increased DPP-IV and α-glucosidase inhibitory activities in chickpeas, faba beans and yellow peas. Compared to germination, SSF with Lactobacillus plantarum changed the content and the profile of phenolic compounds mainly in yellow peas and green lentils because of greater disruption of the seed cell wall. In the same pulses, heat treatment and SSF of flour increased DPP-IV and α-glucosidase inhibitory activities. The results of this study suggest that germination and SSF with L. plantarum are effective and simple methods for modulating phenolic and protein profiles of common pulses and improve the action on DPP-IV and α-glucosidase.

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.

Mapping the diversity of microbial lignin catabolism: experiences from the eLignin database

Lignin is a heterogeneous aromatic biopolymer and a major constituent of lignocellulosic biomass, such as wood and agricultural residues. Despite the high amount of aromatic carbon present, the severe recalcitrance of the lignin macromolecule makes it difficult to convert into value-added products. In nature, lignin and lignin-derived aromatic compounds are catabolized by a consortia of microbes specialized at breaking down the natural lignin and its constituents. In an attempt to bridge the gap between the fundamental knowledge on microbial lignin catabolism, and the recently emerging field of applied biotechnology for lignin biovalorization, we have developed the eLignin Microbial Database ( www.elignindatabase.com ), an openly available database that indexes data from the lignin bibliome, such as microorganisms, aromatic substrates, and metabolic pathways. In the present contribution, we introduce the eLignin database, use its dataset to map the reported ecological and biochemical diversity of the lignin microbial niches, and discuss the findings.

Biotransformation of industrial tannins by filamentous fungi

Tannins are secondary metabolites that are widely distributed in the plant kingdom. They act as growth inhibitors for many microorganisms: they are released upon microbial attack, helping to fight infection in plant tissues. Extraction of tannins from plants is an active industrial sector with several applications, including oenology, animal feeding, mining, the chemical industry, and, in particular, the tanning industry. However, tannins are also considered very recalcitrant pollutants in wastewater of diverse origin. The ability to grow on plant substrates rich in tannins and on industrial tannin preparations is usually considered typical of some species of fungi. These organisms are able to tolerate the toxicity of tannins thanks to the production of enzymes that transform or degrade these substrates, mainly through hydrolysis and oxidation. Filamentous fungi capable of degrading tannins could have a strong environmental impact as bioremediation agents, in particular in the treatment of tanning wastewaters.

Expression of genes involved in metabolism of phenolic compounds by Lactobacillus pentosus and its relevance for table-olive fermentations

Genes with the potential to code for enzymes involved in phenolic compound metabolism were detected in the genome of Lactobacillus pentosus IG1, isolated from a green olive fermentation. Based on homology, these genes could code for a 6-P-β Glucosidase, two different Tannases, a Gallate decarboxylase and a p-Coumaric decarboxylase. Expression of up to seven of these genes was studied in L. pentosus IG1 (olive fermentation) and CECT4023^T (corn silage), including responses upon exposure to relevant phenolic compounds and different olive extracts. Genes potentially coding Tannase, Gallate decarboxylase and p-Coumaric acid decarboxylase significatively increased their expression upon exposure to such compounds and extracts, although it was strain dependent. In general, both the genetic organization and the characteristics of gene expression resembled very much those described for Lactobacillus plantarum. In accordance to the observed induced gene expression, metabolism of specific phenolic compounds was achieved by L. pentosus. Thus, methyl gallate, gallic acid and the hydroxycinamic acids p-coumaric, caffeic and ferulic were metabolized. In addition, the amount of phenolics such as tyrosol, oleuropein, rutin and verbascoside included in a minimal culture medium was noticeably reduced, again dependent on the strain considered.

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.

Bacterial catabolism of lignin-derived aromatics: New findings in a recent decade: Update on bacterial lignin catabolism

Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalysed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: (i) funnelling of a wide variety of lignin-derived aromatics into vanillate and syringate, (ii) O demethylation of vanillate and syringate to form catecholic derivatives and (iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates. Knowledge regarding bacterial catabolic systems for lignin-derived aromatic compounds is not only important for understanding the terrestrial carbon cycle but also valuable for promoting the shift to a low-carbon economy via biological lignin valorisation. This review summarizes recent progress in bacterial catabolic systems for lignin-derived aromatic compounds, including newly identified catabolic pathways and genes for decomposition of lignin-derived biaryls, transcriptional regulation and substrate uptake systems. Recent omics approaches on catabolism of lignin-derived aromatic compounds are also described.