Transcriptome-based characterization of interactions between Saccharomyces cerevisiae and Lactobacillus delbrueckii subsp. bulgaricus in lactose-grown chemostat cocultures

Effects of fructooligosaccharides and Saccharomyces boulardii on the compositional structure and metabolism of gut microbiota in students

Fructooligosaccharides (FOS) are a common prebiotic widely used in functional foods. Meanwhile, Saccharomyces boulardii is a fungal probiotic frequenly used in the clinical treatment of diarrhea. Compared with single use, the combination of prebiotics and probiotics as symbiotics may be more effective in regulating gut microbiota as recently reported in the literature. The present study aimed to investigate the effects of FOS, S. boulardii and their combination on the structure and metabolism of the gut microbiota in healthy primary and secondary school students using an in vitro fermentation model. The results indicated that S. boulardii alone could not effectively regulate the community structure and metabolism of the microbiota. However, both FOS and the combination of FOS and S. boulardii could effectively regulate the microbiota, significantly inhibiting the growth of Escherichia-Shigella and Bacteroides, and controlling the production of the gases including H2S and NH3. In addition, both FOS and the combination could significantly promote the growth of Bifidobacteria and Lactobacillus, lower environmental pH, and enhance several physiological functions related to synthesis and metabolism. Nevertheless, the combination had more unique benefits as it promoted the growth of Lactobacillus, significantly increased CO2 production and enhanced the functional pathways of carbon metabolism and pyruvic acid metabolism. These findings provide guidance for clinical application and a theoretical basis for the development of synbiotic preparations.

Effect of Yeast Inoculation on the Bacterial Community Structure in Reduced-Salt Harbin Dry Sausages: A Perspective of Fungi-Bacteria Interactions

Yeast strains are promising starters to compensate for the flavor deficiencies of reduced-salt dry sausages, but their influence on the bacterial community's structure has not yet been clarified. In this study, the effect of separately inoculating Pichia kudriavzevii MDJ1 (Pk) and Debaryomyces hansenii HRB3 (Dh) on the bacterial community structure in reduced-salt dry sausage was investigated. The results demonstrated that the inoculation of two yeast strains significantly reduced the pH, and enhanced the total acid content, lactic acid bacteria (LAB) counts, and total bacterial counts of reduced-salt sausages after a 12-day fermentation (p < 0.05). Furthermore, high-throughput sequencing results elucidated that the inoculation of yeast strains significantly affected the bacterial composition of the dry sausages. Especially, the relative abundance of bacteria at the firmicute level in the Pk and Dh treatments exhibited a significant increase of 83.22% and 82.19%, respectively, compared to the noninoculated reduced-salt dry sausage treatment (Cr). The relative abundance of Latilactobacillus, especially L. sakei (0.46%, 2.80%, 65.88%, and 33.41% for the traditional dry sausage (Ct), Cr, Pk, and Dh treatments, respectively), increased significantly in the reduced-salt sausages inoculated with two yeast strains. Our work demonstrates the dynamic changes in the bacterial composition of reduced-salt sausages inoculated with different yeast strains, which could provide the foundation for the in-depth study of fungi-bacteria interactions in fermented foods.

Influence of metabolic guilds on a temporal scale in an experimental fermented food derived microbial community

The influence of community diversity, which can be measured at the level of metabolic guilds, on community function is a central question in ecology. Particularly, the long-term temporal dynamic between a community's function and its diversity remains unclear. We investigated the influence of metabolic guild diversity on associated community function by propagating natural microbial communities from a traditionally fermented milk beverage diluted to various levels. Specifically, we assessed the influence of less abundant microbial types, such as yeast, on community functionality and bacterial community compositions over repeated propagation cycles amounting to ∼100 generations. The starting richness of metabolic guilds had a repeatable effect on bacterial community compositions, metabolic profiles, and acidity. The influence of a single metabolic guild, yeast in our study, played a dramatic role on function, but interestingly not on long-term species sorting trajectories of the remaining bacterial community. Our results together suggest an unexpected niche division between yeast and bacterial communities and evidence ecological selection on the microbial communities in our system.

Quantification and mitigation of byproduct formation by low-glycerol-producing Saccharomyces cerevisiae strains containing Calvin-cycle enzymes

BACKGROUND

Anaerobic Saccharomyces cerevisiae cultures require glycerol formation to re-oxidize NADH formed in biosynthetic processes. Introduction of the Calvin-cycle enzymes phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) has been shown to couple re-oxidation of biosynthetic NADH to ethanol production and improve ethanol yield on sugar in fast-growing batch cultures. Since growth rates in industrial ethanol production processes are not constant, performance of engineered strains was studied in slow-growing cultures.

RESULTS

In slow-growing anaerobic chemostat cultures (D = 0.05 h^-1), an engineered PRK/RuBisCO strain produced 80-fold more acetaldehyde and 30-fold more acetate than a reference strain. This observation suggested an imbalance between in vivo activities of PRK/RuBisCO and formation of NADH in biosynthesis. Lowering the copy number of the RuBisCO-encoding cbbm expression cassette from 15 to 2 reduced acetaldehyde and acetate production by 67% and 29%, respectively. Additional C-terminal fusion of a 19-amino-acid tag to PRK reduced its protein level by 13-fold while acetaldehyde and acetate production decreased by 94% and 61%, respectively, relative to the 15 × cbbm strain. These modifications did not affect glycerol production at 0.05 h^-1 but caused a 4.6 fold higher glycerol production per amount of biomass in fast-growing (0.29 h^-1) anaerobic batch cultures than observed for the 15 × cbbm strain. In another strategy, the promoter of ANB1, whose transcript level positively correlated with growth rate, was used to control PRK synthesis in a 2 × cbbm strain. At 0.05 h^-1, this strategy reduced acetaldehyde and acetate production by 79% and 40%, respectively, relative to the 15 × cbbm strain, without affecting glycerol production. The maximum growth rate of the resulting strain equalled that of the reference strain, while its glycerol production was 72% lower.

CONCLUSIONS

Acetaldehyde and acetate formation by slow-growing cultures of engineered S. cerevisiae strains carrying a PRK/RuBisCO bypass of yeast glycolysis was attributed to an in vivo overcapacity of PRK and RuBisCO. Reducing the capacity of PRK and/or RuBisCO was shown to mitigate this undesirable byproduct formation. Use of a growth rate-dependent promoter for PRK expression highlighted the potential of modulating gene expression in engineered strains to respond to growth-rate dynamics in industrial batch processes.

Physiology, quorum sensing, and proteomics of lactic acid bacteria were affected by Saccharomyces cerevisiae YE4

The interaction mode between lactic acid bacteria (LAB) and yeast in a fermentation system directly determines the quality of the products, thus understanding their mode of interaction can improve product quality. The present study investigated the effects of Saccharomyces cerevisiae YE4 on LAB from the perspectives of physiology, quorum sensing (QS), and proteomics. The presence of S. cerevisiae YE4 slowed down the growth of Enterococcus faecium 8-3 but had no significant effect on acid production or biofilm formation. S. cerevisiae YE4 significantly reduced the activity of autoinducer-2 at 19 h in E. faecium 8-3 and at 7-13 h in Lactobacillus fermentum 2-1. Expression of the QS-related genes luxS and pfs was also inhibited at 7 h. Moreover, a total of 107 E. faecium 8-3 proteins differed significantly in coculture with S. cerevisiae YE4-these proteins are involved in metabolic pathways including biosynthesis of secondary metabolites; biosynthesis of amino acids; alanine, aspartate, and glutamate metabolism; fatty acid metabolism; and fatty acid biosynthesis. Among them, proteins involved in cell adhesion, cell wall formation, two-component systems, and ABC transporters were detected. Therefore, S. cerevisiae YE4 might affect the physiological metabolism of E. faecium 8-3 by affecting cell adhesion, cell wall formation, and cell-cell interactions.

Metabolomic analysis of the effects of a mixed culture of Saccharomyces cerevisiae and Lactiplantibacillus plantarum on the physicochemical and quality characteristics of apple cider vinegar

Introduction

This study compared differences in physicochemical characteristics of the vinegar made by a mixed culture (MC) of Saccharomyces cerevisiae and Lactiplantibacillus plantarum and a pure culture (PC) of Saccharomyces cerevisiae.

Methods

The fermentation process was monitored, and metabolomics analysis by Liquid Chromagraphy-Mass Spectrometry (LC-MS) was applied to the compositional differences between PC and MC vinegars, combined with quantification of organic acids, amino acids and B vitamins.

Results

A total of 71 differential metabolites including amino acids, organic acids and carbohydrates, and six possible key metabolic pathways were identified. MC enhanced the malic acid utilization and pyruvate acid metabolism during fermentation, increasing substrate-level phosphorylation, and supplying more energy for cellular metabolism. Higher acidity at the beginning of acetic acid fermentation, resulting from lactic acid production by Lactiplantibacillus plantarum in MC, suppressed the cellular metabolism and growth of Acetobacter pasteurianus, but enhanced its alcohol metabolism and acetic acid production in MC. MC vinegar contained more vitamin B, total flavonoids, total organic acids, amino acids and had a higher antioxidant capacity. MC enhanced the volatile substances, particularly ethyl lactate, ethyl caprate and ethyl caproate, which contributed to a stronger fruity aroma.

Discussion

These results indicated the mixed culture in alcoholic fermentation can effectively enhance the flavor and quality of apple cider vinegar.

Differential Amino Acid Uptake and Depletion in Mono-Cultures and Co-Cultures of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus in a Novel Semi-Synthetic Medium

The mechanistic understanding of the physiology and interactions of microorganisms in starter cultures is critical for the targeted improvement of fermented milk products, such as yogurt, which is produced by Streptococcus thermophilus in co-culture with Lactobacillus delbrueckii subsp. bulgaricus. However, the use of complex growth media or milk is a major challenge for quantifying metabolite production, consumption, and exchange in co-cultures. This study developed a synthetic medium that enables the establishment of defined culturing conditions and the application of flow cytometry for measuring species-specific biomass values. Time courses of amino acid concentrations in mono-cultures and co-cultures of L. bulgaricus ATCC BAA-365 with the proteinase-deficient S. thermophilus LMG 18311 and with a proteinase-positive S. thermophilus strain were determined. The analysis revealed that amino acid release rates in co-culture were not equivalent to the sum of amino acid release rates in mono-cultures. Data-driven and pH-dependent amino acid release models were developed and applied for comparison. Histidine displayed higher concentrations in co-cultures, whereas isoleucine and arginine were depleted. Amino acid measurements in co-cultures also confirmed that some amino acids, such as lysine, are produced and then consumed, thus being suitable candidates to investigate the inter-species interactions in the co-culture and contribute to the required knowledge for targeted shaping of yogurt qualities.

Effect of microbial interaction on flavor quality in Chinese baijiu fermentation

Chinese baijiu brewing is an open, complex, and synergetic functional microbiota fermentation process. Microbial interaction is pivotal for the regulation of microbial structure and function in the brewing microecosystem, consequently affecting the flavor and quality of baijiu. This article mainly summarizes the effect of microbial interactions among functional microbiota on the growth performance, flavor formation, and safe quality of baijiu fermentation process. In addition, the review specifically emphasizes on the microbial interactions for the regulation of “Ethyl Caproate-Increasing and Ethyl Lactate-Decreasing” in Chinese strong-flavor baijiu. Furthermore, the construction of synthetic microbiota by metabolic characteristics of the functional microbes and their interactions for regulating and controlling flavor quality of Chinese baijiu is also reviewed and prospected.

Engineered Microbial Cell Factories for Sustainable Production of L-Lactic Acid: A Critical Review

With the increasing demand for the biodegradable polymer material polylactic acid and its advantage of being metabolized by the human body, L-lactic acid (L-LA) is becoming increasingly attractive in environmental protection and food industry applications. However, the supply of L-LA is not satisfied, and the price is still high. Compared to enzymatic and chemical synthesis methods, L-LA production by microbial fermentation has the advantages of low cost, large yield, simple operation, and environmental protection. This review summarizes the advances in engineering microbial cell factories to produce L-LA. First, the synthetic pathways and microorganisms for L-LA production are outlined. Then, the metabolic engineering strategies for constructing cell factories to overproduce L-LA are summarized and fermentation modes for L-LA production are also given. Finally, the challenges and prospects of the microbial production of L-LA are discussed. This review provides theoretical guidance for researchers engaged in L-LA production.

The production and biochemical characterization of α-carbonic anhydrase from Lactobacillus rhamnosus GG

Abstract

We report the production and biochemical characterization of an α-carbonic anhydrase (LrhCA) from gram-positive probiotic bacteria Lactobacillus rhamnosus GG. CAs form a family of metalloenzymes that catalyze hydration of CO₂/interconversion between CO₂ and water to bicarbonate ions and protons. They are divided into eight independent gene families (α, β, γ, δ, ζ, η, θ, and ι). Interestingly, many pathogens have been identified with only β- and/or γ-CAs, which can be targeted with CA-specific inhibitors (CAIs) acting as anti-pathogen drugs. Since it is important to study the potential off-target effects of CAIs for both the human body and its commensal bacteria, we took L. rhamnosus GG as our study subject. To date, only a single α-CA has been identified in L. rhamnosus GG, which was successfully produced and biochemically characterized. LrhCA showed moderate catalytic activity with the following kinetic parameters: k_cat of 9.86 × 10⁵ s⁻¹ and k_cat/K_M of 1.41 × 10⁷ s⁻¹ M⁻¹. Moderate inhibition was established with 11 of the 39 studied sulfonamides. The best inhibitors were 5-((4-aminophenyl)sulfonamido)-1,3,4-thiadiazole-2-sulfonamide, 4-(2-hydroxymethyl-4-nitrophenyl-sulfonamidoethyl)-benzenesulfonamide, and benzolamide with K_i values of 319 nM, 378 nM, and 387 nM, respectively. The other compounds showed weaker inhibitory effects. The K_i of acetazolamide, a classical CAI, was 733 nM. In vitro experiments with acetazolamide showed that it had no significant effect on cell growth in L. rhamnosus GG culture. Several sulfonamides, including acetazolamide, are in use as clinical drugs, making their inhibition data highly relevant to avoid any adverse off-target effects towards the human body and its probiotic organisms.

Key points

• The α-carbonic anhydrase from Lactobacillus rhamnosus GG (LrhCA) is 24.3 kDa.

• LrhCA has significant catalytic activity with a kcat of 9.9 × 105 s-1.

• Acetazolamide resulted in a marginal inhibitory effect on cell growth.

Tradition as a Stepping Stone for a Microbial Defined Water Kefir Fermentation Process: Insights in Cell Growth, Bioflavoring, and Sensory Perception

A process development from a traditional grain-based fermentation to a defined water kefir fermentation using a co-culture of one lactic acid bacterium and one yeast was elaborated as a prerequisite for an industrially scalable, controllable, and reproducible process. Further, to meet a healthy lifestyle, a low ethanol-containing product was aimed for. Five microbial strains—Hanseniaspora valbyensis, Dekkera bruxellensis, Saccharomyces cerevisiae, Liquorilactobacillus nagelii, and Leuconostoc mesenteroides—were used in pairs in order to examine their influence on the fermentation progress and the properties of the resulting water kefir products against grains as a control. Thereby, the combination of H. valbyensis and L. mesenteroides provided the best-rated water kefir beverage in terms of taste and low ethanol concentrations at the same time. As a further contribution to harmonization and reduction of complexity, the usage of dried figs in the medium was replaced by fig syrup, which could have been proven as an adequate substitute. However, nutritional limitations were faced afterward, and thus, an appropriate supplementation strategy for yeast extract was established. Finally, comparative trials in 5-L scale applying grains as well as a defined microbial consortium showed both water kefir beverages characterized by a pH of 3.14, and lactic acid and aromatic sensory properties. The product resulting from co-culturing outperformed the grain-based one, as the ethanol level was considerably lower in favor of an increased amount of lactic acid. The possibility of achieving a water kefir product by using only two species shows high potential for further detailed research of microbial interactions and thus functionality of water kefir.

Probiotic and Potentially Probiotic Yeasts-Characteristics and Food Application

Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Besides the well-known and tested lactic acid bacteria, yeasts may also be probiotics. The subject of probiotic and potentially probiotic yeasts has been developing and arising potential for new probiotic products with novel properties, which are not offered by bacteria-based probiotics available on the current market. The paper reviews the first probiotic yeast Saccharomyces cerevisiae var. boulardii, its characteristics, pro-healthy activities and application in functional food production. This species offers such abilities as improving digestion of certain food ingredients, antimicrobial activities and even therapeutic properties. Besides Saccharomyces cerevisiae var. boulardii, on this background, novel yeasts with potentially probiotic features are presented. They have been intensively investigated for the last decade and some species have been observed to possess probiotic characteristics and abilities. There are yeasts from the genera Debaryomyces, Hanseniaspora, Pichia, Meyerozyma, Torulaspora, etc. isolated from food and environmental habitats. These potentially probiotic yeasts can be used for production of various fermented foods, enhancing its nutritional and sensory properties. Because of the intensively developing research on probiotic yeasts in the coming years, we can expect many discoveries and possibly even evolution in the segment of probiotics available on the market.

Polymicrobial interaction between Lactobacillus and Saccharomyces cerevisiae: coexistence-relevant mechanisms

The coordination of single or multiple microorganisms are required for the manufacture of traditional fermented foods, improving the flavour and nutrition of the food materials. However, both the additional economic benefits and safety concerns have been raised by microbiotas in fermented products. Among the fermented products, Lactobacillus and Saccharomyces cerevisiae are one of the stable microbiotas, suggesting their interaction is mediated by coexistence-relevant mechanisms and prevent to be excluded by other microbial species. Thus, aiming to guide the manufacture of fermented foods, this review will focus on interactions of coexistence-relevant mechanisms between Lactobacillus and S. cerevisiae, including metabolites communications, aggregation, and polymicrobial biofilm. Also, the molecular regulatory network of the coexistence-relevant mechanisms is discussed according to omics researches.

Development of the yeast and lactic acid bacteria co-culture agent for atmospheric ammonia removing: Genomic features and on-site applications

Odorous gas (e.g. atmospheric ammonia) in low ventilation public places, such as public toilets and waste transfer stations, causes severe health problems. Many technologies are developed to purify the atmospheric ammonia, among which the microbial agents are supposed to be a green and economical approach. In this study, we developed a yeast, Pichia sp. J1, and a lactic acid bacterium (LAB), Lactobacillus paracasei B1, co-culture agent for atmospheric ammonia removing. The on-site application results indicated the yeast and LAB mixed fermented agent had a maximum ammonia removing efficiency of 98.78%, which is significantly higher than the pure cultures (78.93% for B1 and 75.00% for J1), indicating the co-culture agent is an excellent biological product for ammonia removal. The excellent performance of the agent is closely related to the synergy behaviors between the yeast and LAB. In the co-culture agents, some of the LAB cells adhered closely to the yeast, and the growth and lactic acid producing ability of LAB were significantly promoted by yeast. Genomic analysis indicated the complementary of nutrients, i.e. carbon and nitrogen resources, signal transduction, and adhesion proteins (regulates adhesion behavior) played roles in regulating the synergy effects. Our study offers a novel biological solution of odorous gas purification.

Survey of microbes in industrial-scale second-generation bioethanol production for better process knowledge and operation

The microbes present in bioethanol production processes have been previously studied in laboratory-scale experiments, but there is a lack of information on full-scale industrial processes. In this study, the microbial communities of three industrial bioethanol production processes were characterized using several methods. The samples originated from second-generation bioethanol plants that produce fuel ethanol from biowaste, food industry side streams, or sawdust. Amplicon sequencing targeting bacteria, archaea, and fungi was used to explore the microbes present in biofuel production and anaerobic digestion of wastewater and sludge. Biofilm-forming lactic acid bacteria and wild yeasts were identified in fermentation samples of a full-scale plant that uses biowaste as feedstock. During the 20-month monitoring period, the anaerobic digester adapted to the bioethanol process waste with a shift in methanogen profile indicating acclimatization to high concentrations of ammonia. Amplicon sequencing does not specifically target living microbes. The same is true for indirect parameters, such as low pH, metabolites, or genes of lactic acid bacteria. Since rapid identification of living microbes would be indispensable for process management, a commercial method was tested that detects them by measuring the rRNA of selected microbial groups. Small-scale testing indicated that the method gives results comparable with plate counts and microscopic counting, especially for bacterial quantification. The applicability of the method was verified in an industrial bioethanol plant, inspecting the clean-in-place process quality and detecting viability during yeast separation. The results supported it as a fast and promising tool for monitoring microbes throughout industrial bioethanol processes.

Enforced Mutualism Leads to Improved Cooperative Behavior between Saccharomyces cerevisiae and Lactobacillus plantarum

Saccharomyces cerevisiae and Lactobacillus plantarum are responsible for alcoholic and malolactic fermentation, respectively. Successful completion of both fermentations is essential for many styles of wine, and an understanding of how these species interact with each other, as well as the development of compatible pairings of these species, will help to manage the process. However, targeted improvements of species interactions are difficult to perform, in part because of the chemical and biological complexity of natural grape juice. Synthetic ecological systems reduce this complexity and can overcome these difficulties. In such synthetic systems, mutualistic growth of different species can be enforced through the reciprocal exchange of essential nutrients. Here, we implemented a novel approach to evolve mutualistic traits by establishing a co-dependent relationship between S. cerevisiae BY4742Δthi4 and Lb. plantarum IWBT B038 by omitting different combinations of amino acids from a chemically defined synthetic medium simulating standard grape juice. After optimization, the two species were able to support the growth of each other when grown in the absence of appropriate combinations of amino acids. In these obligatory mutualistic conditions, BY4742Δthi4 and IWBT B038 were co-evolved for approximately 100 generations. The selected evolved isolates showed improved mutualistic growth and the growth patterns under non-selective conditions indicate the emergence of mutually beneficial adaptations independent of the synthetic selection pressure. The combined use of synthetic ecology and co-evolution is a promising strategy to better understand and biotechnologically improve microbial interactions.

Kefir microbial composition is a deciding factor in the physiological impact of kefir in a mouse model of obesity

Kefir consumption has been demonstrated to improve lipid and cholesterol metabolism; however, our previous study identified that benefits vary between different commercial and traditional kefir. Here, we investigate the ability of pitched culture kefir, that is, kefir produced by a small number of specific strains, to recapitulate health benefits of a traditional kefir, in a diet-induced obesity mouse model, and examine how microbial composition of kefir impacts these benefits. Eight-week-old female C57BL/6 mice were fed a high-fat diet (40 % energy from fat) supplemented with one of five kefir varieties (traditional, pitched, pitched with no Lactobacillus, pitched with no yeast and commercial control) at 2 ml in 20 g of food for 8 weeks prior to analysis of plasma and liver lipid profiles, and liver gene expression profiles related to lipid metabolism. Both traditional and pitched kefir lowered plasma cholesterol by about 35 % (P = 0·0005) and liver TAG by about 55 % (P = 0·0001) when compared with commercial kefir despite no difference in body weight. Furthermore, pitched kefir produced without either yeast or Lactobacillus did not lower cholesterol. The traditional and pitched kefir with the full complement of microbes were able to impart corresponding decreases in the expression of the cholesterol and lipid metabolism genes encoding 3-hydroxy-3-methylglutaryl-coenzyme A reductase, PPARγ and CD36 in the liver. These results demonstrate that traditional kefir organisms can successfully be utilised in a commercial process, while highlighting the importance of microbial interactions during fermentation in the ability of fermented foods to benefit host health.

The microbial challenge of winemaking: yeast-bacteria compatibility

The diversity and complexity of wine environments present challenges for predicting success of fermentation. In particular, compatibility between yeast and lactic acid bacteria is affected by chemical and physical parameters that are strain and cultivar specific. This review focuses on the impact of compound production by microbes and physical interactions between microbes that ultimately influence how yeast and bacteria may work together during fermentation. This review also highlights the importance of understanding microbial interactions for yeast-bacteria compatibility in the wine context.

Cooperative Response of Pichia kudriavzevii and Saccharomyces cerevisiae to Lactic Acid Stress in Baijiu Fermentation

Lactic acid is a universal metabolite, as well as a growth inhibitor of ethanol producers in Baijiu fermentation. Revealing the mechanism of lactic acid tolerance is essential for the yield of fermented foods. Here, we employed reverse transcription-quantitative polymerase chain reaction to explore the degradation mechanism of lactic acid, based on the coculture of Pichia kudriavzevii and Saccharomyces cerevisiae. Under high lactic acid stress, P. kudriavzevii decreased lactic acid from 40.00 to 35.46 g L^-1 within 24 h. Then, S. cerevisiae restored its capacity to degrade lactic acid. Finally, lactic acid decreased to 26.29 g L^-1. Coculture significantly enhanced lactic acid consumption compared to the monoculture of P. kudriavzevii (90% higher) or S. cerevisiae (209% higher). We found that lactate catabolism, H⁺ extrusion, and glycerol transport were the lactic acid tolerance pathways in yeasts. This study reveals the novel acid tolerance mechanisms of microbiota and would provide new strategies for ethanol production under acid stress.

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.

From Microbial Ecology to Innovative Applications in Food Quality Improvements: the Case of Sourdough as a Model Matrix

Since millennia, humankind has exploited microbial diversity associated to give food matrices in order to obtain fermented foods and beverages, resulting in products with improved quality and extended shelf life. This topic has received deserved and continuous interest in the scientific community, for the reason of its significance as a driver of innovation in the food and beverage sector. In this review paper, using sourdough as a model matrix, we provide some insights into the field, testifying the relevance as a transdisciplinary subject. Firstly, we encompassed the prokaryotic and eukaryotic microbial diversity associated with the sourdough ecosystems. The importance of this micro-biodiversity in the light of flour-related chemical diversity was examined. Finally, we highlighted the increasing interest in microbial-based applications oriented toward biocontrol solution in the field of sourdough-based products (i.e., bread).

Physiological responses of Saccharomyces cerevisiae to industrially relevant conditions: Slow growth, low pH, and high CO2 levels

Engineered strains of Saccharomyces cerevisiae are used for industrial production of succinic acid. Optimal process conditions for dicarboxylic‐acid yield and recovery include slow growth, low pH, and high CO₂. To quantify and understand how these process parameters affect yeast physiology, this study investigates individual and combined impacts of low pH (3.0) and high CO₂ (50%) on slow‐growing chemostat and retentostat cultures of the reference strain S. cerevisiae CEN.PK113‐7D. Combined exposure to low pH and high CO₂ led to increased maintenance‐energy requirements and death rates in aerobic, glucose‐limited cultures. Further experiments showed that these effects were predominantly caused by low pH. Growth under ammonium‐limited, energy‐excess conditions did not aggravate or ameliorate these adverse impacts. Despite the absence of a synergistic effect of low pH and high CO₂ on physiology, high CO₂ strongly affected genome‐wide transcriptional responses to low pH. Interference of high CO₂ with low‐pH signaling is consistent with low‐pH and high‐CO₂ signals being relayed via common (MAPK) signaling pathways, notably the cell wall integrity, high‐osmolarity glycerol, and calcineurin pathways. This study highlights the need to further increase robustness of cell factories to low pH for carboxylic‐acid production, even in organisms that are already applied at industrial scale.

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.

Interaction with Pantoea agglomerans Modulates Growth and Melanization of Sporothrix brasiliensis and Sporothrix schenckii

Sporothrix brasiliensis and Sporothrix schenckii stand as the most virulent agents of sporotrichosis, a worldwide-distributed subcutaneous mycosis. The origin of Sporothrix virulence seems to be associated with fungal interactions with organisms living in the same environment. To assess this hypothesis, the growth of these two species in association with Pantoea agglomerans, a bacterium with a habitat similar to Sporothrix spp., was evaluated. Growth, melanization, and gene expression of the fungus were compared in the presence or absence of the bacterium in the same culture medium. Both S. brasiliensis and S. schenckii grew in contact with P. agglomerans yielding heavily melanized conidia after 5 days of incubation at 30 °C in Sabouraud agar. This increased melanin production occurred around bacterial colonies, suggesting that fungal melanization is triggered by a diffusible bacterial product, which is also supported by a similar pattern of melanin production during Sporothrix spp. growth in contact with heat-killed P. agglomerans. Growth of P. agglomerans was similar in the presence or absence of the fungus. However, the growth of S. brasiliensis and S. schenckii was initially inhibited, but further enhanced when these species were co-cultured with P. agglomerans. Moreover, fungi were able to use killed bacteria as both carbon and nitrogen sources for growth. Representational difference analysis identified overexpressed genes related to membrane transport when S. brasiliensis was co-cultured with the bacteria. The down-regulation of metabolism-related genes appears to be related to nutrient availability during bacterial exploitation. These findings can lead to a better knowledge on Sporothrix ecology and virulence.

Dissecting the Ecology of Microbes Using a Systems Toolbox

Study of simplified microbial consortia shows that nitrogen overflow by yeast is a mechanism that supports the stable co-existence of yeasts and lactic acid bacteria.

Food Spoilage-Associated Leuconostoc, Lactococcus, and Lactobacillus Species Display Different Survival Strategies in Response to Competition

Psychrotrophic lactic acid bacteria (LAB) are the prevailing spoilage organisms in packaged cold-stored meat products. Species composition and metabolic activities of such LAB spoilage communities are determined by the nature of the meat product, storage conditions, and interspecies interactions. Our knowledge of system level responses of LAB during such interactions is very limited. To expand it, we studied interactions between three common psychrotrophic spoilage LAB (Leuconostoc gelidum, Lactococcus piscium, and Lactobacillus oligofermentans) by comparing their time course transcriptome profiles obtained during their growth in individual, pairwise, and triple cultures. The study revealed how these LAB employed different strategies to cope with the consequences of interspecies competition. The fastest-growing bacterium, Le. gelidum, attempted to enhance its nutrient-scavenging and growth capabilities in the presence of other LAB through upregulation of carbohydrate catabolic pathways, pyruvate fermentation enzymes, and ribosomal proteins, whereas the slower-growing Lc. piscium and Lb. oligofermentans downregulated these functions. These findings may explain the competitive success and predominance of Le. gelidum in a variety of spoiled foods. Peculiarly, interspecies interactions induced overexpression of prophage genes and restriction modification systems (mechanisms of DNA exchange and protection against it) in Lc. piscium and Lb. oligofermentans but not in Le. gelidum Cocultivation induced also overexpression of the numerous putative adhesins in Lb. oligofermentans These adhesins might contribute to the survival of this slowly growing bacterium in actively growing meat spoilage communities.IMPORTANCE Despite the apparent relevance of LAB for biotechnology and human health, interactions between members of LAB communities are not well known. Knowledge of such interactions is crucial for understanding how these communities function and, consequently, whether there is any possibility to develop new strategies to interfere with their growth and to postpone spoilage of packaged and refrigerated foods. With the help of controlled experiments, detailed regulation events can be observed. This study gives an insight into the system level interactions and the different competition-induced survival strategies related to enhanced uptake and catabolism of carbon sources, overexpression of adhesins and putative bacteriocins, and the induction of exchange of genetic material. Even though this experiment dealt with only three LAB strains in vitro, these findings agreed well with the relative abundance patterns typically reported for these species in natural food microbial communities.

Lactobacillus kefiranofaciens, the sole dominant and stable bacterial species, exhibits distinct morphotypes upon colonization in Tibetan kefir grains

Tibetan kefir grains (TKGs), natural starters for milk fermentation, are believed to comprise diverse microflora of lactic acid and acetic acid bacteria. In order to better understand the bacterial community in TKGs, TKGs that had been cultured continuously either naturally or aseptically for 10 months were subject to analysis using both culture-dependent and various culture-independent methods. Results of DGGE, metagenomics, FISH, qPCR and isolation all demonstrated that Lactobacillus kefiranofaciens is the only dominant and stable bacterial species in TKGs regardless of culture conditions and time. FISH and SEM showed that L. kefiranofaciens exhibited two distinct morphotypes of short rod (3.0 μm in length) and long rod (10.0 μm in length) upon colonization of either the outer surface or inner component of TKGs, providing evidence for its trophic adaptation to the hollow globular grain structure of TKGs. These findings pave ways for further study of the specific symbiotic interaction between L. kefiranofaciens and the dominant Saccharomyces cerevisiae yeast in TKGs in vivo.

Synergistic Effect in Core Microbiota Associated with Sulfur Metabolism in Spontaneous Chinese Liquor Fermentation

Microbial sulfur metabolism plays crucial roles in various food and alcoholic beverage fermentations. 3-(Methylthio)-1-propanol and dimethyl disulfide are important sulfur compounds in fermented foods and alcoholic beverages. Here, we studied the dynamics of these two compounds during spontaneous Chinese liquor fermentation. The two compounds reached the maximum concentration at day 10 and the maximum production rate at day 3. Metatranscriptomic analysis at days 3 and 10 revealed a total of 354 metabolically active microorganisms. Saccharomyces and Lactobacillus were identified as core microbiota critical for sulfur compound production based on both the transcript abundances of the principal genes and the distribution frequencies of 31 enzymes involved in sulfur metabolism. Saccharomyces transcribed genes encoding 23 enzymes related to the generation of 3-(methylthio)-1-propanol and dimethyl disulfide, and Lactobacillus was active in the methyl cycle, which recycles methionine, the precursor of the two sulfur compounds. Furthermore, the sulfur metabolism-related characteristics of two representative species were studied in coculture during a simulated fermentation. Saccharomyces cerevisiae JZ109 produced 158.4 μg/liter 3-(methylthio)-1-propanol and 58.5 μg/liter dimethyl disulfide in monoculture, whereas Lactobacillus buchneri JZ-JN-2017 could not produce these two compounds in monoculture. Their coculture significantly enhanced the generation of 3-(methylthio)-1-propanol (350.0 μg/liter) and dimethyl disulfide (123.8 μg/liter). In addition, coculture significantly enhanced the gene transcriptions (fold change, 1.5 to ∼55.0) that convert methionine to these two compounds in S. cerevisiae and in the methyl cycle of L. buchneri This study reveals a novel synergistic effect between members of the core microbiota in the production of sulfur compounds via methionine recycling in spontaneous Chinese liquor fermentation.IMPORTANCE Sulfur compounds play a crucial role in the aroma quality of various fermented foods and alcoholic beverages. However, it is unclear how these compounds are produced by microbes during their spontaneous fermentations. Here, we identified the core microbiota (Saccharomyces and Lactobacillus) associated with sulfur metabolism by determining both transcript abundance and distribution frequency of each genus in spontaneous Chinese liquor fermentation. This study provides a system-level analysis of sulfur metabolism by the metatranscriptomic analysis and culture-dependent methods. It sheds new light on how the metabolic behavior of the microbiota contributes to the liquor aroma quality. Furthermore, this work reveals a novel synergistic effect between Saccharomyces and Lactobacillus in the production of sulfur compounds, in which Lactobacillus regenerates the precursor methionine for sulfur compound production by Saccharomyces Our findings can contribute to the enhancement of aroma characteristics in Chinese liquor and open new avenues for improving various food and alcoholic beverage fermentation processes.

Yeast Creates a Niche for Symbiotic Lactic Acid Bacteria through Nitrogen Overflow

Many microorganisms live in communities and depend on metabolites secreted by fellow community members for survival. Yet our knowledge of interspecies metabolic dependencies is limited to few communities with small number of exchanged metabolites, and even less is known about cellular regulation facilitating metabolic exchange. Here we show how yeast enables growth of lactic acid bacteria through endogenous, multi-component, cross-feeding in a readily established community. In nitrogen-rich environments, Saccharomyces cerevisiae adjusts its metabolism by secreting a pool of metabolites, especially amino acids, and thereby enables survival of Lactobacillus plantarum and Lactococcus lactis. Quantity of the available nitrogen sources and the status of nitrogen catabolite repression pathways jointly modulate this niche creation. We demonstrate how nitrogen overflow by yeast benefits L. plantarum in grape juice, and contributes to emergence of mutualism with L. lactis in a medium with lactose. Our results illustrate how metabolic decisions of an individual species can benefit others.

Adjacent-possible ecological niche: growth of Lactobacillus species co-cultured with Escherichia coli in a synthetic minimal medium

In certain conditions, members of the Lactobacillus genus are auxotrophs that have fastidious requirements for growth. Notably, Lactobacillus cannot grow in M9 medium, a minimal synthetic medium used for Escherichia coli. However, we found that some Lactobacillus strains can be grown in M9 when co-cultured with E. coli K-12. In the co-culture, L. casei proliferates exponentially, reaching cell densities of 108 CFU (colony-forming unit) ml-1 in 6 h and dominating E. coli in the late growth phase. Spent medium from E. coli grown overnight lacked this growth-promoting effect on L. casei. Similarly, the effect was not observed when the species were separated by a 0.4-µm membrane. Microscopic observations showed that L. casei are embedded in the micro-scale clusters of E. coli in the early growth phase. This study describes for the first time the ability of a Lactobacillus species to grow in minimal medium when in close proximity with co-cultured bacteria.

Wine microbiome: A dynamic world of microbial interactions

Most fermented products are generated by a mixture of microbes. These microbial consortia perform various biological activities responsible for the nutritional, hygienic, and aromatic qualities of the product. Wine is no exception. Substantial yeast and bacterial biodiversity is observed on grapes, and in both must and wine. The diverse microorganisms present interact throughout the winemaking process. The interactions modulate the hygienic and sensorial properties of the wine. Many studies have been conducted to elucidate the nature of these interactions, with the aim of establishing better control of the two fermentations occurring during wine processing. However, wine is a very complex medium making such studies difficult. In this review, we present the current state of research on microbial interactions in wines. We consider the different kinds of interactions between different microorganisms together with the consequences of these interactions. We underline the major challenges to obtaining a better understanding of how microbes interact. Finally, strategies and methodologies that may help unravel microbe interactions in wine are suggested.

Effects of Exogenous Yeast and Bacteria on the Microbial Population Dynamics and Outcomes of Olive Fermentations

Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be improved by the deliberate addition of starter culture microbes that accelerate or beneficially modify product outcomes, the impact of either of those microbial additions on community dynamics within the fermentations is not well understood at strain-specific or global scales. Herein, we show how exogenous spoilage yeast or starter lactic acid bacteria confer very different effects on microbial numbers and diversity in olive fermentations. Introduced microbes have long-lasting consequences and result in changes that are apparent even when levels of those inoculants and their major enzymatic activities decline. This work has direct implications for understanding bacterial and fungal invasions of microbial habitats resulting in pivotal changes to community structure and function.

In this study, we examined Sicilian-style green olive fermentations upon the addition of Saccharomyces cerevisiae UCDFST 09-448 and/or Pichia kudriazevii UCDFST09-427 or the lactic acid bacteria (LAB) Lactobacillus plantarum AJ11R and Leuconostoc pseudomesenteroides BGM3R. Olives containing S. cerevisiae UCDFST 09-448, a strain able to hydrolyze pectin, but not P. kudriazevii UCDFST 09-427, a nonpectinolytic strain, exhibited excessive tissue damage within 4 weeks. DNA sequencing of fungal internal transcribed spacer (ITS) regions and comparisons to a yeast-specific ITS sequence database remarkably showed that neither S. cerevisiae UCDFST 09-448 nor P. kudriazevii UCDFST 09-427 resulted in significant changes to yeast species diversity. Instead, Candida boidinii constituted the majority (>90%) of the total yeast present, independent of whether S. cerevisiae or P. kudriazevii was added. By comparison, Lactobacillus species were enriched in olives inoculated with potential starter LAB L. plantarum AJ11R and L. pseudomesenteroides BGM3R according to community 16S rRNA gene sequence analysis. The bacterial diversity of those olives was significantly reduced and resembled control fermentations incubated for a longer period of time. Importantly, microbial populations were highly dynamic at the strain level, as indicated by the large variations in AJ11R and BGM3R cell numbers over time and reductions in the numbers of yeast isolates expressing polygalacturonase activity. These findings show the distinct effects of exogenous spoilage and starter microbes on indigenous communities in plant-based food fermentations that result in very different impacts on product quality.

IMPORTANCE Food fermentations are subject to tremendous selective pressures resulting in the growth and persistence of a limited number of bacterial and fungal taxa. Although these foods are vulnerable to spoilage by unintended contamination of certain microorganisms, or alternatively, can be improved by the deliberate addition of starter culture microbes that accelerate or beneficially modify product outcomes, the impact of either of those microbial additions on community dynamics within the fermentations is not well understood at strain-specific or global scales. Herein, we show how exogenous spoilage yeast or starter lactic acid bacteria confer very different effects on microbial numbers and diversity in olive fermentations. Introduced microbes have long-lasting consequences and result in changes that are apparent even when levels of those inoculants and their major enzymatic activities decline. This work has direct implications for understanding bacterial and fungal invasions of microbial habitats resulting in pivotal changes to community structure and function.

Saccharomyces cerevisiae metabolism in ecological context

The architecture and regulation of Saccharomyces cerevisiae metabolic network are among the best studied owing to its widespread use in both basic research and industry. Yet, several recent studies have revealed notable limitations in explaining genotype-metabolic phenotype relations in this yeast, especially when concerning multiple genetic/environmental perturbations. Apparently unexpected genotype-phenotype relations may originate in the evolutionarily shaped cellular operating principles being hidden in common laboratory conditions. Predecessors of laboratory S. cerevisiae strains, the wild and the domesticated yeasts, have been evolutionarily shaped by highly variable environments, very distinct from laboratory conditions, and most interestingly by social life within microbial communities. Here we present a brief review of the genotypic and phenotypic peculiarities of S. cerevisiae in the context of its social lifestyle beyond laboratory environments. Accounting for this ecological context and the origin of the laboratory strains in experimental design and data analysis would be essential in improving the understanding of genotype-environment-phenotype relationships.

Transcriptomic Responses of the Interactions between Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009 in a Cellulose-Grown Coculture for Enhanced Hydrogen Production

Coculturing dark- and photofermentative bacteria is a promising strategy for enhanced hydrogen (H2) production. In this study, next-generation sequencing was used to query the global transcriptomic responses of an artificial coculture of Clostridium cellulovorans 743B and Rhodopseudomonas palustris CGA009. By analyzing differentially regulated gene expression, we showed that, consistent with the physiological observations of enhanced H2 production and cellulose degradation, the nitrogen fixation genes in R. palustris and the cellulosomal genes in C. cellulovorans were upregulated in cocultures. Unexpectedly, genes related to H2 production in C. cellulovorans were downregulated, suggesting that the enhanced H2 yield was contributed mainly by R. palustris A number of genes related to biosynthesis of volatile fatty acids (VFAs) in C. cellulovorans were upregulated, and correspondingly, a gene that mediates organic compound catabolism in R. palustris was also upregulated. Interestingly, a number of genes responsible for chemotaxis in R. palustris were upregulated, which might be elicited by the VFA concentration gradient created by C. cellulovorans In addition, genes responsible for sulfur and thiamine metabolism in C. cellulovorans were downregulated in cocultures, and this could be due to a response to pH changes. A conceptual model illustrating the interactions between the two organisms was constructed based on the transcriptomic results.

IMPORTANCE

The findings of this study have important biotechnology applications for biohydrogen production using renewable cellulose, which is an industrially and economically important bioenergy process. Since the molecular characteristics of the interactions of a coculture when cellulose is the substrate are still unclear, this work will be of interest to microbiologists seeking to better understand and optimize hydrogen-producing coculture systems.

Maintenance-energy requirements and robustness of Saccharomyces cerevisiae at aerobic near-zero specific growth rates

Background

Saccharomyces cerevisiae is an established microbial platform for production of native and non-native compounds. When product pathways compete with growth for precursors and energy, uncoupling of growth and product formation could increase product yields and decrease formation of biomass as a by-product. Studying non-growing, metabolically active yeast cultures is a first step towards developing S. cerevisiae as a robust, non-growing cell factory. Microbial physiology at near-zero growth rates can be studied in retentostats, which are continuous-cultivation systems with full biomass retention. Hitherto, retentostat studies on S. cerevisiae have focused on anaerobic conditions, which bear limited relevance for aerobic industrial processes. The present study uses aerobic, glucose-limited retentostats to explore the physiology of non-dividing, respiring S. cerevisiae cultures, with a focus on industrially relevant features.

Results

Retentostat feeding regimes for smooth transition from exponential growth in glucose-limited chemostat cultures to near-zero growth rates were obtained by model-aided experimental design. During 20 days of retentostats cultivation, the specific growth rate gradually decreased from 0.025 h⁻¹ to below 0.001 h⁻¹, while culture viability remained above 80 %. The maintenance requirement for ATP (m_ATP) was estimated at 0.63 ± 0.04 mmol ATP (g biomass)⁻¹ h⁻¹, which is ca. 35 % lower than previously estimated for anaerobic retentostats. Concomitant with decreasing growth rate in aerobic retentostats, transcriptional down-regulation of genes involved in biosynthesis and up-regulation of stress-responsive genes resembled transcriptional regulation patterns observed for anaerobic retentostats. The heat-shock tolerance in aerobic retentostats far exceeded previously reported levels in stationary-phase batch cultures. While in situ metabolic fluxes in retentostats were intentionally low due to extreme caloric restriction, off-line measurements revealed that cultures retained a high metabolic capacity.

Conclusions

This study provides the most accurate estimation yet of the maintenance-energy coefficient in aerobic cultures of S. cerevisiae, which is a key parameter for modelling of industrial aerobic, glucose-limited fed-batch processes. The observed extreme heat-shock tolerance and high metabolic capacity at near-zero growth rates demonstrate the intrinsic potential of S. cerevisiae as a robust, non-dividing microbial cell factory for energy-intensive products.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0501-z) contains supplementary material, which is available to authorized users.

Oxygen availability strongly affects chronological lifespan and thermotolerance in batch cultures of Saccharomyces cerevisiae

Stationary-phase (SP) batch cultures of Saccharomyces cerevisiae, in which growth has been arrested by carbon-source depletion, are widely applied to study chronological lifespan, quiescence and SP-associated robustness. Based on this type of experiments, typically performed under aerobic conditions, several roles of oxygen in aging have been proposed. However, SP in anaerobic yeast cultures has not been investigated in detail. Here, we use the unique capability of S. cerevisiae to grow in the complete absence of oxygen to directly compare SP in aerobic and anaerobic bioreactor cultures. This comparison revealed strong positive effects of oxygen availability on adenylate energy charge, longevity and thermotolerance during SP. A low thermotolerance of anaerobic batch cultures was already evident during the exponential growth phase and, in contrast to the situation in aerobic cultures, was not substantially increased during transition into SP. A combination of physiological and transcriptome analysis showed that the slow post-diauxic growth phase on ethanol, which precedes SP in aerobic, but not in anaerobic cultures, endowed cells with the time and resources needed for inducing longevity and thermotolerance. When combined with literature data on acquisition of longevity and thermotolerance in retentostat cultures, the present study indicates that the fast transition from glucose excess to SP in anaerobic cultures precludes acquisition of longevity and thermotolerance. Moreover, this study demonstrates the importance of a preceding, calorie-restricted conditioning phase in the acquisition of longevity and stress tolerance in SP yeast cultures, irrespective of oxygen availability.

Fluorescence-based bioassays for the detection and evaluation of food materials

We summarize here the recent progress in fluorescence-based bioassays for the detection and evaluation of food materials by focusing on fluorescent dyes used in bioassays and applications of these assays for food safety, quality and efficacy. Fluorescent dyes have been used in various bioassays, such as biosensing, cell assay, energy transfer-based assay, probing, protein/immunological assay and microarray/biochip assay. Among the arrays used in microarray/biochip assay, fluorescence-based microarrays/biochips, such as antibody/protein microarrays, bead/suspension arrays, capillary/sensor arrays, DNA microarrays/polymerase chain reaction (PCR)-based arrays, glycan/lectin arrays, immunoassay/enzyme-linked immunosorbent assay (ELISA)-based arrays, microfluidic chips and tissue arrays, have been developed and used for the assessment of allergy/poisoning/toxicity, contamination and efficacy/mechanism, and quality control/safety. DNA microarray assays have been used widely for food safety and quality as well as searches for active components. DNA microarray-based gene expression profiling may be useful for such purposes due to its advantages in the evaluation of pathway-based intracellular signaling in response to food materials.

Growth-rate dependency of de novo resveratrol production in chemostat cultures of an engineered Saccharomyces cerevisiae strain

Introduction

Saccharomyces cerevisiae has become a popular host for production of non-native compounds. The metabolic pathways involved generally require a net input of energy. To maximize the ATP yield on sugar in S. cerevisiae, industrial cultivation is typically performed in aerobic, sugar-limited fed-batch reactors which, due to constraints in oxygen transfer and cooling capacities, have to be operated at low specific growth rates. Because intracellular levels of key metabolites are growth-rate dependent, slow growth can significantly affect biomass-specific productivity. Using an engineered Saccharomyces cerevisiae strain expressing a heterologous pathway for resveratrol production as a model energy-requiring product, the impact of specific growth rate on yeast physiology and productivity was investigated in aerobic, glucose-limited chemostat cultures.

Results

Stoichiometric analysis revealed that de novo resveratrol production from glucose requires 13 moles of ATP per mole of produced resveratrol. The biomass-specific production rate of resveratrol showed a strong positive correlation with the specific growth rate. At low growth rates a substantial fraction of the carbon source was invested in cellular maintenance-energy requirements (e.g. 27 % at 0.03 h⁻¹). This distribution of resources was unaffected by resveratrol production. Formation of the by-products coumaric, phloretic and cinnamic acid had no detectable effect on maintenance energy requirement and yeast physiology in chemostat. Expression of the heterologous pathway led to marked differences in transcript levels in the resveratrol-producing strain, including increased expression levels of genes involved in pathways for precursor supply (e.g. ARO7 and ARO9 involved in phenylalanine biosynthesis). The observed strong differential expression of many glucose-responsive genes in the resveratrol producer as compared to a congenic reference strain could be explained from higher residual glucose concentrations and higher relative growth rates in cultures of the resveratrol producer.

Conclusions

De novo resveratrol production by engineered S. cerevisiae is an energy demanding process. Resveratrol production by an engineered strain exhibited a strong correlation with specific growth rate. Since industrial production in fed-batch reactors typically involves low specific growth rates, this study emphasizes the need for uncoupling growth and product formation via energy-requiring pathways.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0321-6) contains supplementary material, which is available to authorized users.

Genomic expression program of Saccharomyces cerevisiae along a mixed-culture wine fermentation with Hanseniaspora guilliermondii

Background

The introduction of yeast starter cultures consisting in a blend of Saccharomyces cerevisiae and non-Saccharomyces yeast strains is emerging for production of wines with improved complexity of flavor. The rational use of this approach is, however, dependent on knowing the impact that co-inoculation has in the physiology of S. cerevisiae. In this work the transcriptome of S.cerevisiae was monitored throughout a wine fermentation, carried out in single culture or in a consortium with Hanseniasporaguilliermondii, this being the first time that this relevant yeast–yeast interaction is examined at a genomic scale.

Results

Co-inoculation with H. guilliermondii reduced the overall genome-wide transcriptional response of S. cerevisiae throughout the fermentation, which was attributable to a lower fermentative activity of S. cerevisiae while in the mixed-fermentation. Approximately 350 genes S. cerevisiae genes were found to be differently expressed (FDR < 0.05) in response to the presence of H. guilliermondii in the fermentation medium. Genes involved in biosynthesis of vitamins were enriched among those up-regulated in the mixed-culture fermentation, while genes related with the uptake and biosynthesis of amino acids were enriched among those more expressed in the single-culture. The differences in the aromatic profiles of wines obtained in the single and in the mixed-fermentations correlated with the differential expression of S. cerevisiae genes encoding enzymes required for formation of aroma compounds.

Conclusions

By integrating results obtained in the transcriptomic analysis performed with physiological data our study provided, for the first time, an integrated view into the adaptive responses of S. cerevisiae to the challenging environment of mixed culture fermentation. The availability of nutrients, in particular, of nitrogen and vitamins, stands out as a factor that may determine population dynamics, fermentative activity and by-product formation.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-015-0318-1) contains supplementary material, which is available to authorized users.

Fine structure of Tibetan kefir grains and their yeast distribution, diversity, and shift

Tibetan kefir grains (TKGs), a kind of natural starter for fermented milk in Tibet, China, host various microorganisms of lactic acid bacteria, yeasts, and occasionally acetic acid bacteria in a polysaccharide/protein matrix. In the present study, the fine structure of TKGs was studied to shed light on this unusual symbiosis with stereomicroscopy and thin sections. The results reveal that TKGs consist of numerous small grain units, which are characterized by a hollow globular structure with a diameter between 2.0 and 9.0 mm and a wall thickness of approximately 200 µm. A polyhedron-like net structure, formed mainly by the bacteria, was observed in the wall of the grain units, which has not been reported previously to our knowledge. Towards the inside of the grain unit, the polyhedron-like net structures became gradually larger in diameter and fewer in number. Such fine structures may play a crucial role in the stability of the grains. Subsequently, the distribution, diversity, and shift of yeasts in TKGs were investigated based on thin section, scanning electron microscopy, cloning and sequencing of D1/D2 of the 26S rRNA gene, real-time quantitative PCR, and in situ hybridization with specific fluorescence-labeled oligonucleotide probes. These show that (i) yeasts appear to localize on the outer surface of the grains and grow normally together to form colonies embedded in the bacterial community; (ii) the diversity of yeasts is relatively low on genus level with three dominant species – Saccharomyces cerevisiae, Kluyveromyces marxianus, and Yarrowia lipolytica; (iii) S. cerevisiae is the stable predominant yeast species, while the composition of Kluyveromyces and Yarrowia are subject to change over time. Our results indicate that TKGs are relatively stable in structure, and culture conditions to some extent shape the microbial community and interaction in kefir grains. These findings pave the way for further study of the specific symbiotic associations between S. cerevisiae and Lactobacillus bacteria in TKGs.

Physiological and transcriptional responses of anaerobic chemostat cultures of Saccharomyces cerevisiae subjected to diurnal temperature cycles

Diurnal temperature cycling is an intrinsic characteristic of many exposed microbial ecosystems. However, its influence on yeast physiology and the yeast transcriptome has not been studied in detail. In this study, 24-h sinusoidal temperature cycles, oscillating between 12°C and 30°C, were imposed on anaerobic, glucose-limited chemostat cultures of Saccharomyces cerevisiae. After three diurnal temperature cycles (DTC), concentrations of glucose and extracellular metabolites as well as CO2 production rates showed regular, reproducible circadian rhythms. DTC also led to waves of transcriptional activation and repression, which involved one-sixth of the yeast genome. A substantial fraction of these DTC-responsive genes appeared to respond primarily to changes in the glucose concentration. Elimination of known glucose-responsive genes revealed an overrepresentation of previously identified temperature-responsive genes as well as genes involved in the cell cycle and de novo purine biosynthesis. In-depth analysis demonstrated that DTC led to a partial synchronization of the cell cycle of the yeast populations in chemostat cultures, which was lost upon release from DTC. Comparison of DTC results with data from steady-state cultures showed that the 24-h DTC was sufficiently slow to allow S. cerevisiae chemostat cultures to acclimate their transcriptome and physiology at the DTC temperature maximum and to approach acclimation at the DTC temperature minimum. Furthermore, this comparison and literature data on growth rate-dependent cell cycle phase distribution indicated that cell cycle synchronization was most likely an effect of imposed fluctuations of the relative growth rate (μ/μmax) rather than a direct effect of temperature.

Functional characterization of a Penicillium chrysogenum mutanase gene induced upon co-cultivation with Bacillus subtilis

BACKGROUND

Microbial gene expression is strongly influenced by environmental growth conditions. Comparison of gene expression under different conditions is frequently used for functional analysis and to unravel regulatory networks, however, gene expression responses to co-cultivation with other microorganisms, a common occurrence in nature, is rarely studied under laboratory conditions. To explore cellular responses of the antibiotic-producing fungus Penicillium chrysogenum to prokaryotes, the present study investigates its transcriptional responses during co-cultivation with Bacillus subtilis.

RESULTS

Steady-state glucose-limited chemostats of P. chrysogenum grown under penillicin-non-producing conditions were inoculated with B. subtilis. Physiological and transcriptional responses of P. chrysogenum in the resulting mixed culture were monitored over 72 h. Under these conditions, B. subtilis outcompeted P. chrysogenum, as reflected by a three-fold increase of the B. subtilis population size and a two-fold reduction of the P. chrysogenum biomass concentration. Genes involved in the penicillin pathway and in synthesis of the penicillin precursors and side-chain were unresponsive to the presence of B. subtilis. Moreover, Penicillium polyketide synthase and nonribosomal peptide synthase genes were either not expressed or down-regulated. Among the highly responsive genes, two putative α-1,3 endoglucanase (mutanase) genes viz Pc12g07500 and Pc12g13330 were upregulated by more than 15-fold and 8-fold, respectively. Measurement of enzyme activity in the supernatant of mixed culture confirmed that the co-cultivation with B. subtilis induced mutanase production. Mutanase activity was neither observed in pure cultures of P. chrysogenum or B. subtilis, nor during exposure of P. chrysogenum to B. subtilis culture supernatants or heat-inactivated B. subtilis cells. However, mutanase production was observed in cultures of P. chrysogenum exposed to filter-sterilized supernatants of mixed cultures of P. chrysogenum and B. subtilis. Heterologous expression of Pc12g07500 and Pc12g13330 genes in Saccharomyces cerevisiae confirmed that Pc12g07500 encoded an active α-1,3 endoglucanase.

CONCLUSION

Time-course transcriptional profiling of P. chrysogenum revealed differentially expressed genes during co-cultivation with B. subtilis. Penicillin production was not induced under these conditions. However, induction of a newly characterized P. chrysogenum gene encoding α-1,3 endoglucanase may enhance the efficacy of fungal antibiotics by degrading bacterial exopolysaccharides.