Impact of quorum sensing on the quality of fermented foods

The key quorum sensing gene luxS in Lactobacillus acidophilus CICC 6074 and Lactobacillus helveticus R0052 mediates organic acid production and promotes protein hydrolysis in yogurt

In this study, the effect of luxS, a key gene involved in quorum sensing, on the characteristic flavor of yogurt and its molecular mechanisms during the cofermentation of yogurt with engineered probiotics was investigated. The luxS gene overexpression strain was constructed by the homologous recombination technique, and its effect on the expression of population sensing signaling molecules and luxS gene was determined by bioluminescence and quantitative real-time PCR, and finally, headspace solid-phase micro extraction-GC-MS (HS-SPME-GC-MS) and metabolomics were used to determine the mechanism of its effect on the characteristic flavor of yogurt. The results demonstrated that the overexpression strains of Lactobacillus acidophilus CICC 6074-pMG36e-luxS and Lactobacillus helveticus R0052-pMG36e-luxS were successfully constructed. The expression of the luxS gene was upregulated by 2.25-fold and 3.16-fold, respectively. Compared with the wild-type strains, yogurt fermented by the overexpression strains showed a significant increase in AI-2 content, acidity, viable bacterial count, and protein hydrolysis, whereas pH, water-holding capacity, and hardness were significantly reduced. The HS-SPME-GC-MS results revealed the presence of 31 volatile flavor substances in yogurt. Among them, benzaldehyde (almond and burned sugar flavors), 2,4-dimethyl- (almond, cherry, and naphthalene flavors), dibutyl phthalate (a faint aromatic odor), and n-decanoic acid (rancid and fatty notes) were identified as the key differential flavor substances mediated by the luxS gene. Metabolomics results showed that the luxS gene mediates the production of organic acids in yogurt through arginine and proline metabolism, phenylalanine metabolism, and tryptophan metabolism. This study provides a theoretical basis for a deeper understanding of the molecular mechanisms underlying yogurt flavor formation.

Insights into the flavor contribution, mechanisms of action, and future trends of coagulase-negative staphylococci in fermented meat products: A review

During fermentation, meat is pre-treated and cured to cultivate a diverse microflora, resulting in fermented meat products with distinctive flavors. Coagulase-negative staphylococcus holds a crucial role in all fermented meat products, contributing to the breakdown of proteins, carbohydrates, and fats, and the creation of flavor compounds. Fermentation technology has important research value and significance in fermented meat products. The optimization and improvement of flavor by CNS can be achieved by regulating the fermentation environment, initial microflora and processing conditions. The review explores the ways in which coagulase-negative staphylococci contribute to the flavors in fermented meat products. The mechanism of flavor substance formation and means of regulation in coagulase-negative staphylococci were also investigated. The review concludes by summarizing future development trends and drawing conclusions.

Harnessing microbial division of labor for biomanufacturing: a review of laboratory and formal modeling approaches

Bioprocess industries aim to meet the increasing demand for product complexity by designing enhanced cellular and metabolic capabilities for the host. Monocultures, standard biomanufacturing workhorses, are often restricted in their capability to meet these demands, and the solution often involves the genetic modification of the host. Synthetic microbial communities are a promising alternative to monocultures because they exhibit division of labor, enabling efficient resource utilization and pathway modularity. This specialization minimizes metabolic burden and enhances robustness to perturbations, providing a competitive advantage. Despite this potential, their utilization in biotechnological or bioprocessing applications remains limited. The recent emergence of new and innovative community design tools and strategies, particularly those harnessing the division of labor, holds promise to change this outlook. Understanding the microbial interactions governing natural microbial communities can be used to identify complementary partners, informing synthetic community design. Therefore, we particularly consider engineering division of labor in synthetic microbial communities as a viable solution to accelerate progress in the field. This review presents the current understanding of how microbial interactions enable division of labor and how this information can be used to design synthetic microbial communities to perform tasks otherwise unfeasible to individual organisms. We then evaluate laboratory and formal modeling approaches specifically developed to: elucidate microbial community physiology, guide experimental design, and improve our understanding of complex community interactions assisting synthetic community design. By synthesizing these insights, we aim to present a comprehensive framework that advances the use of microbial communities in biomanufacturing applications.

Harnessing Microbial Signal Transduction Systems in Natural and Synthetic Consortia for Biotechnological Applications

Signal transduction is crucial for communication and cellular response in microbial communities. Consortia rely on it for effective communication, responding to changing environmental conditions, establishing community structures, and performing collective behaviors. Microbial signal transduction can be through quorum sensing (QS), two-component signal transduction systems, biofilm formation, nutrient sensing, chemotaxis, horizontal gene transfer stress response, and so forth. The consortium uses small signaling molecules in QS to regulate gene expression and coordinate intercellular communication and behaviors. Biofilm formation allows cells to adhere and aggregate, promoting species interactions and environmental stress resistance. Chemotaxis enables directional movement toward or away from chemical gradients, promoting efficient resource utilization and community organization within the consortium. In recent years, synthetic microbial consortia have gained attention for their potential applications in biotechnology and bioremediation. Understanding signal transduction in natural and synthetic microbial consortia is important for gaining insights into community dynamics, evolution, and ecological function. It can provide strategies for biotechnological innovation for enhancing biosensors, biodegradation, bioenergy efficiency, and waste reduction. This review provides compelling insight that will advance our understanding of microbial signal transduction dynamics and its role in orchestrating microbial interactions, which facilitate coordination, cooperation, gene expression, resource allocation, and trigger specific responses that determine community success.

Fermentation process of tobacco leaves drives the specific changes of microbial community

BACKGROUND

The changes of microbial community on tobacco leaves are affected by several factors during fermentation. However, the relative contribution of different factors in determining microbial community is not clear. This study investigated the effects of fermentation time (fermentation for 0, 3, 6, 9 and 12 months), leaf position (middle and top tobacco leaves) and fermentation site (Longyan and Xiamen warehouses) on bacterial community of tobacco leaves using 16 S rDNA sequencing.

RESULTS

The results demonstrated that fermentation time had a much stronger impact on bacterial diversity, composition, co-occurrence network and functional profiles than leaf position and fermentation site. With the fermentation progressed, the difference of bacterial community between middle and top tobacco leaves was gradually reduced or even disappeared. The bacterial community diversity and network complexity at three, six and nine months of fermentation were significantly lower than those at fermentation initiation. Specific bacterial genera with desired functions were recruited at different fermentation stages, such as Terribacillus, Pantoea and Franconibacter at three or six months of fermentation and Pseudomonas at nine months of fermentation. The recruited microorganisms would form biofilms on tobacco leaves and compete for polysaccharide or protein substances to accelerate the degradation of tobacco macromolecular substances.

CONCLUSIONS

In conclusion, fermentation time was an important factor in determining the composition and function of microbial community on tobacco leaves during the fermentation process.

Effect of photostimulation through red LED light radiation on natural fermentation of table olives: An innovative case study with Negrinha the Freixo variety

In this study, for the first time, red LED light radiation was applied to the fermentation process of table olives using the Negrinha de Freixo variety. Photostimulation using LED light emission (630 ± 10 nm) is proposed to shorten and speed up this stage and reduce time to market. Several physical-chemical characteristics and microorganisms (total microbial count of mesophilic aerobic, molds, yeasts, and lactic acid bacteria) and their sequence during fermentation were monitored. The fermentation occurred for 122 days, with two irradiation periods for red LED light. The nutritional composition and sensory analysis were performed at the end of the process. Fermentation under red LED light increased the viable yeast and lactic acid bacteria (LAB) cell counts and decreased the total phenolics in olives. Even though significant differences were observed in some color parameters, the hue values were of the same order of magnitude and similar for both samples. Furthermore, the red LED light did not play a relevant change in the texture profile, preventing the softening of the fruit pulp. Similarly, LED light did not modify the existing type of microflora but increased species abundance, resulting in desirable properties and activities. The species identified were yeasts - Candida boidinii, Pichia membranifaciens, and Saccharomyces cerevisiae, and bacteria - Lactobacillus plantarum and Leuconostoc mesenteroides, being the fermentative process dominated by S. cerevisiae and L. plantarum. At the end of fermentation (122 days), the irradiated olives showed less bitterness and acidity, higher hardness, and lower negative sensory attributes than non-irradiated. Thus, the results of this study indicate that red LED light application can be an innovative technology for table olives production.

Genomic exploration of the fermented meat isolate Staphylococcus shinii IMDO-S216 with a focus on competitiveness-enhancing secondary metabolites

BACKGROUND

Staphylococcus shinii appears as an umbrella species encompassing several strains of Staphylococcus pseudoxylosus and Staphylococcus xylosus. Given its phylogenetic closeness to S. xylosus, S. shinii can be found in similar ecological niches, including the microbiota of fermented meats where the species may contribute to colour and flavour development. In addition to these conventional functionalities, a biopreservation potential based on the production of antagonistic compounds may be available. Such potential, however, remains largely unexplored in contrast to the large body of research that is available on the biopreservative properties of lactic acid bacteria. The present study outlines the exploration of the genetic basis of competitiveness and antimicrobial activity of a fermented meat isolate, S. shinii IMDO-S216. To this end, its genome was sequenced, de novo assembled, and annotated.

RESULTS

The genome contained a single circular chromosome and eight plasmid replicons. Focus of the genomic exploration was on secondary metabolite biosynthetic gene clusters coding for ribosomally synthesized and posttranslationally modified peptides. One complete cluster was coding for a bacteriocin, namely lactococcin 972; the genes coding for the pre-bacteriocin, the ATP-binding cassette transporter, and the immunity protein were also identified. Five other complete clusters were identified, possibly functioning as competitiveness factors. These clusters were found to be involved in various responses such as membrane fluidity, iron intake from the medium, a quorum sensing system, and decreased sensitivity to antimicrobial peptides and competing microorganisms. The presence of these clusters was equally studied among a selection of multiple Staphylococcus species to assess their prevalence in closely-related organisms.

CONCLUSIONS

Such factors possibly translate in an improved adaptation and competitiveness of S. shinii IMDO-S216 which are, in turn, likely to improve its fitness in a fermented meat matrix.

Screening of a potential probiotic Lactiplantibacillus plantarum NUC08 and its synergistic effects with yogurt starter

This study aims to identify lactic acid bacteria (LAB) isolates possessing physiological characteristics suitable for use as probiotics in yogurt fermentation. Following acid and bile salt tolerance tests, Lactiplantibacillus plantarum (NUC08 and NUC101), Lacticaseibacillus rhamnosus (NUC55 and NUC201), and Lacticaseibacillus paracasei (NUC159, NUC216, and NUC351) were shortlisted based on intraspecies distribution for further evaluation. Their physiological probiotic properties, including transit tolerance, adhesion, autoaggregation, surface hydrophobicity, biofilm formation, and antibacterial activity, were assessed. Principal component analysis indicated that Lactiplantibacillus plantarum NUC08 was the preferred choice among the evaluated strains. Subsequent investigations revealed that co-culturing Lactiplantibacillus plantarum NUC08 with 2 yogurt starter strains resulted in a cooperative and synergistic effect, enhancing the growth of mixed strains and increasing their tolerance to simulated gastric and intestinal conditions. Additionally, when Vibrio harveyi bioluminescent reporter strain was used, the 3 cocultured strains cooperated to induce the activity of a quorum sensing (QS) molecule autoinducer-2 (AI-2), hinting a potential connection between phenotypic traits and QS in the cocultured strains. Importantly, LAB viable counts were significantly higher in yogurt co-fermented with Lactiplantibacillus plantarum NUC08, consistently throughout the storage period. In conclusion, the study demonstrates that the probiotic strain Lactiplantibacillus plantarum NUC08 can be employed in synergy with yogurt starter strains, affirming its potential for use in the development of functional fermented dairy products.

Investigating luxS gene expression in lactobacilli along lab-scale cocoa fermentations

Previous metagenomic analyses have suggested that lactobacilli present potential for Quorum Sensing (QS) in cocoa fermentation, and in the present research, laboratory scale fermentations were carried out to monitor the expression of luxS, a universal marker of QS. For that, 96 h-fermentations were studied, as follows: F0 (non inoculated control), F1 (inoculated with yeasts, lactic acid bacteria, and acetic acid bacteria), F2 (inoculated with yeasts and acetic acid bacteria), F3 (inoculated with yeasts only). The parameters evaluated were: plate counting, quantification of key enzymes and analysis of volatile organic compounds associated with key sensory descriptors, using headspace gas chromatography-mass spectrometry (GC-MS). Furthermore, QS was estimated by the quantification of the expression of luxS genes by Reverse Transcriptase Real-Time PCR. The results demonstrated that microbial succession occurred in pilot scale fermentations, but no statistical differences for microbial enumeration and α-diversity index were observed among experiments and control. Moreover, it was not possible to make conclusive correlations of enzymatic profile and fermenting microbiota, likely due to the intrinsic activity of plant hydrolases. Regarding to the expression of luxS genes, in Lactiplantibacillus plantarum they were active along the fermentation, but for Limosilactobacillus fermentum, luxS was expressed only at early and middle phases. Correlation analysis of luxS expression and production of volatile metabolites evidenced a possible negative association of Lp. Plantarum with fermentation quality. In conclusion, these data corroborate former shotgun metagenomic analysis by demonstrating the expression of luxS by lactobacilli in pilot scale cocoa fermentation and evidence Lp. Plantarum is the main lactic acid bacteria related to its expression.

The intricate symbiotic relationship between lactic acid bacterial starters in the milk fermentation ecosystem

Fermentation is one of the most effective methods of food preservation. Since ancient times, food has been fermented using lactic acid bacteria (LAB). Fermented milk is a very intricate fermentation ecosystem, and the microbial metabolism of fermented milk largely determines its metabolic properties. The two most frequently used dairy starter strains are Streptococcus thermophilus (S. thermophilus) and Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus). To enhance both the culture growth rate and the flavor and quality of the fermented milk, it has long been customary to combine S. thermophilus and L. bulgaricus in milk fermentation due to their mutually beneficial and symbiotic relationship. On the one hand, the symbiotic relationship is reflected by the nutrient co-dependence of the two microbes at the metabolic level. On the other hand, more complex interaction mechanisms, such as quorum sensing between cells, are involved. This review summarizes the application of LAB in fermented dairy products and discusses the symbiotic mechanisms and interactions of milk LAB starter strains from the perspective of nutrient supply and intra- and interspecific quorum sensing. This review provides updated information and knowledge on microbial interactions in a fermented milk ecosystem.

Diversity and succession of contaminating yeasts in white-brined cheese during cold storage

Contamination of white-brined cheeses (WBCs) with yeasts is of major concern in the dairy industry. This study aimed to identify yeast contaminants and characterize their succession in white-brined cheese during a shelf-life of 52 weeks. White-brined cheeses added herbs (WBC1) or sundried tomatoes (WBC2) were produced at a Danish dairy and incubated at 5 °C and 10 °C. An increase in yeast counts was observed for both products within the first 12-14 weeks of incubation and stabilized afterwards varying in a range of 4.19-7.08 log CFU/g. Interestingly, higher incubation temperature, especially in WBC2, led to lower yeast counts, concurrently with higher diversity of yeast species. Observed decrease in yeast counts was, most likely, due to negative interactions between yeast species leading to growth inhibition. In total, 469 yeast isolates from WBC1 and WBC2 were genotypically classified using the (GTG)₅-rep-PCR technique. Out of them, 132 representative isolates were further identified by sequencing the D1/D2 domain of the 26 S rRNA gene. Predominant yeast species in WBCs were Candida zeylanoides and Debaryomyces hansenii, while Candida parapsilosis, Kazachstania bulderi, Kluyveromyces lactis, Pichia fermentans, Pichia kudriavzevii, Rhodotorula mucilaginosa, Torulaspora delbrueckii, and Wickerhamomyces anomalus were found in lower frequency. Heterogeneity of yeast species in WBC2 was generally larger compared to WBC1. This study indicated that, along with contamination levels, taxonomic heterogeneity of yeasts is an important factor influencing yeast cell counts, as well as product quality during storage.

Quorum sensing-mediated microbial interactions: Mechanisms, applications, challenges and perspectives

Microbial community in natural or artificial environments playes critical roles in substance cycles, products synthesis and species evolution. Although microbial community structures have been revealed via culture-dependent and culture-independent approaches, the hidden forces driving the microbial community are rarely systematically discussed. As a mode of cell-to-cell communication that modifies microbial interactions, quorum sensing can regulate biofilm formation, public goods secretion, and antimicrobial substances synthesis, directly or indirectly influencing microbial community to adapt to the changing environment. Therefore, the current review focuses on microbial community in the different habitats from the quorum sensing perspective. Firstly, the definition and classification of quorum sensing were simply introduced. Subsequently, the relationships between quorum sensing and microbial interactions were deeply explored. The latest progressives regarding the applications of quorum sensing in wastewater treatment, human health, food fermentation, and synthetic biology were summarized in detail. Finally, the bottlenecks and outlooks of quorum sensing driving microbial community were adequately discussed. To our knowledge, this current review is the first to reveal the driving force of microbial community from the quorum sensing perspective. Hopefully, this review provides a theoretical basis for developing effective and convenient approaches to control the microbial community with quorum sensing approaches.

The mixed biofilm formed by Listeria monocytogenes and other bacteria: Formation, interaction and control strategies

Listeria monocytogenes is an important foodborne pathogen. It can adhere to food or food contact surface for a long time and form biofilm, which will lead to equipment damage, food deterioration, and even human diseases. As the main form of bacteria to survive, the mixed biofilms often exhibit higher resistance to disinfectants and antibiotics, including the mixed biofilms formed by L. monocytogenes and other bacteria. However, the structure and interspecific interaction of the mixed biofilms are very complex. It remains to be explored what role the mixed biofilm could play in the food industry. In this review, we summarized the formation and influence factors of the mixed biofilm developed by L. monocytogenes and other bacteria, as well as the interspecific interactions and the novel control measures in recent years. Moreover, the future control strategies are prospected, in order to provide theoretical basis and reference for the research of the mixed biofilms and the targeted control measures.

Transcriptomics Reveals the Effect of Strain Interactions on the Growth of A. Oryzae and Z. Rouxii

The microbial community structure in traditional fermented foods is quite complex, making the relationship between strains unclear. In this regard, the co-culture system can simulate microbial interactions during food fermentation and reveal the morphological changes, metabolic processes, and gene expression of microbial communities. The present study sought to investigate the effects of microbial interactions on the growth of Aspergillus oryzae and Zygosaccharomyces rouxii through omics. After co-cultivation, the pH value and dry weight were consistent with the pure culture of Z. rouxii. Additionally, the consumption of reducing sugar decreased, and the enzymatic activity increased compared with the pure culture of fungus. The analysis of volatile organic compounds (VOCs) and transcriptomics showed that co-culture significantly promoted the effect on Z. rouxii. A total of 6 different VOCs and 2202 differentially expressed genes were identified in the pure and co-culture of Z. rouxii. The differentially expressed genes were mainly related to the endonucleolytic cleavage of rRNA, ribosome biogenesis in eukaryotes, and RNA polymerase metabolic pathways. The study results will provide insights into the effect of microbial interactions on the growth of A. oryzae and Z. rouxii.

Quorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting

Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.

Metagenomic and Functional Characterization of Two Chilean Kefir Beverages Reveals a Dairy Beverage Containing Active Enzymes, Short-Chain Fatty Acids, Microbial β-Amyloids, and Bio-Film Inhibitors

Kefir beverage is a probiotic food associated with health benefits, containing probiotic microorganisms and biomolecules produced during fermentation. The microbial composition of these beverages varies among countries, geographical regions, and the substrates, therefore, the characterization of kefir beverages is of great relevance in understanding their potential health-promoting and biotechnological applications. Therefore, this study presents the metagenomic and functional characterization of two Chilean kefir beverages, K02 and K03, through shotgun and amplicon-based metagenomic, microbiological, chemical, and biochemical studies. Results show that both beverages’ microbiota were mainly formed by Bacteria (>98%), while Eukarya represented less than 2%. Regarding Bacteria, the most abundant genera were Acetobacter (93.43% in K02 and 80.99% in K03) and Lactobacillus (5.72% in K02 and 16.75% in K03), while Kazachstania was the most abundant genus from Eukarya (42.55% and 36.08% in K02 and K03). Metagenomic analyses revealed metabolic pathways for lactose and casein assimilation, biosynthesis of health-promoting biomolecules, and clusters for antibiotic resistance, quorum sensing communication, and biofilm formation. Enzymatic activities, microbial β-amyloids, and short-chain fatty acids (acetic acid and propionic acid) were also detected in these beverages. Likewise, both kefir beverages inhibited biofilm formation of the opportunistic pathogen Pseudomonas aeruginosa.

Growth of Salmonella Enteritidis in the presence of quorum sensing signaling compounds produced by Pseudomonas aeruginosa

Quorum sensing (QS) can exist in food-related bacteria and potentially affect bacterial growth through acyl-homoserine lactones (AHLs). To verify the role of QS compounds in the cell-free supernatant, this study examined the effect of supernatant extracted from Pseudomonas aeruginosa culture on the growth kinetics of Salmonella Enteritidis. The results showed that the lag time (λ) of S. Enteritidis was apparently reduced (p < 0.05) under the influence of P. aeruginosa culture supernatant compared with the S. Enteritidis culture supernatant. HPLC-MS/MS test demonstrated that AHLs secreted by P. aeruginosa were mainly C14-HSL with a content of 85.71 μg/mL and a small amount of 3-oxo-C12-HSL. In addition, the commercially synthetic C14-HSL had positive effects on the growth of S. Enteritidis, confirming once again that the growth of S. Enteritidis was affected by AHL metabolized by other bacteria and the complexity of bacterial communication.

Quinolone Signals Related to Pseudomonas Quinolone Signal-Quorum Sensing Inhibits the Predatory Activity of Bdellovibrio bacteriovorus

Bdellovibrio bacteriovorus is one of the predatory bacteria; therefore, it can act as a novel “living antibiotic,” unlike the current antibiotics. Here the predation of Escherichia coli by B. bacteriovorus was inhibited in the presence of Pseudomonas aeruginosa. This study investigated whether P. aeruginosa-induced predation inhibition is associated with bacterial quorum sensing (QS). Each las, rhl, or pqs QS mutant in P. aeruginosa was used to check the predatory activity of E. coli cells using B. bacteriovorus. As a result, the predatory activity of B. bacteriovorus increased in a mutant pqs QS system, whereas wild-type PA14 inhibited the predatory activity. Moreover, the addition of 4-hydroxy-2-heptylquinoline (HHQ) or the analog triggered the low predatory activity of B. bacteriovorus and killed B. bacteriovorus cells. Therefore, a defensive action of P. aeruginosa against B. bacteriovorus is activated by the pqs QS system, which produces some quinolone compounds such as HHQ.

Metagenomic Investigation Uncovers Presence of Probiotic-Type Microbiome in Kalparasa® (Fresh Unfermented Coconut Inflorescence Sap)

The phloem sap tapped from unopened inflorescence (spadix) of coconut palm using a novel collecting device, "coco-sap chiller," has been branded Kalparasa® (henceforth as Kalparasa in the text) to distinguish its properties not found in sap harvested by traditional methods. To know its hitherto unidentified microbiome profile, we employed high-throughput sequencing to uncover the bacteriome and mycobiome in fresh and 12-h fermented samples. Fresh Kalparasa had a pH of 7.2, which dropped to 4.5 after 12 h, signifying fermentation of the sap. Diversity analysis indicated fresh Kalparasa having higher bacterial species than the fermented one. Contrary to this, fresh sap had lower fungal/yeast diversity than the fermented sample. Fresh Kalparasa had relatively higher abundance of probiotic-type Leuconostoc genus followed by equal proportions of Gluconobacter, Acetobacter, and Fructobacillus. The 12-h fermented Kalparasa showed a significant increase in Gluconobacter with a sharp decrease in Leuconostoc. Mycobiome data revealed fresh Kalparasa to be preponderant in Saccharomyces and Hanseniaspora genera of yeasts while the fermented sap had higher representation of Hanseniaspora and Cortinarius and lesser Saccharomyces. This suggested that the fermentation of Kalparasa was probably driven by symbiotic culture of bacteria and yeasts (SCOBY), particularly acetic acid bacteria and non-Saccharomyces yeasts. The bacteriome-function predictions highlighted the enrichment of glycerophospholipid, ABC transporters, purine, and pyrimidine metabolisms. Based on our findings, Kalparasa containing large population of Leuconostoc mesenteroides, Fructobacillus fructosus, Saccharomyces cerevisiae, and Hanseniaspora guilliermondii can be promoted as a healthy "unfermented" plant edible food containing live probiotic-type microbiome during its consumption.

Pangenome analyses of LuxS-coding genes and enzymatic repertoires in cocoa-related lactic acid bacteria

Lactobacillaceae presents potential for interspecific Quorum Sensing (QS) in spontaneous cocoa fermentation, correlated with high abundance of luxS. Three Brazilian isolates from cocoa fermentation were characterized by Whole Genome Sequencing and luxS gene was surveyed in their genomes, in comparison with public databases. They were classified as Lactiplantibacillus plantarum, Limosilactobacillus fermentum and Pediococcus acidilactici. LuxS genes were conserved in core genomes of the novel isolates, but in some non-cocoa related Lactic Acid Bacteria (LAB) it was accessory and plasmid-borne. The conservation and horizontal acquisition of luxS reinforces that QS is determinant for bacterial adaptation in several environments, especially taking into account the luxS has been correlated with modulation of bacteriocin production, stress tolerance and biofilm formation. Therefore, in this paper, new clade and species-specific primers were designed for future application for screening of luxS gene in LAB to evaluate the adaptive potential to diverse food fermentations.

Understanding the Mechanisms of Positive Microbial Interactions That Benefit Lactic Acid Bacteria Co-cultures

Microorganisms grow in concert, both in natural communities and in artificial or synthetic co-cultures. Positive interactions between associated microbes are paramount to achieve improved substrate conversion and process performance in biotransformation and fermented food production. The mechanisms underlying such positive interactions have been the focus of numerous studies in recent decades and are now starting to be well characterized. Lactic acid bacteria (LAB) contribute to the final organoleptic, nutritional, and health properties of fermented food products. However, interactions in LAB co-cultures have been little studied, apart from the well-characterized LAB co-culture used for yogurt manufacture. LAB are, however, multifunctional microorganisms that display considerable potential to create positive interactions between them. This review describes why LAB co-cultures are of such interest, particularly in foods, and how their extensive nutritional requirements can be used to favor positive interactions. In that respect, our review highlights the benefits of co-cultures in different areas of application, details the mechanisms underlying positive interactions and aims to show how mechanisms based on nutritional interactions can be exploited to create efficient LAB co-cultures.

Unambiguous determination of farnesol and tyrosol in vaginal fluid using fast and sensitive UHPLC-MS/MS method

The new ultra-high performance liquid chromatography method with tandem mass spectrometry detection (UHPLC-MS/MS) has been optimized to allow fast, selective, and high-throughput analysis of two Candida albicans quorum sensing molecules (QSM), farnesol and tyrosol. The problem of the presence of the interference in the samples and system was successfully solved by careful optimization of chromatographic conditions. Charged hybrid stationary phase modified with pentafluorophenyl group and optimized gradient elution provided adequate separation selectivity and peak shapes. The impurity was identified as dibutyl phthalate and had the same m/z ions as farnesol leading to an important interference on selected reaction monitoring channel. Two different types of biological matrices originating from vaginal fluid, supernatant and sediment, were analysed. Micro-solid phase extraction in pipette tips was optimized for the selective isolation of QSM from the supernatant. The insufficient retention of farnesol on the extraction sorbent was improved when 1% of organic solvent was added prior to extraction, while the retention of tyrosol was only possible when using combined C8 and polymer sorbent type. Strong retention of farnesol had to be solved by increasing elution solvent strength and volume up to 600 μL. However, this approach did not allow the pretreatment of sediment samples due to the sorbent clogging. Therefore, our previously developed protein precipitation method was modified and validated to analyse the sediments. New developed UHPLC-MS/MS method provided suitable accuracy and precision for the determination of QSM in vaginal fluid while using only 50 μL sample volume and two different sample preparation methods.

The Search for Quorum Sensing in Botrytis cinerea: Regulatory Activity of Its Extracts on Its Development

Botrytis cinerea is a phytopathogenic fungus that causes large crop and post-harvest losses. Therefore, new and effective strategies are needed to control the disease and to reduce resistance to fungicides. Modulating pathogenicity and virulence by manipulating microbial communication is a promising strategy. This communication mechanism, called Quorum Sensing (QS), has already been reported in bacteria and yeasts; however, it has not yet been studied in B. cinerea. To establish the existence of this biochemical process in B. cinerea, we prepared extracts at different growth times (D1-D12), which were applied to fresh cultures of the same fungi. The chemical analysis of the extracts obtained from several fermentations showed different compositions and biological activities. We confirmed the presence of several phytotoxins, as well as compounds 1-phenylethanol and 3-phenylpropanol. Day five extract (0.1%) inhibited conidia germination and elongation of germ tubes, day seven extract (1%) produced the greatest phytotoxic effect in tomato leaves, and day nine extract (0.1%) was a sporulation inhibitor. In contrast, the extracts from days 7, 9, and 12 of fermentation (0.1% and 0.01%) promoted pellet and biofilm formation. Sporulation was slightly induced at 0.01%, while at 0.1% there was a great inhibition. At the highest extract concentrations, a biocidal effect was detected, but at the lowest, we observed a QS-like effect, regulating processes such as filamentation, morphogenesis, and pathogenesis. These results of the biological activity and composition of extracts suggest the existence of a QS-like mechanism in B. cinerea, which could lead to new non-biocidal alternatives for its control through interference in the pathogenicity and virulence mechanisms of the fungi.

A Big World in Small Grain: A Review of Natural Milk Kefir Starters

Milk kefir is a traditional fermented milk product whose consumption is becoming increasingly popular. The natural starter for kefir production is kefir grain, which consists of various bacterial and yeast species. At the industrial scale, however, kefir grains are rarely used due to their slow growth, complex application, bad reproducibility and high costs. Instead, mixtures of defined lactic acid bacteria and sometimes yeasts are applied, which alter sensory and functional properties compared to natural grain-based milk kefir. In order to be able to mimic natural starter cultures for authentic kefir production, it is a prerequisite to gain deep knowledge about the nature of kefir grains, its microbial composition, morphologic structure, composition of strains on grains and the impact of environmental parameters on kefir grain characteristics. In addition, it is very important to deeply investigate the numerous multi-dimensional interactions among different species, which play important roles on the formation and the functionality of grains.

Does Quorum Sensing play a role in microbial shifts along spontaneous fermentation of cocoa beans? An in silico perspective

Cocoa fermentation is a spontaneous process shaped by a variable microbial ecosystem which is assembled due to cross-feeding relationship among yeasts and bacteria, resulting in a synchronized microbial succession started by yeasts, followed by lactic acid bacteria (LAB) and finalized by acetic acid bacteria (AAB). Several studies have indicated the effect of microbial interactions in food ecosystems highlighting the importance of quorum sensing (QS) in bacterial adaptation in harsh environments modulating several phenotypes such as biofilm formation, tolerance to acid stress, bacteriocin production, competence, morphological modifications, motility, among others. However, antagonic interactions also occur, and can be marked by Quorum Quenching (QQ) activity, negatively impacting QS regulated phenotypes. Our current knowledge regarding microbial cocoa composition and functioning is based on culture-based analysis and culture-independent PCR-based methods. Therefore, we set out to investigate the application of metagenomics analysis on a classical spontaneous cocoa fermentation in order to describe: (I) the microbial taxonomic composition; (II) the functional potential of the cocoa microbiome; (III) the microbiome putative QS potential; and (IV) the microbiome QQ potential. Both aims III and IV are related to the expression of effectors that may confer advantageous traits along fermentation which can explain their dominance in specific time zones during the entire process. We have observed a bacterial succession shaped by yeasts and filamentous fungi and then Enterobacteriaceales, LAB and AAB, as well as a diverse genetic metabolic potential related to proteins and carbohydrates metabolism associated to the yeast Saccharomyces cerevisiae and members of the Enterobacteriaceales order and LAB and AAB groups. In addition, in silico evidences of interspecific QS arsenal were found in members of the genera Enterobacter, Lactobacillus, Bacillus and Pantoea, while inferences of intraspecific QS potential were found in the members of the genera Bacillus, Enterobacter, Komagataeibacter, Lactobacillus and Pantoea. In addition, a QQ potential was detected in Lactobacillus and in AAB members. These findings indicate that QS and QQ may modulate bacterial dominance in different time points during fermentation, along with cross-feeding, being responsible for their maintenance in a large time range.

Ιn Vitro Screening of γ-Aminobutyric Acid and Autoinducer-2 Signalling in Lactic Acid Bacteria Exhibiting Probiotic Potential Isolated from Natural Black Conservolea Olives

In the present study, 33 strains of lactic acid bacteria (LAB) previously isolated from natural black Conservolea olives were assessed for their probiotic potential in vitro, as well as for their autoinducer-2 (AI-2) activity under standard growth conditions and the production of γ-aminobutyric acid (GABA). The probiotic tests included the in vitro resistance to low pH and resistance to bile salts, the evaluation of bile salt hydrolase activity, as well as safety tests regarding their possible haemolytic activity and their antimicrobial activity against pathogens. The results indicated that 17 strains were able to survive in low pH and in the presence of bile, with 15 of them also exhibiting partial bile salt hydrolase activity. None of the strains exhibited haemolytic activity or inhibited the growth of any of the examined pathogens. Moreover, the strains displayed generally low AI-2 activity under the growth conditions tested, regardless of the species. Interestingly, in contrast to what has been found in most foods, none of the isolates were found to produce GABA after 48 h of growth. The results from the AI-2 activity and extracellular GABA detection were considered as unexpected for LAB with probiotic attributes.

Occurrence and Importance of Yeasts in Indigenous Fermented Food and Beverages Produced in Sub-Saharan Africa

Indigenous fermented food and beverages represent a valuable cultural heritage in sub-Saharan Africa, having one of the richest selections of fermented food products in the world. In many of these indigenous spontaneously fermented food and beverages, yeasts are of significant importance. Several factors including raw materials, processing methods, hygienic conditions as well as the interactions between yeasts and other commensal microorganisms have been shown to influence yeast species diversity and successions. Both at species and strain levels, successions take place due to the continuous change in intrinsic and extrinsic growth factors. The selection pressure from the microbial stress factors leads to niche adaptation and both yeast species and strains with traits deviating from those generally acknowledged in current taxonomic keys, have been isolated from indigenous sub-Saharan African fermented food products. Yeasts are important for flavor development, impact shelf life, and nutritional value and do, in some cases, even provide host-beneficial effects. In order to sustain and upgrade these traditional fermented products, it is quite important to obtain detailed knowledge on the microorganisms involved in the fermentations, their growth requirements and interactions. While other publications have reported on the occurrence of prokaryotes in spontaneously fermented sub-Saharan food and beverages, the present review focuses on yeasts considering their current taxonomic position, relative occurrence and successions, interactions with other commensal microorganisms as well as beneficial effects and importance in human diet. Additionally, the risk of opportunistic yeasts is discussed.

Fungal Quorum-Sensing Molecules and Inhibitors with Potential Antifungal Activity: A Review

The theory of persisting independent and isolated regarding microorganisms is no longer accepted. To survive and reproduce they have developed several communication platforms within the cells which facilitates them to adapt the surrounding environmental changes. This cell-to-cell communication is termed as quorum sensing; it relies upon the cell density and can stimulate several traits of microbes including biofilm formation, competence, and virulence factors secretion. Initially, this sophisticated mode of communication was discovered in bacteria; later, it was also confirmed in eukaryotes (fungi). As a consequence, many quorum-sensing molecules and inhibitors have been identified and characterized in various fungal species. In this review article, we will primarily focus on fungal quorum-sensing molecules and the production of inhibitors from fungal species with potential applications for combating fungal infections.

Effect of quorum sensing molecules and natamycin on biofilms of Candida tropicalis and other yeasts isolated from industrial juice filtration membranes

AIMS

Cells limit the cell number of dense biofilms by releasing self-inhibitory molecules. Here, we aim to assess the effectiveness of yeast quorum sensing (QS) molecules and the antifungal agent natamycin against yeast biofilms of strains commonly isolated from fruit juice ultrafiltration membranes.

METHODS AND RESULTS

Yeast QS molecules, such as tyrosol, 2-phenylethanol and farnesol, were detected by solvent extraction and HS-SPME GC-MS in Candida tropicalis cultures. The effect of QS molecules on mono- and multispecies biofilms formed by Rhodotorula mucilaginosa, C. tropicalis, Candida krusei and Candida kefyr was evaluated by plate count and epifluorescence microscopy. Farnesol caused a decrease in cell number and disrupted mono- and multispecies yeast biofilms during adhesion (0·6 mmol l^-1 ). 2-phenyl ethanol 1·2 mmol l^-1 stimulated biofilm density and increased cell number in both mono- and multispecies biofilms, while tyrosol did not show effects when tested against C. tropicalis biofilms (0·05-1·2 mmol l^-1 ). Natamycin caused a strong decrease in cell number and disruption of biofilm structure in C. tropicalis biofilms at high concentrations (0·3-1·2 mmol l^-1 ). The combination of farnesol 0·6 mmol l^-1 and natamycin at 0·01 mmol l^-1 , the maximum concentration of natamycin accepted for direct addition into fruit juices, effectively reduced cell counts and disrupted the structure of C. tropicalis biofilms.

CONCLUSION

Farnesol 0·6 mmol l^-1 significantly increased the inhibition exerted by natamycin 0·01 mmol l^-1 (~5 ppm) reducing biofilm development from juice on stainless steel surfaces.

SIGNIFICANCE AND IMPACT OF THE STUDY

These results support the use of QS molecules as biofilm inhibitors in beverages and would certainly inspire the design of novel preservative and cleaning products for the food industry based on combinatory approaches.

Natural Compounds That Modulate the Development of the Fungus Botrytis cinerea and Protect Solanum lycopersicum

Botrytis cinerea is the causal agent of gray mold disease and is responsible for the loss of millions of dollars in crops in worldwide. Currently, this pathogen exhibits increasing resistance to conventional fungicides; therefore, better control methods and novel compounds with a more specific mechanism of action but without biocidal effects, are required. In this work, several natural compounds to control B. cinerea were analyzed in vitro. Detected effects were dependent on the stage of fungus development, and 3-phenyl-1-propanol displayed the most potent inhibition of in vitro germination, germ tube development, and sporulation. However, it had lower protection of leaves and postharvest fruit in plant infection. Isoeugenol and 1-phenylethanol exhibited lower inhibition of in vitro germination and sporulation, but at the highest concentrations, they inhibited germ tube elongation. Although the lowest rates of foliage infection were recorded using isoeugenol and 3-phenyl-1-propanol, 1-phenylethanol significantly decreased the disease in postharvest tomato fruit, with an efficacy like Mancozeb, but at 18 times lower micromolar concentration. All compounds resulted in high cell viability after spores were removed from the treatment solution exhibited high cell viability, suggesting a non-biocidal effect. The diversity of in vitro and in-plant effects seems to indicate a different mechanism of action.