Co-culture-inducible bacteriocin production in lactic acid bacteria

Bacteriocins sourced from traditional fermented foods for ensuring food safety: the microbial guards

Concerns about food safety have consistently driven the exploration of potent antimicrobials with probiotic origins. Identification of probiotic-derived bacteriocins as robust alternatives to antibiotics has gained traction following the COVID-19 pandemic. Additionally, the global market is witnessing an increasing preference for minimally processed food products free from chemical additives. Another contributing factor to the search for potent antimicrobials is the escalating number of infections caused by antibiotic-resistant bacteria and the need to mitigate the significant damage inflicted on the commensal human microbiota by broad-spectrum antibiotics. As an alternative bio-preservation strategy, there is substantial enthusiasm for the use of bacteriocins or starter cultures producing bacteriocins in preserving a variety of food items. This review specifically focuses on bacteriocins originating from lactic acid bacteria associated with fermented foods and explores their technological applications as nanobiotics. The food-grade antibiotic alternatives, whether utilized independently or in combination with other antimicrobials and administered directly or encapsulated, are anticipated to possess qualities of safety, stability and non-toxicity suitable for application in the food sector. © 2024 Society of Chemical Industry.

Enhancing food preservation with postbiotic metabolites γ-aminobutyric acid (GABA) and bacteriocin-like inhibitory substances (BLIS) produced by Lactobacillus brevis C23 co-cultures in plant-based medium

Lactic acid bacteria (LAB) can produce γ-aminobutyric acid (GABA) with antioxidant properties and sedative effects when it binds to the GABA receptor in the human brain. LAB can also produce bacteriocin-like inhibitory substances (BLIS) with antimicrobial capabilities during carbohydrate fermentation. GABA and BLIS are natural compounds with potential health benefits and food preservation properties. Lactobacillus brevis C23 was co-cultured with three different LABs as inducers, which produced the highest GABA content and BLIS activity. They were cultured in various plant-based media to obtain an edible and better-tasting final product over commercially available media like MRS broth. A coconut-based medium with additives was optimized using response surface methodology (RSM) to increase GABA and BLIS production. The optimized medium for maximum GABA production (3.22 ± 0.01 mg/mL) and BLIS activity (84.40 ± 0.44%) was a 5.5% coconut medium containing 0.23% glucose, 1.44% Tween 20, 0.48% L-glutamic acid, and 0.02% pyridoxine. Due to the presence of GABA, the cell-free supernatant (CFS) as a postbiotic showed higher antioxidant activity than other food preservatives like nisin and potassium sorbate. Finally, microbiological tests on food samples showed that the postbiotic was more effective than other preservatives at combating the growth of LAB, molds and coliform bacteria, making it a possible food preservative.

Cocultures of Enterococcus faecium and Aeromonas veronii Induce the Secretion of Bacteriocin-like Substances against Aeromonas

Lactic acid bacteria (LAB) were screened from Lutjanus russellii (red sea bass), and their antimicrobial activities were evaluated against two Aeromonas species isolated from the Nile tilapia, namely, Aeromonas veronii (AV) and Aeromonas jandaei (AJ). Three LAB isolates, Enterococcus faecium MU8 (EF_8), Enterococcus faecalis MU2 (EFL_2), and E. faecalis MU9 (EFL_9), were found to inhibit both AV and AJ; however, their cell-free supernatant (CFS) did not do so. Interestingly, bacteriocin-like substances (BLS) induced by cocultures of EF_8 with AV exhibited the highest antimicrobial activity against both Aeromonas sp. The size of BLS was less than 1.0 kDa; the purified BLS were susceptible to proteinase K digestion, indicating that they are peptides. BLS contained 13 identified peptides derived from E. faecium, as determined by liquid chromatography-tandem mass spectrometry. Cocultures of Gram-positive-producing and -inducing LAB strains have been used to increase bacteriocin yields. To our knowledge, this is the first report describing inducible BLS produced by cocultures of Gram-positive-producing and Gram-negative-inducing strains.

Fungal–Lactobacteria Consortia and Enzymatic Catalysis for Polylactic Acid Production

Polylactic acid (PLA) is the main biobased plastic manufactured on an industrial scale. This polymer is synthetized by chemical methods, and there is a strong demand for the implementation of clean technologies. This work focuses on the microbial fermentation of agro-industrial waste rich in starch for the production of lactic acid (LA) in a consolidated bioprocess, followed by the enzymatic synthesis of PLA. Lactic acid bacteria (LAB) and the fungus Rhizopus oryzae were evaluated as natural LA producers in pure cultures or in fungal–lactobacteria co-cultures formed by an LAB and a fungus selected for its metabolic capacity to degrade starch and to form consortia with LAB. Microbial interaction was analyzed by scanning electron microscopy and biofilm production was quantified. The results show that the fungus Talaromyces amestolkiae and Lactiplantibacillus plantarum M9MG6-B2 establish a cooperative relationship to exploit the sugars from polysaccharides provided as carbon sources. Addition of the quorum sensing molecule dodecanol induced LA metabolism of the consortium and resulted in improved cooperation, producing 99% of the maximum theoretical yield of LA production from glucose and 65% from starch. Finally, l-PLA oligomers (up to 19-LA units) and polymers (greater than 5 kDa) were synthetized by LA polycondensation and enzymatic ring-opening polymerization catalyzed by the non-commercial lipase OPEr, naturally produced by the fungus Ophiostoma piceae.

Probiotic Potential and Safety Assessment of Type Strains of Weissella and Periweissella Species

Although numerous strains belonging to the Weissella genus have been described in the last decades for their probiotic and biotechnological potential, others are known to be opportunistic pathogens of humans and animals. Here, we investigated the probiotic potential of two Weissella and four Periweissella type strains belonging to the species Weissella diestrammenae, Weissella uvarum, Periweissella beninensis, Periweissella fabalis, Periweissella fabaria, and Periweissella ghanensis by genomic and phenotypic analyses, and performed a safety assessment of these strains. Based on the results of the survival to simulated gastrointestinal transit, autoaggregation and hydrophobicity characteristics, as well as adhesion to Caco-2 cells, we showed that the P. beninensis, P. fabalis, P. fabaria, P. ghanensis, and W. uvarum type strains exhibited a high probiotic potential. The safety assessment, based on the genomic analysis, performed by searching for virulence and antibiotic resistance genes, as well as on the phenotypic evaluation, by testing hemolytic activity and antibiotic susceptibility, allowed us to identify the P. beninensis type strain as a safe potential probiotic microorganism. IMPORTANCE A comprehensive analysis of safety and functional features of six Weissella and Periweissella type strains was performed. Our data demonstrated the probiotic potential of these species, indicating the P. beninensis type strain as the best candidate based on its potential probiotic features and the safety assessment. The presence of different antimicrobial resistance profiles in the analyzed strains highlighted the need to establish cutoff values to perform a standardized safety evaluation of these species, which, in our opinion, should be mandatory on a strain-specific basis.

Enhancing chemical and biological diversity by co-cultivation

In natural product research, microbial metabolites have tremendous potential to provide new therapeutic agents since extremely diverse chemical structures can be found in the nearly infinite microbial population. Conventionally, these specialized metabolites are screened by single-strain cultures. However, owing to the lack of biotic and abiotic interactions in monocultures, the growth conditions are significantly different from those encountered in a natural environment and result in less diversity and the frequent re-isolation of known compounds. In the last decade, several methods have been developed to eventually understand the physiological conditions under which cryptic microbial genes are activated in an attempt to stimulate their biosynthesis and elicit the production of hitherto unexpressed chemical diversity. Among those, co-cultivation is one of the most efficient ways to induce silenced pathways, mimicking the competitive microbial environment for the production and holistic regulation of metabolites, and has become a golden methodology for metabolome expansion. It does not require previous knowledge of the signaling mechanism and genome nor any special equipment for cultivation and data interpretation. Several reviews have shown the potential of co-cultivation to produce new biologically active leads. However, only a few studies have detailed experimental, analytical, and microbiological strategies for efficiently inducing bioactive molecules by co-culture. Therefore, we reviewed studies applying co-culture to induce secondary metabolite pathways to provide insights into experimental variables compatible with high-throughput analytical procedures. Mixed-fermentation publications from 1978 to 2022 were assessed regarding types of co-culture set-ups, metabolic induction, and interaction effects.

Genetic and phenotypic assessment of the antimicrobial activity of three potential probiotic lactobacilli against human enteropathogenic bacteria

Introduction

Lactobacilli are avid producers of antimicrobial compounds responsible for their adaptation and survival in microbe-rich matrices. The bactericidal or bacteriostatic ability of lactic acid bacteria (LAB) can be exploited for the identification of novel antimicrobial compounds to be incorporated in functional foodstuffs or pharmaceutical supplements. In this study, the antimicrobial and antibiofilm properties of Lactiplantibacillus pentosus L33, Lactiplantibacillus plantarum L125 and Lacticaseibacillus paracasei SP5, previously isolated form fermented products, were examined, against clinical isolates of Staphylococcus aureus, Salmonella enterica subsp. enterica serovar Enteritidis and Escherichia coli.

Methods

The ability of viable cells to inhibit pathogen colonization on HT-29 cell monolayers, as well as their co-aggregation capacity, were examined utilizing the competitive exclusion assay. The antimicrobial activity of cell-free culture supernatants (CFCS) was determined against planktonic cells and biofilms, using microbiological assays, confocal microscopy, and gene expression analysis of biofilm formation-related genes. Furthermore, in vitro analysis was supplemented with in silico prediction of bacteriocin clusters and of other loci involved in antimicrobial activity.

Results

The three lactobacilli were able to limit the viability of planktonic cells of S. aureus and E. coli in suspension. Greater inhibition of biofilm formation was recorded after co-incubation of S. enterica with the CFCS of Lc. paracasei SP5. Predictions based on sequence revealed the ability of strains to produce single or two-peptide Class II bacteriocins, presenting sequence and structural conservation with functional bacteriocins.

Discussion

The efficiency of the potentially probiotic bacteria to elicit antimicrobial effects presented a strain- and pathogen-specific pattern. Future studies, utilizing multi-omic approaches, will focus on the structural and functional characterization of molecules involved in the recorded phenotypes.

Bacteriocin production enhancing mechanism of Lactiplantibacillus paraplantarum RX-8 response to Wickerhamomyces anomalus Y-5 by transcriptomic and proteomic analyses

Plantaricin is a kind of bacteriocin with broad-spectrum antibacterial activity on several food pathogens and spoilage microorganisms, showing potential in biopreservation applications. However, the low yield of plantaricin limits its industrialization. In this study, it was found that the co-culture of Wickerhamomyces anomalus Y-5 and Lactiplantibacillus paraplantarum RX-8 could enhance plantaricin production. To investigate the response of L. paraplantarum RX-8 facing W. anomalus Y-5 and understand the mechanisms activated when increasing plantaricin yield, comparative transcriptomic and proteomic analyses of L. paraplantarum RX-8 were performed in mono-culture and co-culture. The results showed that different genes and proteins in the phosphotransferase system (PTS) were improved and enhanced the uptake of certain sugars; the key enzyme activity in glycolysis was increased with the promotion of energy production; arginine biosynthesis was downregulated to increase glutamate mechanism and then promoted plantaricin yield; and the expression of several genes/proteins related to purine metabolism was downregulated and those related to pyrimidine metabolism was upregulated. Meanwhile, the increase of plantaricin synthesis by upregulation of plnABCDEF cluster expression under co-culture indicated that the PlnA-mediated quorum sensing (QS) system took part in the response mechanism of L. paraplantarum RX-8. However, the absence of AI-2 did not influence the inducing effect on plantaricin production. Mannose, galactose, and glutamate were critical metabolites and significantly simulate plantaricin production (p < 0.05). In summary, the findings provided new insights into the interaction between bacteriocin-inducing and bacteriocin-producing microorganisms, which may serve as a basis for further research into the detailed mechanism.

Multi-Costimulatory Pathways Drive the Antagonistic Pseudoalteromonas piscicida against the Dominant Pathogenic Vibrio harveyi in Mariculture: Insights from Proteomics and Metabolomics

Vibrio harveyi is the dominant pathogen in mariculture, and biocontrol of this pathogen using antagonistic probiotics is a long-standing biological challenge. Here, Pseudoalteromonas piscicida WCPW15003 as a probiotic effectively antagonized dominant pathogenic V. harveyi in a mariculture, with a growth-of-inhibition ratio of 6.3 h-1. The antagonistic activities of cells and intracellular components of WCPW15003 made a greater contribution to the antagonistic process than did extracellular metabolites and caused the dominance of WCPW15003 during the antagonistic process in vitro. WCPW15003 was safe for the pearl gentian grouper (♀ Epinephelus fuscoguttatus × ♂ Epinephelus lanceolatus) and, as a consequence of the antagonistic effect on V. harveyi, protected the fish from an immune response in vivo. A comprehensive combined proteomics and metabolomics analysis of antagonistic WCPW15003 and pathogenic V. harveyi in a coculture compared to a monoculture was performed to investigate the antagonistic molecular mechanisms. The results showed that during the antagonistic process, WCPW15003 in a coculture had significantly downregulated metabolic pathways for histidine metabolism, arginine biosynthesis, and phenylalanine metabolism, and upregulated glycerophospholipid metabolism, leading to a competitive advantage against the co-occurring species, V. harveyi. This defined a mechanism by which multi-costimulatory pathways drove P. piscicida WCPW15003 against V. harveyi. IMPORTANCE V. harveyi as a dominant pathogen has become a major hazard in mariculture development and seafood safety, and biocontrol of this pathogen using antagonistic probiotic agents is a long-standing biological challenge. P. piscicida WCPW15003 has promise as a novel, safe, and effective bioagent for specifically inhibiting dominant pathogenic V. harveyi and protects mariculture animals from infection by this pathogen by moderating the host immune response, which is heavily driven by multi-costimulatory pathways in a coculture of WCPW15003 and V. harveyi. This work identified a direction for comprehensively elucidating the molecular mechanism of WCPW15003 antagonism against the dominant pathogen in mariculture using modern molecular biology techniques and provided deep insights into the advantages and potential of this antagonistic probiotic against V. harveyi for the construction of an environmentally friendly, recirculating mariculture system.

Food and gut originated bacteriocins involved in gut microbe-host interactions

The gut microbes interact with each other as well as host, influencing human health and some diseases. Many gut commensals and food originated bacteria produce bacteriocins which can inhibit pathogens and modulate gut microbiota. Bacteriocins have comparable narrow antimicrobial spectrum and are attractive potentials for precision therapy of gut disorders. In this review, the bacteriocins from food and gut microbiomes and their involvement in the interaction between producers and gut ecosystem, along with their characteristics, types, biosynthesis, and functions are described and discussed. Bacteriocins are produced by many intestinal commensals and food microbes among which lactic acid bacteria (many are probiotics) has been paid more attention. Bacteriocin production has been generally regarded as a probiotic trait. They give a competitive advantage to bacteria, enabling their colonization in human gut, and mediating the interaction between the producers and host ecosystem. They fight against unwanted bacteria and pathogens without significant impact on the composition of commensal microbiota. Bacteriocins assist the producers to survive and colonize in the gut microbial populations. There is a great need to evaluate and utilize the potential of bacteriocins for improved therapeutic implications for intestinal health.

An overview on inactivated and live-attenuated SARS-CoV-2 vaccines

After about 2 years since severe acute respiratory syndrome coronavirus 2 (SARS‑CoV‑2), first infections were detected in Wuhan city of China in December 2019, which was followed by a worldwide pandemic with a record of 5.41 million deaths. Due to urgent need for the development of a safe and effective vaccine for coronavirus disease 2019 (COVID‐19), attempts for producing efficient vaccines are inexhaustibly continuing. According to a report by the World Health Organization (WHO) on COVID‐19 vaccine tracker and landscape, there are 149 vaccine candidates all over the world. Inactivated SARS‐CoV‐2 vaccines as a conventional vaccine platform consist of whole virus particles grown in cell culture and inactivated by chemicals. Because of benefits such as antigenic similarity to real virion inducing humoral and cellular immune responses and ease for transport and storage, these vaccines, including the vaccines produced by Bharat Biotech, Sinopharm, and Sinovac, are in use at large scales. In this study, we have a review on inactivated SARS‐CoV‐2 vaccines that are passing their phase 3 and 4 clinical trials, population which was included in the trials, vaccine producers, the efficiency, adverse effects, and components of vaccines, and other vaccine features.

Postbiotics as the new frontier in food and pharmaceutical research

Food is the essential need of human life and has nutrients that support growth and health. Gastrointestinal tract microbiota involves valuable microorganisms that develop therapeutic effects and are characterized as probiotics. The investigations on appropriate probiotic strains have led to the characterization of specific metabolic byproducts of probiotics named postbiotics. The probiotics must maintain their survival against inappropriate lethal conditions of the processing, storage, distribution, preparation, and digestion system so that they can exhibit their most health effects. Conversely, probiotic metabolites (postbiotics) have successfully overcome these unfavorable conditions and may be an appropriate alternative to probiotics. Due to their specific chemical structure, safe profile, long shelf-life, and the fact that they contain various signaling molecules, postbiotics may have anti-inflammatory, immunomodulatory, antihypertensive properties, inhibiting abnormal cell proliferation and antioxidative activities. Consequently, present scientific literature approves that postbiotics can mimic the fundamental and clinical role of probiotics, and due to their unique characteristics, they can be applied in an oral delivery system (pharmaceutical/functional foods), as a preharvest food safety hurdle, to promote the shelf-life of food products and develop novel functional foods or/and for developing health benefits, and therapeutic aims. This review addresses the latest postbiotic applications with regard to pharmaceutical formulations and commercial food-based products. Potential postbiotic applications in the promotion of host health status, prevention of disease, and complementary treatment are also reviewed.

Insights into the Composition of a Co-Culture of 10 Probiotic Strains (OMNi BiOTiC® AAD10) and Effects of Its Postbiotic Culture Supernatant

Background: We aimed to gain insights in a co-culture of 10 bacteria and their postbiotic supernatant. Methods: Abundances and gene expression were monitored by shotgun analysis. The supernatant was characterized by liquid chromatography mass spectroscopy (LC-MS) and gas chromatography mass spectroscopy (GC-MS). Supernatant was harvested after 48 h (S48) and 196 h (S196). Susceptibility testing included nine bacteria and C. albicans. Bagg albino (BALBc) mice were fed with supernatant or culture medium. Fecal samples were obtained for 16S analysis. Results: A time-dependent decrease of the relative abundances and gene expression of L. salivarius, L. paracasei, E. faecium and B. longum/lactis and an increase of L. plantarum were observed. Substances in LC-MS were predominantly allocated to groups amino acids/peptides/metabolites and nucleotides/metabolites, relating to gene expression. Fumaric, panthotenic, 9,3-methyl-2-oxovaleric, malic and aspartic acid, cytidine monophosphate, orotidine, phosphoserine, creatine, tryptophan correlated to culture time. Supernatant had no effect against anaerobic bacteria. S48 was reactive against S. epidermidis, L. monocytogenes, P. aeruginosae, E. faecium and C. albicans. S196 against S. epidermidis and Str. agalactiae. In vivo S48/S196 had no effect on alpha/beta diversity. Linear discriminant analysis effect size (LEfSe) and analysis of composition of microbiomes (ANCOM) revealed an increase of Anaeroplasma and Faecalibacterium prausnitzii. Conclusions: The postbiotic supernatant had positive antibacterial and antifungal effects in vitro and promoted the growth of distinct bacteria in vivo.

Amino Acid-Derived Quorum Sensing Molecule Alanine on the Gastrointestinal Tract Tolerance of the Lactobacillus Strains in the Cocultured Fermentation Model

More and more people are aware of the importance of intestinal flora to human health, and people are interested in the regulation of intestinal flora and its interaction with the host. The survival status of the probiotics in the gastrointestinal environment and the microbial interactions between the lactic acid bacteria have also received considerable attention. In this study, the gastrointestinal environment tolerance, adhesion ability, and biofilm formation of the Lactobacillus strain in the coculture system were explored through the real-time fluorescence-based quantitative PCR, UPLC-MS/MS metabolic profiling analysis, and Live/Dead BacLight cell staining methods. The results showed that the coculture system could promote the release of signal molecules autoinducer-2 and effectively protect the viability of the Lactobacillus acidophilus in the gastrointestinal environment. Meanwhile, amino acid-derived characteristic metabolite l-alanine (1%) could effectively enhance the communication of the cells in the complex fermentation model, which led to an increase in the tolerance ability of the L. acidophilus by 28% in the gastrointestinal-like environment.

IMPORTANCE It was deduced from the study that amino acid-derived metabolites play an important role in cell communication in the gastrointestinal tract (GIT) environment, thus enhancing the communication of Lactobacillus strains in the complex fermentation model. Meanwhile, the viability of Lactobacillus acidophilus can be increased in the coculture system during the gastrointestinal stress environment treated with the amino acid-derived quorum sensing (QS) molecule l-alanine. It will shed some light on the application of amino acid-derived QS molecules in the fermentation stater industry.

Bacillus subtilis BS-15 Effectively Improves Plantaricin Production and the Regulatory Biosynthesis in Lactiplantibacillus plantarum RX-8

Plantaricin is a broad-spectrum bacteriocin produced by Lactiplantibacillus plantarum with significant food industry application potential. It was found that the plantaricin production of L. plantarum RX-8 was enhanced when co-culturing with Bacillus subtilis BS-15. This study, therefore, set out to explore how B. subtilis BS-15 induces biosynthesis of plantaricin. The effect of co-culturing with B. subtilis BS-15 on cell growth, plantaricin production, quorum-sensing (QS) signal molecule PlnA/autoinducer-2 (AI-2) secretion, as well as plantaricin biosynthesis gene cluster and AI-2 synthesis-associated gene expression, was investigated in bacteriocin-producer L. plantarum RX-8. When L. plantarum RX-8 and B. subtilis BS-15 were co-inoculated in Man–Rogosa–Sharp (MRS) for 20 h at an inoculum ratio of 1:1 (10⁶:10⁶ CFU/ml), the greatest plantaricin output (2,048 AU/ml) was obtained, rising by 32-fold compared with the monoculture of L. plantarum RX-8. Additionally, co-culture increased PlnA-inducing activity and AI-2 activity by 8- and 1.14-fold, respectively, over monoculture. RT-qPCR findings generated every 4 h (4–32 h) demonstrated that B. subtilis BS-15 remarkably improved the transcription of plnABCD and plnEF, and increased pfs and luxS transcription, even when using 200 mM D-ribose, a kind of AI-2 inhibitor. Based on the above findings, co-culturing with B. subtilis BS-15 as an environmental stimulus could activate the plantaricin induction via the PlnA-mediated intraspecies QS system and the AI-2-mediated interspecies QS system. Moreover, the inducing effect of PlnA and AI-2 in co-culture was independent. Differential proteomics analysis of B. subtilis BS-15 in co-culture indicated that bacteriocin-inducing regulatory mechanism may be related to flagellar assembly, peptidoglycan biosynthesis, anaerobic respiration, glycine cleavage system, or thiamin pyrophosphate biosynthesis.

Bacteriocin-like inhibitory substances production by Enterococcus faecium 135 in co-culture with Ligilactobacillus salivarius and Limosilactobacillus reuteri

The use of lactic acid bacteria (LAB) and probiotic cultures in the breeding of animals such as poultry and swine are quite common. It is known that those strains can produce bacteriocins when grown in pure culture. However, the production of bacteriocin using co-culture of microorganisms has not been much studied so far. The present study contributes with innovation in this area by embracing the production of bacteriocin-like inhibitory substances (BLIS) by a newly isolated strain of Enterococcus faecium 135. Additionally, the co-cultivation of this strain with Ligilactobacillus salivarius and Limosilactobacillus reuteri was also investigated. The antimicrobial activity of the produced BLIS was evaluated against Listeria monocytogenes, Listeria innocua, Salmonella enterica, and Salmonella enterica serovar Typhimurium using two methods: turbidimetric and agar diffusion. In addition, the presence of enterocin genes was also evaluated. The BLIS produced showed a bacteriostatic effect against the bio-indicator strains, and the highest antimicrobial activities expressed by arbitrary units per mL (AU/mL) were obtained against L. monocytogenes in monoculture (12,800 AU/mL), followed by the co-culture of E. faecium with Limosilactobacillus reuteri (400 AU/mL). After concentration with ammonium sulfate, the antimicrobial activity raised to 25,600 AU/mL. Assays to determine the proteinaceous nature of the BLIS showed susceptibility to trypsin and antimicrobial activity until 90 °C. Finally, analysis of the presence of structural genes of enterocins revealed that four enterocin genes were present in E. faecium 135. These results suggest that BLIS produced by E. faecium 135 has potential to be a bacteriocin and, after purification, could potentially be used as an antimicrobial agent in animal breeding.

CRISPR/Cas9-Based Genome Editing Platform for Companilactobacillus crustorum to Reveal the Molecular Mechanism of Its Probiotic Properties

Companilactobacillus crustorum usually serves as a starter culture for the food industry. Recent studies revealed that this species also possesses probiotic properties. Genome engineering, including point mutation or gene deletion, is desired to understand the mechanisms of its probiotic and fermentation properties. To tackle the hurdle in genetic manipulation in C. crustorum, here, we established a fast and easy CRISPR/Cas9-based platform for precise genome editing in this species. The platform includes two CRISPR/Cas9 systems and a CRISPR/Cas9-based editing system. Using the developed methods, we were able to knockout 12 genes in C. crustorum by deleting a fragment located in the open reading frames. The editing efficiency ranged from 14.3 to 100%. Moreover, we developed a CRISPR-assisted cytidine base-editing system, enabling programmed C to T conversion in the chromosome for gene inactivation or point mutation. To further exploit this platform, we investigated the role of nine putative bacteriocin-encoding genes and found that bacteriocins BM173 and BM1157 mostly contributed to the antimicrobial activity of C. crustorum MN047 against Staphylococcus aureus and Escherichia coli. In addition, the regulation of bacteriocin expression was also revealed to be linked with the quorum-sensing modulator luxS. This work will dramatically accelerate the genetic engineering of C. crustorum and close-related species.

The microbiome-shaping roles of bacteriocins

The microbiomes on human body surfaces affect health in multiple ways. They include not only commensal or mutualistic bacteria but also potentially pathogenic bacteria, which can enter sterile tissues to cause invasive infection. Many commensal bacteria produce small antibacterial molecules termed bacteriocins that have the capacity to eliminate specific colonizing pathogens; as such, bacteriocins have attracted increased attention as potential microbiome-editing tools. Metagenome-based and activity-based screening approaches have strongly expanded our knowledge of the abundance and diversity of bacteriocin biosynthetic gene clusters and the properties of a continuously growing list of bacteriocin classes. The dynamic acquisition, diversification or loss of bacteriocin genes can shape the fitness of a bacterial strain that is in competition with bacteriocin-susceptible bacteria. However, a bacteriocin can only provide a competitive advantage if its fitness benefit exceeds the metabolic cost of production, if it spares crucial mutualistic partner strains and if major competitors cannot develop resistance. In contrast to most currently available antibiotics, many bacteriocins have only narrow activity ranges and could be attractive agents for precision therapy and prevention of infections. A common scientific strategy involving multiple disciplines is needed to uncover the immense potential of microbiome-shaping bacteriocins.

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

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

Recipe for Success: Suggestions and Recommendations for the Isolation and Characterisation of Bacteriocins

Bacteriocins are bacterially produced antimicrobial peptides. Although only two peptides have been approved for use as natural preservatives foods, current research is focusing on expanding their application as potential therapeutics against clinical pathogens. Our laboratory group has been working on bacteriocins for over 25 years, and during that time, we have isolated bacteriocin-producing microorganisms from a variety of sources including human skin, human faeces, and various foods. These bacteriocins were purified and characterised, and their potential applications were examined. We have also identified bioengineered derivatives of the prototype lantibiotic nisin which possess more desirable properties than the wild-type, such as enhanced antimicrobial activity. In the current communication, we discuss the main methods that were employed to identify such peptides. Furthermore, we provide a step-by-step guide to carrying out these methods that include accompanying diagrams. We hope that our recommendations and advice will be of use to others in their search for, and subsequent analysis of, novel bacteriocins, and derivatives thereof.

Expression of five class II bacteriocins with activity against Escherichia coli in Lacticaseibacillus paracasei CNCM I-5369, and in a heterologous host

Five open reading frames viz orf010, orf12, orf023, orf030 and orf038 coding class II bacteriocins in Lacticaseibacillus paracasei CNCM I-5369 strain previously isolated from an Algerian dairy product, were found to be expressed after 24 h of growth. The strain has also shown anti-E. coli activity in a narrow pH range between 4.5 and 5. Then, expression and purification of these bacteriocins was conducted in the heterologous host E. coli. This strategy enabled us to purify the peptide encoded by orf030 in large quantities, in contrast to other peptides that were produced but required to be released from the insoluble fraction following 4 M urea and desalting treatments. All peptides heterologously produced were characterized by MALDI TOF Mass spectrometry and successfully tested for their anti-E. coli activity. Furthermore, in silico transcriptional analysis was determined by Findterm tool and with Bagel4 software permitted to locate potential promoters and co-transcription events.

The occurrence, growth, and biocontrol of Listeria monocytogenes in fresh and surface-ripened soft and semisoft cheeses

Listeria monocytogenes continues to pose a food safety risk in ready-to-eat foods, including fresh and soft/semisoft cheeses. Despite L. monocytogenes being detected regularly along the cheese production continuum, variations in cheese style and intrinsic/extrinsic factors throughout the production process (e.g., pH, water activity, and temperature) affect the potential for L. monocytogenes survival and growth. As novel preservation strategies against the growth of L. monocytogenes in susceptible cheeses, researchers have investigated the use of various biocontrol strategies, including bacteriocins and bacteriocin-producing cultures, bacteriophages, and competition with native microbiota. Bacteriocins produced by lactic acid bacteria (LAB) are of particular interest to the dairy industry since they are often effective against Gram-positive organisms such as L. monocytogenes, and because many LAB are granted Generally Regarded as Safe (GRAS) status by global food safety authorities. Similarly, bacteriophages are also considered a safe form of biocontrol since they have high specificity for their target bacterium. Both bacteriocins and bacteriophages have shown success in reducing L. monocytogenes populations in cheeses in the short term, but regrowth of surviving cells can commonly occur in the finished cheeses. Competition with native microbiota, not mediated by bacteriocin production, has also shown potential to inhibit the growth of L. monocytogenes in cheeses, but the mechanisms are still unclear. Here, we have reviewed the current knowledge on the growth of L. monocytogenes in fresh and surface-ripened soft and semisoft cheeses, as well as the various methods used for biocontrol of this common foodborne pathogen.

Case-Control Microbiome Study of Chronic Otitis Media with Effusion in Children Points at Streptococcus salivarius as a Pathobiont-Inhibiting Species

Chronic otitis media with effusion (OME) has been associated with a shift in microbiome composition and microbial interaction in the upper respiratory tract (URT). While most studies have focused on potential pathogens, this study aimed to find bacteria that could be protective against OME through a case-control microbiome study and characterization of isolates from healthy subjects. The URT and ear microbiome profiles of 70 chronic OME patients and 53 controls were compared by 16S rRNA amplicon sequencing. Haemophilus influenzae was the most frequent classic middle ear pathobiont. However, other taxa, especially Alloiococcus otitis, were also frequently detected in the ear canal of OME patients. Streptococci of the salivarius group and Acinetobacter lwoffii were more abundant in the nasopharynx of healthy controls than in OME patients. In addition to the microbiome analysis, 142 taxa were isolated from healthy individuals, and 79 isolates of 13 different Streptococcus species were tested for their pathobiont-inhibiting potential. Of these, Streptococcus salivarius isolates showed a superior capacity to inhibit the growth of H. influenzae, Moraxella catarrhalis, Streptococcus pneumoniae, Streptococcus pyogenes, Staphylococcus aureus, A. otitis, and Corynebacterium otitidis. S. salivarius strains thus show potential as a probiotic for prevention or treatment of OME based on their overrepresentation in the healthy nasopharynx and their ability to inhibit the growth of respiratory pathobionts. (This study has been registered at ClinicalTrials.gov under registration no. NCT03109496.)

IMPORTANCE The majority of probiotics marketed today target gastrointestinal health. This study searched for bacteria native to the human upper respiratory tract, with a beneficial potential for respiratory and middle ear health. Comparison of the microbiomes of children with chronic otitis media with effusion (OME) and of healthy controls identified Streptococcus salivarius as a health-associated and prevalent inhabitant of the human nasopharynx. However, beneficial potential should be assessed at strain level. Here, we also isolated specific S. salivarius strains from the healthy individuals in our study. These isolates showed a beneficial safety profile and efficacy potential to inhibit OME pathogens in vitro. These properties will now have to be evaluated and confirmed in human clinical studies.

A New Approach to Harness Probiotics Against Common Bacterial Skin Pathogens: Towards Living Antimicrobials

In this study, the potential of certain lactic acid bacteria—classified as probiotics and known to be antimicrobially active against pathogens or food-poisoning microorganisms—was evaluated with respect to their activity against bacterial skin pathogens. The aim of the study was to develop a plaster/bandage for the application of inhibitory substances produced by these probiotics when applied to diseased skin. For this purpose, two Streptococcus salivarius strains and one Lactobacillus plantarum were tested for production of antimicrobials (bacteriocin-like substances) active against Gram-positive and Gram-negative pathogens using established methods. A newly designed membrane test ensured that the probiotics produce antimicrobials diffusible through membranes. Target organisms used were Cutibacterium acnes, Staphylococcus aureus, and Pseudomonas aeruginosa. Moreover, the L. plantarum 8P-A3 strain was tested against additional bacteria involved in skin disorders. The Lactobacillales used were active against all potential skin pathogens tested. These probiotics could be enclosed between polymer membranes—one tight, the other permeable for their products, preserved by vacuum drying, and reactivated after at least three months storage. Importantly, the reactivated pads containing the probiotics demonstrated antibacterial activity on agar plates against all pathogens tested. This suggests that the probiotic containing pads may be topically applied for the treatment of skin disorders without the need for a regular antibiotic treatment or as an adjunctive therapy.

Microbial co-culturing strategies for the production high value compounds, a reliable framework towards sustainable biorefinery implementation - an overview

The microbial co-cultures or consortia are a natural set of microorganisms formed from different species or the same species but different strains, in which members can interact with each other. The co-culture systems have wide variety of technological applications such as the production of foods, treatment of wastewater, removal of toxic substances, environmental recovery, and all these without the need to work in sterile conditions. Therefore, the need of understanding communication mechanisms between cell-to-cell within co-culture will allow to construct and to program their biological behavior from the use of complex substrates to produce biocompounds. The technology of co-culture systems enables the development of biorefinery platforms to obtain biofuels, and high value compounds through biomass transformation by sustainable process. This review focuses on understanding the roles of consortia microbial to design and built co-culture systems to produce high value compounds in terms a sustainable biorefinery.

Enhancement of the antibacterial potential of plantaricin by incorporation into silver nanoparticles

Background

Bacteriocins are proteinaceous compounds produced from lactic acid bacteria. Bacteriocins are well-known for their antibacterial potential and safety for application in food. However, the commercial availability of bacteriocin is facing several limitations; among them is the low yield and short stability period. That calls for a new strategy for overcoming these hurdles. Among these approaches is incorporating bacteriocin in nanoparticles. So, the aim of this study was to enhance the plantaricin produced from isolated Lactobacillus plantarum strain using nanotechnology.

Results

In this study, the plnEF genes encoding plantaricin EF have been identified and sequenced (accession number of MN172264.1). The extracted bacteriocin (EX-PL) was obtained by the ammonium sulfate method. Then, it was used for biosynthesizing plantaricin-incorporated silver nanoparticles (PL-SNPs). The synthesized nanoparticles were confirmed by SEM-EDAX analysis. The antibacterial activity of both combined (PL-SNPs) and extracted plantaricin (EX-PL) were tested against some strains of foodborne pathogenic bacteria. The results revealed that the antibacterial activities were increased by 99.2% on the combination of bacteriocin with the silver nanoparticle. The MIC of EX-PL (7.6 mg/mL) has been lowered after incorporating into silver nanoparticles and reached 0.004 mg/mL for PL-SNPs. Despite that extracted plantaricin showed no inhibitory activity towards Listeria monocytogenes, plantaricin-incorporated silver nanoparticles displayed inhibitory activity against this strain. Furthermore, the stability period at 4 °C was increased from 5 days to 60 days for EX-PL and PL-SNPs, respectively.

Conclusions

Plantaricin-incorporated silver nanoparticles possess higher antibacterial activity and more stability than the free one, which makes it more fitting for combating foodborne pathogens and open more fields for applications in both food and pharmaceutical industries.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s43141-020-00093-z.

Toward understanding the signals of bacteriocin production by Streptococcus spp. and their importance in current applications

Microorganisms have developed quorum sensing (QS) systems to detect small signaling molecules that help to control access to additional nutrients and space in highly competitive polymicrobial niches. Many bacterial processes are QS-regulated; two examples are the highly related traits of the natural genetic competence state and the production of antimicrobial peptides such as bacteriocins. The Streptococcus genus is widely studied for its competence and for its ability to produce bacteriocins, as these antimicrobial peptides have significant potential in the treatment of infections caused by multiple-resistant pathogens, a severe public health issue. The transduction of a two-component system controls competence in streptococci: (1) ComD/E, which controls the competence in the Mitis and Anginosus groups, and (2) ComR/S, which performs the same function in the Bovis, Mutans, Salivarius, and Pyogenic groups. The cell-to-cell communication required for bacteriocin production in the Streptococcus groups is controlled mainly by a paralog of the ComD/E system. The relationships between pheromone signals and induction pathways are related to the bacteriocin production systems. In this review, we discuss the recent advances in the understanding of signaling and the induction of bacteriocin biosynthesis by QS regulation in streptococci. This information could aid in the design of better methods for the development and production of these antimicrobial peptides. It could also contribute to the analysis and emerging applications of bacteriocins in terms of their safety, quality, and human health benefits.

A review on preparation and chemical analysis of postbiotics from lactic acid bacteria

Postbiotics may be defined as soluble metabolites released by food-grade microorganisms during the growth and fermentation in complex microbiological culture, food or gut. It is rich in high and low molecular weight biologically active metabolites. There are still gaps concerning these substances, mainly how to use them for food applications. Although the most recent work on preparation and application of postbiotics from several probiotics are very encouraging, the suitability of postbiotics to combat microorganisms that deal with food safety should be tested mainly by analyzing the chemical composition and conducting antagonistic tests. Consequently, foods can effectively benefit from an identified postbiotic with a defined effect. This review approached the recent advances in relation to the preparation of postbiotics from lactic acid bacteria. The function of different instrumental analysis techniques and factors affecting the chemical composition of postbiotics were also comprehensively reviewed.

The effect of co-cultivation of Rhodococcus erythropolis with other bacterial strains on biological activity of synthesized surface-active substances

Surface-active substances synthesized by Rhodococcus erythropolis ІMВ Ас-5017 during co-cultivation with inducing bacteria either Bacillus subtilis BT-2 or Escherichia coli ІЕM-1 (SASI) had the higher antimicrobial and antiadhesive activities in comparison with surface-active substances synthesized in the medium without cells of inducing bacteria (SAS). Minimum inhibitory concentrations of SASI ranged from 3 to12 μg/mL and were in 4-32 times lower than the same parameter for SAS. Treatment of abiotic surfaces (ceramic, steel, and glass) with SASI decreased adhesion of bacteria Staphylococcus aureus BMC-1 or yeasts Candida albicans D-6 to the level of 10-32 % in comparison with 32-87 % after treatment of surfaces with SAS. Destruction of bacterial and yeast biofilms treated with SASI was in the range from 40 to 94 %, while it was 32-65 % in the case when SAS was used. Increasing of biological activity of surface-active substances synthesized by R. erythropolis in co-culture with inducing bacteria E. coli or B. subtilis was shown for the first time.

Pediocin AcH Is Transcriptionally Regulated by a Two-Component System in Lactobacillus plantarum subsp. plantarum

ABSTRACT

The quorum-sensing regulation of class II bacteriocin (AcH) synthesis in Lactobacillus plantarum subsp. plantarum Zhang-LL was studied. No detectable inhibition zone was formed by the supernatant of L. plantarum subsp. plantarum Zhang-LL culture in skim milk (SM) with an inoculum size of 7 × 102 CFU/mL after incubation for 36 h. Hence, this culture system was used to investigate the induced regulation mechanism of bacteriocin production in L. plantarum subsp. plantarum Zhang-LL. Bacteriocin production by this bacterium in SM medium was induced by treatment with inactivated culture supernatant from de Man Rogosa Sharpe (MRS) medium (supernatant-MRS). Pediocin AcH encoded by the papA gene in a plasmid in strain Zhang-LL was the inducer present in supernatant-MRS. This is the first report of the role of pediocin AcH in the quorum-sensing regulation of class II bacteriocin synthesis. The mRNA of the papA, papB, papC, and papD genes involved in bacteriocin synthesis by strain Zhang-LL in SM medium was upregulated significantly after being induced by pediocin AcH. This study offers the first evidence that the ABT40_05745, ABT40_05750, and ABT40_11975 components of two-component systems in L. plantarum subsp. plantarum Zhang-LL are involved in the induced regulation of AcH bacteriocin production.

HIGHLIGHTS

Fermentation of Wheat Bran and Whey Permeate by Mono-Cultures of Lacticaseibacillus rhamnosus Strains and Co-culture With Yeast Enhances Bioactive Properties

The aim of this work was to obtain a bioingredient (BI) with bioactive properties through the solid fermentation of a wheat bran-whey permeate (WB/WP) mixture with three strains of Lacticaseibacillus rhamnosus (R0011, ATCC 9595, and RW-9595M) in mono or co-culture with Saccharomyces cerevisiae. The choice of these strains was based on their capacity to produce the same exopolysaccharide (EPS), but at different yields. The solid fermentation of WB/WP revealed a similar growth pattern, sugar utilization and metabolite production between strains and types of culture. Lactic acid, soluble protein, free amino acid and phenolic compound content in BI were compared to NFWB. Water soluble polysaccharides (including EPS) were significantly increased in co-culture for (44%) ATCC 9595, (40%) R0011 and (27%) RW-9595M. The amount of bound Total Phenolic Content (TPC) as well as the antioxidant activity in BI were higher after fermentation. The free phenolic acid content was higher after fermentation with ATCC 9595 (53-59%), RW-9595M (45-46%), and R0011 (29-39%) compared to non-fermented NFWB. Fermentation by these strains increased the amounts of free caffeic acid and 4-hydroxybenzoic acid in both types of culture. The bound phenolic acid content was enhanced in co-culture for the BI obtained from the highest EPS producer strain RW-9595M which was 30% higher than NFWB. After in vitro digestion, bioaccessibility of free total phenolic acids was improved by more than 40% in BI compared to NFWB. The co-culture increased recovery of TPC (%) and antioxidant activity compared to monoculture for the strains in digested product. In contrast, the recovery of bound total phenolic acids in co-culture was 33 and 38% lower when compared to monoculture for R0011 and RW-9595M. Our findings provide new insights into the impact of LAB/yeast co-culture on the bioactive properties of fermented wheat bran.

The functional capacity of plantaricin-producing Lactobacillus plantarum SF9C and S-layer-carrying Lactobacillus brevis SF9B to withstand gastrointestinal transit

Background

We evaluated the functional capacity of plantaricin-producing Lactobacillus plantarum SF9C and S-layer-carrying Lactobacillus brevis SF9B to withstand gastrointestinal transit and to compete among the gut microbiota in vivo. Considering the probiotic potential of Lb. brevis SF9B, this study aims to investigate the antibacterial activity of Lb. plantarum SF9C and their potential for in vivo colonisation in rats, which could be the basis for the investigation of their synergistic functionality.

Results

A plantaricin-encoding cluster was identified in Lb. plantarum SF9C, a strain which efficiently inhibited the growth of Listeria monocytogenes ATCC^® 19111™ and Staphylococcus aureus 3048. Homology-based three-dimensional (3D) structures of SF9C plantaricins PlnJK and PlnEF were predicted using SWISS-MODEL workspace and the helical wheel representations of the plantaricin peptide helices were generated by HELIQUEST. Contrary to the plantaricin-producing SF9C strain, the S-layer-carrying SF9B strain excluded Escherichia coli 3014 and Salmonella enterica serovar Typhimurium FP1 from the adhesion to Caco-2 cells. Finally, PCR-DGGE analysis of the V2–V3 regions of the 16S rRNA gene confirmed the transit of the two selected lactobacilli through the gastrointestinal tract (GIT). Microbiome profiling via the Illumina MiSeq platform revealed the prevalence of Lactobacillus spp. in the gut microbiota of the Lactobacillus-treated rats, even on the 10th day after the Lactobacillus application, compared to the microbiota of the healthy and AlCl₃-exposed rats before Lactobacillus treatment.

Conclusion

The combined application of Lb. plantarum SF9C and Lb. brevis SF9B was able to influence the intestinal microbiota composition in rats, which was reflected in the increased abundance of Lactobacillus genus, but also in the altered abundances of other bacterial genera, either in the model of healthy or aberrant gut microbiota of rats. The antibacterial activity and capacity to withstand in GIT conditions contributed to the functional aspects of SF9C and SF9B strains that could be incorporated in the probiotic-containing functional foods with a possibility to positively modulate the gut microbiota composition.

Carnobacterium maltaromaticum as bioprotective culture in vitro and in cooked ham

The bioprotective effects of Carnobacterium maltaromaticum (CM) strains were assessed in vitro and in sliced cooked ham. CM strains were tested in vitro against Listeria monocytogenes (LM), Escherichia coli O157:H7 (EC) and Salmonella Typhimurium (ST). In vitro effect was evaluated using co-culture (with and without EDTA) and cell-free supernatant (CFS). CFS was tested by agar well diffusion and minimum inhibitory concentration. In cooked ham, the inhibitory effect of CM on L. innocua (LI) and on the physicochemical parameters were evaluated for 7 days at 4 °C. In co-cultures at -1 °C and 4 °C, all CM isolates inhibited LM. A slight inhibition was observed against the Gram-negative bacteria with the addition of EDTA. CFS did not show inhibitory effect under the studied conditions. In cooked ham, CM inhibited LI growth and did not affect the physicochemical parameters of the product during storage. CM strains show potential to be used as bioprotective cultures in cold-stored cooked ham and improve its safety.

Competition Among Gardnerella Subgroups From the Human Vaginal Microbiome

Gardnerella spp. are hallmarks of bacterial vaginosis, a clinically significant dysbiosis of the vaginal microbiome. Gardnerella has four subgroups (A, B, C, and D) based on cpn60 sequences. Multiple subgroups are often detected in individual women, and interactions between these subgroups are expected to influence their population dynamics and associated clinical signs and symptoms of bacterial vaginosis. In the present study, contact-independent and contact-dependent interactions between the four Gardnerella subgroups were investigated in vitro. The cell free supernatants of mono- and co-cultures had no effect on growth rates of the Gardnerella subgroups suggesting that there are no contact-independent interactions (and no contest competition). For contact-dependent interactions, mixed communities of 2, 3, or 4 subgroups were created and the initial (0 h) and final population sizes (48 h) were quantified using subgroup-specific PCR. Compared to the null hypothesis of neutral interactions, most (69.3%) of the mixed communities exhibited competition. Competition reduced the growth rates of subgroups A, B, and C. In contrast, the growth rate of subgroup D increased in the presence of the other subgroups. All subgroups were able to form biofilm alone and in mixed communities. Our study suggests that there is scramble competition among Gardnerella subgroups, which likely contributes to the observed distributions of Gardnerella spp. in vaginal microbiomes and the formation of the multispecies biofilms characteristic of bacterial vaginosis.

Enhanced Exopolysaccharide Production by Lactobacillus rhamnosus in Co-Culture with Saccharomyces cerevisiae

Lactobacillus strains are known to produce exopolysaccharides (EPS) with recognized health benefits (i.e. prebiotic and immunomodulation) but production is limited by low yields. Co-culture has been shown to improve metabolite productivity, particularly bacteriocins and EPS. Although lactic acid bacteria (LAB) and yeasts are found in several fermented products, the molecular mechanisms linked to the microbial interactions and their influences on EPS biosynthesis are unclear. The aim of the present study was to investigate the effect of co-culture on EPS production by three Lactobacillus rhamnosus strains (ATCC 9595, R0011, and RW-9595M) in association with Saccharomyces cerevisiae. Fermentation, in both mono and co-culture, was carried out and the expression of key LAB genes was monitored. After 48 h, results revealed that EPS production was enhanced by 39%, 49%, and 42% in co-culture for R0011, ATCC 9595, and RW-9595M, respectively. Each strain showed distinctive gene expression profiles. For a higher EPS production, higher EPS operon expression levels were observed for RW-9595M in co-culture. The construction of gene co-expression networks revealed common correlations between the expression of genes related to the EPS operons, sugar metabolism, and stress during EPS production and microbial growth for the three strains. Our findings provide insight into the positive influence of inter-kingdom interactions in stimulating EPS biosynthesis, representing progress toward the development of a bio-ingredient with broad industrial applications.

Sub-inhibitory Effects of Antimicrobial Peptides

Antimicrobials, and particularly antimicrobial peptides (AMPs), have been thoroughly studied due to their therapeutic potential. The research on their exact mode of action on bacterial cells, especially at under sublethal concentrations, has resulted in a better understanding of the unpredictable nature of bacterial behavior under stress conditions. In this review, we were aiming to gather the wide yet still under-investigated knowledge about various AMPs and their subinhibition effects on cellular and molecular levels. We describe how AMP action is non-linear and unpredictable, also showing that exposure to AMP can lead to antimicrobial resistance via triggering various regulatory systems. Being one of the most known types of antimicrobials, bacteriocins have dual action and can also be utilized by microorganisms as signaling molecules at naturally achievable sub-inhibitory concentrations. The unpredictable nature of AMP action and the pathogenic response triggered by them remains an area of knowledge that requires further investigation.

Biopreservation potential of antimicrobial protein producing Pediococcus spp. towards selected food samples in comparison with chemical preservatives

The present study elucidates biopreservation potential of an antimicrobial protein; bacteriocin, producing Pediococcus spp. isolated from dairy sample and enhancement of their shelf life in comparison with two chemical preservatives. The antimicrobial protein producing Pediococcus spp. was isolated from selected diary samples and characterised by standard microbiology and molecular biology protocols. The cell free supernatant of Pediococcus spp. was applied on the selected food samples and monitored on daily basis. Antimicrobial potential of the partially purified protein from this bacterium was tested against clinical isolates by well diffusion assay. The preservation efficiency of bacteriocin producing isolate at various concentrations was tested against selected food samples and compared with two chemical preservatives such as sodium sulphite and sodium benzoate. The bacteriocin was partially purified and the microbiological qualities of the biopreservative treated food samples were assessed. The present study suggested that 100 μg/l of bacteriocin extract demonstrated antimicrobial potential against E. coli and Shigella spp. The treatment with the Pediococcus spp. showed enhanced preservation at 15 mL/kg of selected samples for a period of 15 days in comparison with sodium sulphite and sodium benzoate. The microbiological quality of food samples treated with biopreservative showed lesser total bacterial count (CFU/g) in comparison with the food samples applied with chemicals (p ≤ 0.05). Thus, the present study suggests that bacteriocin producing Pediococcus probably provides enhanced shelf life to the selected food samples and can be used as biopreservatives.

Enhanced Bacteriocin Production by Pediococcus pentosaceus 147 in Co-culture With Lactobacillus plantarum LE27 on Cheese Whey Broth

The production of bacteriocins by lactic acid bacteria (LAB) has been of wide interest in the food industry due to their potential application in biopreservation. The production of bacteriocins is usually low in single strain fermentation, but can improve when the bacteriocinogenic strain is cultured in association with another bacteria. The present work aims to evaluate the growth and production of bacteriocins by Pediococcus pentosaceus 147 (bacteriocinogenic strain) in co-culture with Lactobacillus plantarum LE27 (inducer strain) using a culture medium based on cheese whey (CW). Strains were inoculated in co-culture in a CW broth at 7.24 Log CFU/mL of initial concentration of P. pentosaceus 147 and incubated at 37°C. Bacteriocin production was measured after 24 h by the critical dilution method, biomass was measured by plating on MRS agar (1% aniline blue), and a mono-culture was used as a control. The titers of bacteriocins produced by P. pentosaceus 147 in mono-culture were 19,200 AU/mL lower than those obtained in co-culture with Lb. plantarum LE27 at 51,200 AU/mL. The effect of adding the inducer strain at different times of incubation (3, 6, 9, and 12 h) was evaluated, with the addition of the induction factor at the beginning of the incubation of P. pentosaceus 147 generating the highest bacteriocin activity. This study shows the potential of inducing bacteriocinogenesis using co-cultures of strains of the genera Pediococcus and Lactobacillus and using alternative substrates such as cheese whey.

Model Microbial Consortia as Tools for Understanding Complex Microbial Communities

A major biological challenge in the postgenomic era has been untangling the composition and functions of microbes that inhabit complex communities or microbiomes. Multi-omics and modern bioinformatics have provided the tools to assay molecules across different cellular and community scales; however, mechanistic knowledge over microbial interactions often remains elusive. This is due to the immense diversity and the essentially undiminished volume of not-yet-cultured microbes. Simplified model communities hold some promise in enabling researchers to manage complexity so that they can mechanistically understand the emergent properties of microbial community interactions. In this review, we surveyed several approaches that have effectively used tractable model consortia to elucidate the complex behavior of microbial communities. We go further to provide some perspectives on the limitations and new opportunities with these approaches and highlight where these efforts are likely to lead as advances are made in molecular ecology and systems biology.

Cooperation of lactic acid bacteria regulated by the AI-2/LuxS system involve in the biopreservation of refrigerated shrimp

Litopenaeus vannamei is an extremely perishable food because of rapid microbial growth and chemical degradation after harvesting. Biopreservation is a food preservation technology based on the addition of "positive" bacteria to kill or prevent the growth of undesirable microorganisms. In this study, the cooperation between lactic acid bacteria (LAB) strains (Lactobacillus plantarum AB-1 and Lactobacillus casei) regulated by the AI-2/LuxS was investigated in vitro and on shrimp. The antimicrobial activity of L. plantarum AB-1 was significantly increased in the co-culture compared with the mono-culture in vitro, and the transcription of the quorum sensing luxS gene and bacteriocin regulatory operons (plnB and plnC) in L. plantarum AB-1 were also significantly increased in co-culture (P < .05), indicating cooperation and that the production of bacteriocin in L. plantarum AB-1 might be related to the LuxS/AI-2 quorum sensing (QS) system. The results were confirmed by adding the exogenous AI-2 molecule signal to L. plantarum AB-1 in vitro. In the on shrimp experiments, the spoilage organisms (mainly Shewanella baltica) in shrimp samples were significantly inhibited after co-inoculation with L. plantarum AB-1 and L. casei, and the values of total volatile basic nitrogen (TVB-N) and pH in co-inoculated shrimp were also significantly decreased (P < .05). In addition, the AI-2 activities in co-inoculated shrimp were significantly higher during refrigerated storage. The results suggest that the cooperation and bacteriocin production of lactic acid bacteria might by regulated by the AI-2/LuxS system, and the co-inoculation of L. plantarum AB-1 and L. casei in shrimp is an effective strategy for biopreservation of shrimp.

Screening of bacterial endophytes as potential biocontrol agents against soybean diseases

AIMS

This research was aimed at identifying and characterizing endophytic micro-organisms associated with soybean that have antimicrobial activity towards soybean pathogens.

METHODS AND RESULTS

Soybean plants were collected from field trials in four locations of southern Brazil that were cultivated with conventional (C) and transgenic glyphosate-resistant (GR) soybeans. Endophytic bacteria isolated from roots, stems and leaves of soybeans were evaluated for their capacity to inhibit fungal and bacterial plant pathogens and 13 micro-organisms were identified with antagonistic activity. Approximately 230 bacteria were isolated and identified based on the 16S rRNA and rpoN gene sequences. Bacteria isolated from conventional and transgenic soybeans were significantly different not only in population diversity but also in their antagonistic capacity. Thirteen isolates showed in vitro antagonism against Sclerotinia sclerotiorum, Phomopsis sojae and Rhizoctonia solani. Bacillus sp. and Burkholderia sp. were the most effective isolates in controlling bacterial and fungal pathogens in vitro. Extracts and precipitates from culture supernatants of isolates showed different patterns of inhibitory activity on growth of fungal and bacterial pathogens.

CONCLUSIONS

Bacillus sp. and Burkholderia sp. were the most effective isolates in controlling fungal pathogens in vitro, and the activity is mainly due to peptides. However, most of the studied bacteria showed the presence of antimicrobial compounds in the culture supernatant, either peptides, bacteriocins or secondary metabolites.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results could be significant to develop tools for the biological control of soybean diseases. The work brought to the identification of micro-organisms such as Bacillus sp. and Burkholderia sp. that have the potential to protect crops in order to enhance a sustainable management system of crops. Furthermore, the study provides the first evidences of the influence of management as well as the genetics of glyphosate-resistant soybean on the diversity of bacterial endophytes of soybean phytobiome.

Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs' gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods

Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery-raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild-born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, because the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery-reared parrs.

Bacteriocins: Not Only Antibacterial Agents

This commentary was aimed at shedding light on the multifunction of bacteriocins mainly those produced by lactic acid bacteria. These antibacterial agents were first used to improve food safety and quality. With the increasing antibiotic resistance concern worldwide, they have been considered as viable agents to replace or potentiate the fading abilities of conventional antibiotics to control human pathogens. Bacteriocins were also shown to have potential as antiviral agents, plant protection agents, and anticancer agents. Bacteriocins were reported to be involved in shaping bacterial communities through inter- and intra-specific interactions, conferring therefore to producing strains a probiotic added value. Furthermore, bacteriocins recently were shown as molecules with a fundamental impact on the resilience and virulence of some pathogens.

Pentocin MQ1: A Novel, Broad-Spectrum, Pore-Forming Bacteriocin From Lactobacillus pentosus CS2 With Quorum Sensing Regulatory Mechanism and Biopreservative Potential

Micrococcus luteus, Listeria monocytogenes, and Bacillus cereus are major food-borne pathogenic and spoilage bacteria. Emergence of antibiotic resistance and consumer demand for foods containing less of chemical preservatives led to a search for natural antimicrobials. A study aimed at characterizing, investigating the mechanism of action and regulation of biosynthesis and evaluating the biopreservative potential of pentocin from Lactobacillus pentosus CS2 was conducted. Pentocin MQ1 is a novel bacteriocin isolated from L. pentosus CS2 of coconut shake origin. The purification strategy involved adsorption-desorption of bacteriocin followed by RP-HPLC. It has a molecular weight of 2110.672 Da as determined by MALDI-TOF mass spectrometry and a molar extinction value of 298.82 M⁻¹ cm⁻¹. Pentocin MQ1 is not plasmid-borne and its biosynthesis is regulated by a quorum sensing mechanism. It has a broad spectrum of antibacterial activity, exhibited high chemical, thermal and pH stability but proved sensitive to proteolytic enzymes. It is potent against M. luteus, B. cereus, and L. monocytogenes at micromolar concentrations. It is quick-acting and exhibited a bactericidal mode of action against its targets. Target killing was mediated by pore formation. We report for the first time membrane permeabilization as a mechanism of action of the pentocin from the study against Gram-positive bacteria. Pentocin MQ1 is a cell wall-associated bacteriocin. Application of pentocin MQ1 improved the microbiological quality and extended the shelf life of fresh banana. This is the first report on the biopreservation of banana using bacteriocin. These findings place pentocin MQ1 as a potential biopreservative for further evaluation in food and medical applications.

Engineering co-culture system for production of apigetrin in Escherichia coli

Microbial cells have extensively been utilized to produce value-added bioactive compounds. Based on advancement in protein engineering, DNA recombinant technology, genome engineering, and metabolic remodeling, the microbes can be re-engineered to produce industrially and medicinally important platform chemicals. The emergence of co-culture system which reduces the metabolic burden and allows parallel optimization of the engineered pathway in a modular fashion restricting the formation of undesired byproducts has become an alternative way to synthesize and produce bioactive compounds. In this study, we present genetically engineered E. coli-based co-culture system to the de novo synthesis of apigetrin (APG), an apigenin-7-O-β-D-glucopyranoside of apigenin. The culture system consists of an upstream module including 4-coumarate: CoA ligase (4CL), chalcone synthase, chalcone flavanone isomerase (CHS, CHI), and flavone synthase I (FNSI) to synthesize apigenin (API) from p-coumaric acid (PCA). Whereas, the downstream system contains a metabolizing module to enhance the production of UDP-glucose and expression of glycosyltransferase (PaGT3) to convert API into APG. To accomplish this improvement in titer, the initial inoculum ratio of strains for making the co-culture system, temperature, and media component was optimized. Following large-scale production, a yield of 38.5 µM (16.6 mg/L) of APG was achieved. In overall, this study provided an efficient tool to synthesize bioactive compounds in microbial cells.