Use of kefir-derived lactic acid bacteria for the preparation of a fermented soy drink with increased estrogenic activity

Fermented foods are receiving growing attention for their health promoting properties. In particular, there is a growing demand for plant-based fermented foods as dairy alternatives. Considering that soy is a vegetal food rich in nutrients and a source of the phytoestrogen isoflavones, the aim of this study was to select safe food microorganisms with the ability to ferment a soy drink resulting in a final product with an increased estrogenic activity and improved functional properties. We used milk kefir grains, a dairy source of microorganisms with proven health-promoting properties, as a starting inoculum for a soymilk. After 14 passages of daily inoculum in fresh soy drink, we isolated four lactic acid bacterial strains: Lactotoccus lactis subsp. lactis K03, Leuconostc pseudomesenteroides K05, Leuconostc mesenteroides K09 and Lentilactobacillus kefiri K10. Isolated strains were proven to be safe for human consumption according to the assessment of their antibiotic resistance profile and comparative genomics. Furthermore, functional characterization of the bacterial strains demonstrated their ability to ferment sugars naturally present in soybeans and produce a creamy texture. In addition, we demonstrated, by means of a yeast-based bioluminescence reporter system, that the two strains belonging to the genus Leuconostoc increased the estrogenic activity of the soybean drink. In conclusion, the proposed application of the bacterial strains characterized in this study meets the growing demand of consumers for health-promoting vegetal food alternatives to dairy products.

Bioactive Properties of the Aqueous Extracts of Endophytic Fungi Associated with Scots Pine (Pinus sylvestris) Roots

Despite the continuing interest in various plant and natural products, only a small portion of the biologically active compounds from nature has been discovered and exploited. In this study, antioxidant and antibacterial properties of aqueous fractions of three endophytic fungi isolated from the roots of 8-year-old Scots pines (Pinus sylvestris) growing on a drained peatland were investigated. The endophytic fungi species were Acephala applanata, Phialocephala fortinii, and Humicolopsis cephalosporioides/Coniochaeta mutabilis. The bioactivities were examined using hydrogen peroxide scavenging and oxygen radical absorbance capacity tests as well as sensitive Escherichia coli-based biosensors, which produce a luminescent signal in the presence of substances with oxidative or genotoxic properties. In addition, cell models for Parkinson's disease, age-related macular degeneration, and osteoarthritis were used to evaluate the potential for pharmaceutical applications. The aqueous extracts of fungi and 19 out of 42 fractions were found to be active in one or more of the tests used. However, no activity was found in the age-related macular degeneration and osteoarthritis cell model tests. Additionally, bioactivity data was connected with metabolites putatively annotated, and out of 330 metabolites, 177 were interesting in view of the bioactivities investigated. A majority of these were peptides and all three fungal species shared a highly similar metabolome. We propose that Scots pine endophytic fungi are a rich source of interesting metabolites, and synergistic effects may cause the bioactivities, as they were found to vary after the fractionation process.

Metabolic Profiling of Water-Soluble Compounds from the Extracts of Dark Septate Endophytic Fungi (DSE) Isolated from Scots Pine (Pinus sylvestris L.) Seedlings Using UPLC-Orbitrap-MS

Endophytes are microorganisms living inside plant hosts and are known to be beneficial for the host plant vitality. In this study, we isolated three endophytic fungus species from the roots of Scots pine seedlings growing on Finnish drained peatland setting. The isolated fungi belonged to dark septate endophytes (DSE). The metabolic profiles of the hot water extracts of the fungi were investigated using Ultrahigh Performance Liquid Chromatography with Diode Array Detection and Electron Spray Ionization source Mass Spectrometry with Orbitrap analyzer (UPLC-DAD-ESI-MS-Orbitrap). Out of 318 metabolites, we were able to identify 220, of which a majority was amino acids and peptides. Additionally, opine amino acids, amino acid quinones, Amadori compounds, cholines, nucleobases, nucleosides, nucleotides, siderophores, sugars, sugar alcohols and disaccharides were found, as well as other previously reported metabolites from plants or endophytes. Some differences of the metabolic profiles, regarding the amount and identity of the found metabolites, were observed even though the fungi were isolated from the same host. Many of the discovered metabolites have been described possessing biological activities and properties, which may make a favorable contribution to the host plant nutrient availability or abiotic and biotic stress tolerance.

A Bioscreening Technique for Ultraviolet Irradiation Protective Natural Substances

Ultraviolet radiation (UV-R) causes genotoxic and aging effects on skin, and sunscreens are used to alleviate the damage. However, sunscreens contain synthetic shielding agents that can cause harmful effects in the environment. Nature-derived substances may have potential as replacement materials for the harmful sunscreen chemicals. However, screening of a broad range of samples is tedious, and often requires a separate genotoxicity assessment. We describe a simple microplate technique for the screening of UV protective substances using a recombinant Escherichia coli biosensor. Both absorbance-based and bioactivity-based shields can be detected with simultaneous information about the sample genotoxicity. With this technique, a controversial sunscreen compound, oxybenzone offers physical or absorbance-based shield but appears genotoxic at higher concentrations (3.3 mg/mL). We also demonstrate that pine needle extract (Pi_Ne ) shields the biosensor from UV-R in a dose-dependent manner without showing genotoxicity. The physical shield of 5 mg/mL Pi_Ne was similar to that of one of the most common UV-shielding compound TiO₂ concentration 0.80 mg/mL. The bioactivity-based shield of Pi_Ne also reaches the extent of the physical shield with the highest concentration (3.3 mg/mL). We conclude that our technique is suitable in detecting the UV-shielding potential of natural substances, and gives simultaneous information on genotoxicity.

Engineering and Characterization of Bacterial Nanocellulose Films as Low Cost and Flexible Sensor Material

Some bacterial strains such as Komagataeibacter xylinus are able to produce cellulose as an extracellular matrix. In comparison to wood-based cellulose, bacterial cellulose (BC) holds interesting properties such as biodegradability, high purity, water-holding capacity, and superior mechanical and structural properties. Aiming toward improvement in BC production titer and tailored alterations to the BC film, we engineered K. xylinus to overexpress partial and complete bacterial cellulose synthase operon that encodes activities for BC production. The changes in cell growth, end metabolite, and BC production titers from the engineered strains were compared with the wild-type K. xylinus. Although there were no significant differences between the growth of wild-type and engineered strains, the engineered K. xylinus strains demonstrated faster BC production, generating 2-4-fold higher production titer (the highest observed titer was obtained with K. xylinus-bcsABCD strain producing 4.3 ± 0.46 g/L BC in 4 days). The mechanical and structural characteristics of cellulose produced from the wild-type and engineered K. xylinus strains were analyzed with a stylus profilometer, in-house built tensile strength measurement system, a scanning electron microscope, and an X-ray diffractometer. Results from the profilometer indicated that the engineered K. xylinus strains produced thicker BC films (wild type, 5.1 μm, and engineered K. xylinus strains, 6.2-10.2 μm). Scanning electron microscope revealed no principal differences in the structure of the different type BC films. The crystallinity index of all films was high (from 88.6 to 97.5%). All BC films showed significant piezoelectric response (5.0-20 pC/N), indicating BC as a promising sensor material.

Growth and wax ester production of an Acinetobacter baylyi ADP1 mutant deficient in exopolysaccharide capsule synthesis

Acinetobacter baylyi ADP1 naturally produces wax esters that could be used as a raw material in industrial applications. We attempted to improve wax ester yield of A. baylyi ADP1 by removing rmlA, a gene involved in exopolysaccharide production. Growth rate, biomass formation and wax ester yield on 4-hydroxybenzoate were not affected, but the rmlA− strain grew slower on acetate, while reaching similar biomass and wax ester yield. The rmlA− cells had malformed shape and large size and grew poorly on glucose without expression of the gene for pyruvate kinase (pykF) from Escherichia coli. The pykF-expressing rmlA− strain had similar growth rate, lowered biomass formation and improved wax ester production on glucose as compared to the wild-type strain expressing pykF. Cultivation of the pykF-expressing rmlA− strain on an elevated glucose concentration in a medium supplemented with amino acids resulted in doubled molar wax ester yield and acetate production.

Effect of source-separated urine storage on estrogenic activity detected using bioluminescent yeast Saccharomyces cerevisiae

The objective was to demonstrate that a microbial whole cell biosensor, bioluminescent yeast, Saccharomyces cerevisiae (BMAEREluc/ERα) can be applied to detect overall estrogenic activity from fresh and stored human urine. The use of source-separated urine in agriculture removes a human originated estrogen source from wastewater influents, subsequently enabling nutrient recycling. Estrogenic activity in urine should be diminished prior to urine usage in agriculture in order to prevent its migration to soil. A storage period of 6 months is required for hygienic reasons; therefore, estrogenic activity monitoring is of interest. The method measured cumulative female hormone-like activity. Calibration curves were prepared for estrone, 17β-estradiol, 17α- ethinylestradiol and estriol. Estrogen concentrations of 0.29-29,640 μg L(-1) were detectable while limit of detection corresponded to 0.28-35 μg L(-1) of estrogens. The yeast sensor responded well to fresh and stored urine and gave high signals corresponding to 0.38-3,804 μg L(-1) of estrogens in different urine samples. Estrogenic activity decreased during storage, but was still higher than in fresh urine implying insufficient storage length. The biosensor was suitable for monitoring hormonal activity in urine and can be used in screening anthropogenic estrogen-like compounds interacting with the receptor.

Cell-based bioreporter assay coupled to HPLC micro-fractionation in the evaluation of antimicrobial properties of the basidiomycete fungus Pycnoporus cinnabarinus

CONTEXT

Identification of bioactive components from complex natural product extracts can be a tedious process that aggravates the use of natural products in drug discovery campaigns.

OBJECTIVE

This study presents a new approach for screening antimicrobial potential of natural product extracts by employing a bioreporter assay amenable to HPLC-based activity profiling.

MATERIALS AND METHODS

A library of 116 crude extracts was prepared from fungal culture filtrates by liquid-liquid extraction with ethyl acetate, lyophilised, and screened against Escherichia coli using TLC bioautography. Active extracts were studied further with a broth microdilution assay, which was, however, too insensitive for identifying the active microfractions after HPLC separation. Therefore, an assay based on bioluminescent E. coli K-12 (pTetLux1) strain was coupled with HPLC micro-fractionation.

RESULTS

Preliminary screening yielded six fungal extracts with potential antimicrobial activity. A crude extract from a culture filtrate of the wood-rotting fungus, Pycnoporus cinnabarinus (Jacq.) P. Karst. (Polyporaceae), was selected for evaluating the functionality of the bioreporter assay in HPLC-based activity profiling. In the bioreporter assay, the IC50 value for the crude extract was 0.10 mg/mL. By integrating the bioreporter assay with HPLC micro-fractionation, the antimicrobial activity was linked to LC-UV peak of a compound in the chromatogram of the extract. This compound was isolated and identified as a fungal pigment phlebiarubrone.

DISCUSSION AND CONCLUSION

HPLC-based activity profiling using the bioreporter-based approach is a valuable tool for identifying antimicrobial compound(s) from complex crude extracts, and offers improved sensitivity and speed compared with traditional antimicrobial assays, such as the turbidimetric measurement.

Fluorescent Protein Based FRET Pairs with Improved Dynamic Range for Fluorescence Lifetime Measurements

Fluorescence Resonance Energy Transfer (FRET) using fluorescent protein variants is widely used to study biochemical processes in living cells. FRET detection by fluorescence lifetime measurements is the most direct and robust method to measure FRET. The traditional cyan-yellow fluorescent protein based FRET pairs are getting replaced by green-red fluorescent protein variants. The green-red pair enables excitation at a longer wavelength which reduces cellular autofluorescence and phototoxicity while monitoring FRET. Despite the advances in FRET based sensors, the low FRET efficiency and dynamic range still complicates their use in cell biology and high throughput screening. In this paper, we utilized the higher lifetime of NowGFP and screened red fluorescent protein variants to develop FRET pairs with high dynamic range and FRET efficiency. The FRET variations were analyzed by proteolytic activity and detected by steady-state and time-resolved measurements. Based on the results, NowGFP-tdTomato and NowGFP-mRuby2 have shown high potentials as FRET pairs with large fluorescence lifetime dynamic range. The in vitro measurements revealed that the NowGFP-tdTomato has the highest Förster radius for any fluorescent protein based FRET pairs yet used in biological studies. The developed FRET pairs will be useful for designing FRET based sensors and studies employing Fluorescence Lifetime Imaging Microscopy (FLIM).

Bioluminescent whole-cell reporter gene assays as screening tools in the identification of antimicrobial natural product extracts

We describe novel tools, bioluminescent whole-cell reporter gene assays, for facilitating the use of natural products in antimicrobial drug discovery. As proof-of-concept, a plant extract library was screened and follow-up experiments were carried out. Primary results can be obtained in 2-4h with high sensitivity, leading to significant improvements of the process.

Rationally engineered synthetic coculture for improved biomass and product formation

In microbial ecosystems, bacteria are dependent on dynamic interspecific interactions related to carbon and energy flow. Substrates and end-metabolites are rapidly converted to other compounds, which protects the community from high concentrations of inhibitory molecules. In biotechnological applications, pure cultures are preferred because of the more straight-forward metabolic engineering and bioprocess control. However, the accumulation of unwanted side products can limit the cell growth and process efficiency. In this study, a rationally engineered coculture with a carbon channeling system was constructed using two well-characterized model strains Escherichia coli K12 and Acinetobacter baylyi ADP1. The directed carbon flow resulted in efficient acetate removal, and the coculture showed symbiotic nature in terms of substrate utilization and growth. Recombinant protein production was used as a proof-of-principle example to demonstrate the coculture utility and the effects on product formation. As a result, the biomass and recombinant protein titers of E. coli were enhanced in both minimal and rich medium simple batch cocultures. Finally, harnessing both the strains to the production resulted in enhanced recombinant protein titers. The study demonstrates the potential of rationally engineered cocultures for synthetic biology applications.

Assessment of metabolic flux distribution in the thermophilic hydrogen producer Caloramator celer as affected by external pH and hydrogen partial pressure

BACKGROUND

Caloramator celer is a strict anaerobic, alkalitolerant, thermophilic bacterium capable of converting glucose to hydrogen (H2), carbon dioxide, acetate, ethanol and formate by a mixed acid fermentation. Depending on the growth conditions C. celer can produce H2 at high yields. For a biotechnological exploitation of this bacterium for H2 production it is crucial to understand the factors that regulate carbon and electron fluxes and therefore the final distribution of metabolites to channel the metabolic flux towards the desired product.

RESULTS

Combining experimental results from batch fermentations with genome analysis, reconstruction of central carbon metabolism and metabolic flux analysis (MFA), this study shed light on glucose catabolism of the thermophilic alkalitolerant bacterium C. celer. Two innate factors pertaining to culture conditions have been identified to significantly affect the metabolic flux distribution: culture pH and partial pressures of H2 (PH2). Overall, at alkaline to neutral pH the rate of biomass synthesis was maximized, whereas at acidic pH the lower growth rate and the less efficient biomass formation are accompanied with more efficient energy recovery from the substrate indicating high cell maintenance possibly to sustain intracellular pH homeostasis. Higher H2 yields were associated with fermentation at acidic pH as a consequence of the lower synthesis of other reduced by-products such as formate and ethanol. In contrast, PH2 did not affect the growth of C. celer on glucose. At high PH2 the cellular redox state was balanced by rerouting the flow of carbon and electrons to ethanol and formate production allowing unaltered glycolytic flux and growth rate, but resulting in a decreased H2 synthesis.

CONCLUSION

C. celer possesses a flexible fermentative metabolism that allows redistribution of fluxes at key metabolic nodes to simultaneously control redox state and efficiently harvest energy from substrate even under unfavorable conditions (i.e. low pH and high PH2). With the H2 production in mind, acidic pH and low PH2 should be preferred for a high yield-oriented process, while a high productivity-oriented process can be achieved at alkaline pH and high PH2.

Processing and sustained in vitro release of rifampicin containing composites to enhance the treatment of osteomyelitis

The objective in this study was to develop an osteoconductive, biodegradable and rifampicin releasing bone filling composite material for the treatment of osteomyelitis, a bacterial infection of bone that is very difficult and expensive to treat. The composite material will be used together with a ciprofloxacin releasing composite, because of the rapid development of resistant bacteria when rifampicin is used alone. Three composites were manufactured by twin-screw extrusion. The polymer matrix for the composites was poly(L-lactide-co-ε-caprolactone) 70/30 and all the composites contained 8 wt% (weight percent) of rifampicin antibiotic. The β-TCP contents of the composites were 0 wt%, 50 wt% and 60 wt%. The composites were sterilized by gamma irradiation before in vitro degradation and drug release tests. The hydrolytical degradation of the studied composites proceeded quickly and the molecular weight of the polymer component of the composites decreased rapidly. Rifampicin release occurred in four phases in which the high β-TCP content of the samples, polymer degradation and mass loss all played a role in determining the phases. The ceramic component was seen to have a positive effect on the drug release. The composite with 50 wt% of β-TCP showed the most promising rifampicin release profile and it also showed activity against a common osteomyelitis causing bacteria Pseudomonas aeruginosa. A clear inhibition zone was formed in 16 h incubation. Overall, the tested materials showed great potential to be developed into a bone filler material for the treatment of osteomyelitis or other bone related infections in combination with the ciprofloxacin releasing materials.

An in vitro study of composites of poly(L-lactide-co-ε-caprolactone), β-tricalcium phosphate and ciprofloxacin intended for local treatment of osteomyelitis

Osteomyelitis is a bacterial disease that can become chronic, and treatment often includes a surgical operation to remove infected bone. The aim of this study was to develop and investigate in vitro bone filling composite materials that release ciprofloxacin to kill any remaining bacteria and contain bioceramic to help the bone to heal. Three composites of poly(L-lactide-co-ε-caprolactone), β-tricalcium phosphate and ciprofloxacin were compounded using twin-screw extrusion and sterilized by gamma irradiation. Drug release and degradation of the composites were investigated in vitro for 52 weeks. The composite with 50 wt% of β-TCP had the most promising ciprofloxacin release profile. The ceramic component accelerated the drug release that occurred in three phases obeying first-order kinetics. Inhibition zone testing using bioluminescence showed that the released ciprofloxacin had effect in eradicating a common osteomyelitis causing bacteria Pseudomonas aeruginosa. During the in vitro degradation test series, molar weight of the polymer matrix of the composites decreased rapidly. Additionally, ¹H-NMR analysis showed that the polymer had blocky structure and the comonomer ratio changed during hydrolysis. The tested composites showed great potential to be developed into bone filler materials for the treatment of osteomyelitis or other bone related infections.

Bioluminescence-based identification of nisin producers - a rapid and simple screening method for nisinogenic bacteria in food samples

We present a simple and rapid method for screening nisin producers that directly identifies nisinogenic bacteria by induction of bioluminescence within the Lactococcus lactis NZ9800lux biosensor strain (Immonen and Karp, 2007, Biosensors and Bioelectronics 22, 1982-7). An overlay of putative nisinogenic colonies with the biosensor strain gives identification results within 1h. Functionality and specificity of the method were verified by screening nisin producers among 144 raw milk colonies and a panel of 91 lactococcal strains. Studies performed on strains and colonies that did not induce bioluminescence but inhibited growth of the biosensor demonstrated that only nisinogenic bacteria can cause induction. Bacteria known to produce bacteriocins other than nisin failed to induce bioluminescence, further verifying the specificity of the assay. We discovered a non-inducing but inhibitory lactococcal strain harboring a modified nisin Z gene, and demonstrated that the source of the inhibitory action is not a non-inducing variant of nisin, but a bacteriocin of lower molecular weight. The concentration of nisin producers in a raw milk sample was 1.3 × 10(2)CFU/ml. We identified from raw milk a total of seven nisin Z producing L. lactis subsp. lactis colonies, which were shown by genetic fingerprinting to belong to three different groups. Among the panel of 91 lactococci, four strains were nisin A producers, and one strain harbored the modified nisin Z gene. The method presented here is robust, cost-effective and simple to perform, and avoids the pitfalls of traditional screening methods by directly specifying the identity of the inhibitory substance.

Monitoring alkane degradation by single BioBrick integration to an optimal cellular framework

Synthetic biology enables rewiring and reconstruction of desirable biochemical routes using well-characterized BioBricks. One goal is to optimize these biological systems in terms of robustness, functionality, and simplicity. Thus, in addition to optimizing the molecular level of the metabolic network, choosing an optimal "chassis" can have a great significance in the constructed system. As an example, this study presents a simplified system for monitoring and studying long-chain n-alkane degradation in Acinetobacter baylyi ADP1 online, provided by a single BioBrick insertion, bacterial luciferase luxAB. The system exploits the natural alkane degradation machinery of ADP1 and a sensitive response of bacterial luciferase to a specific intermediate, providing important aspects to natural alkane degradation kinetics. The study suggests the monitoring system to be applicable in the field of environmental biotechnology and emphasizes the utility of ADP1 as a host in both model systems and applications.

Real-time monitoring of intracellular wax ester metabolism

BACKGROUND

Wax esters are industrially relevant molecules exploited in several applications of oleochemistry and food industry. At the moment, the production processes mostly rely on chemical synthesis from rather expensive starting materials, and therefore solutions are sought from biotechnology. Bacterial wax esters are attractive alternatives, and especially the wax ester metabolism of Acinetobacter sp. has been extensively studied. However, the lack of suitable tools for rapid and simple monitoring of wax ester metabolism in vivo has partly restricted the screening and analyses of potential hosts and optimal conditions.

RESULTS

Based on sensitive and specific detection of intracellular long-chain aldehydes, specific intermediates of wax ester synthesis, bacterial luciferase (LuxAB) was exploited in studying the wax ester metabolism in Acinetobacter baylyi ADP1. Luminescence was detected in the cultivation of the strain producing wax esters, and the changes in signal levels could be linked to corresponding cell growth and wax ester synthesis phases.

CONCLUSIONS

The monitoring system showed correlation between wax ester synthesis pattern and luminescent signal. The system shows potential for real-time screening purposes and studies on bacterial wax esters, revealing new aspects to dynamics and role of wax ester metabolism in bacteria.

Biohydrogen production in alkalithermophilic conditions: Thermobrachium celere as a case study

In the present work the hydrogenesis in the anaerobic alkalithermophilic bacterium Thermobrachium celere was studied. The impact of several factors on hydrogen production during glucose fermentation was investigated in batch conditions. The optimal hydrogen production occurred at pH (67 °C) 8.2 with phosphate buffer concentration of 50 mM. Hydrogen yield reached the highest value of 3.36 mol H2/mol glucose when the partial pressure in the gas headspace was reduced. Supplementation of nitrogen sources and iron affected hydrogen production. Under optimized conditions, the maximum H2 accumulation and H2 production rate were estimated to be respectively 124.3 mmol H2/l culture and 20.7 mmol H2/l/h. Considering the efficient and rapid hydrogen evolution, and the ability to grow in extreme environments, T. celere might be a good candidate for biohydrogen production in open (non-sterile) bioprocess system.

Improved triacylglycerol production in Acinetobacter baylyi ADP1 by metabolic engineering

Background

Triacylglycerols are used in various purposes including food applications, cosmetics, oleochemicals and biofuels. Currently the main sources for triacylglycerol are vegetable oils, and microbial triacylglycerol has been suggested as an alternative for these. Due to the low production rates and yields of microbial processes, the role of metabolic engineering has become more significant. As a robust model organism for genetic and metabolic studies, and for the natural capability to produce triacylglycerol, Acinetobacter baylyi ADP1 serves as an excellent organism for modelling the effects of metabolic engineering for energy molecule biosynthesis.

Results

Beneficial gene deletions regarding triacylglycerol production were screened by computational means exploiting the metabolic model of ADP1. Four deletions, acr1, poxB, dgkA, and a triacylglycerol lipase were chosen to be studied experimentally both separately and concurrently by constructing a knock-out strain (MT) with three of the deletions. Improvements in triacylglycerol production were observed: the strain MT produced 5.6 fold more triacylglycerol (mg/g cell dry weight) compared to the wild type strain, and the proportion of triacylglycerol in total lipids was increased by 8-fold.

Conclusions

In silico predictions of beneficial gene deletions were verified experimentally. The chosen single and multiple gene deletions affected beneficially the natural triacylglycerol metabolism of A. baylyi ADP1. This study demonstrates the importance of single gene deletions in triacylglycerol metabolism, and proposes Acinetobacter sp. ADP1 as a model system for bioenergetic studies regarding metabolic engineering.

Alkalizing reactions streamline cellular metabolism in acidogenic microorganisms

An understanding of the integrated relationships among the principal cellular functions that govern the bioenergetic reactions of an organism is necessary to determine how cells remain viable and optimise their fitness in the environment. Urease is a complex enzyme that catalyzes the hydrolysis of urea to ammonia and carbonic acid. While the induction of urease activity by several microorganisms has been predominantly considered a stress-response that is initiated to generate a nitrogen source in response to a low environmental pH, here we demonstrate a new role of urease in the optimisation of cellular bioenergetics. We show that urea hydrolysis increases the catabolic efficiency of Streptococcus thermophilus, a lactic acid bacterium that is widely used in the industrial manufacture of dairy products. By modulating the intracellular pH and thereby increasing the activity of β-galactosidase, glycolytic enzymes and lactate dehydrogenase, urease increases the overall change in enthalpy generated by the bioenergetic reactions. A cooperative altruistic behaviour of urease-positive microorganisms on the urease-negative microorganisms within the same environment was also observed. The physiological role of a single enzymatic activity demonstrates a novel and unexpected view of the non-transcriptional regulatory mechanisms that govern the bioenergetics of a bacterial cell, highlighting a new role for cytosol-alkalizing biochemical pathways in acidogenic microorganisms.

A dairy bacterium displays in vitro probiotic properties for the pharyngeal mucosa by antagonizing group A streptococci and modulating the immune response

The probiotic approach represents an alternative strategy in the prevention and treatment of infectious diseases, not only at the intestinal level but also at other sites of the body where the microbiota plays a role in the maintenance of physiological homeostasis. In this context, we evaluated in vitro the potential abilities of probiotic and dairy bacteria in controlling Streptococcus pyogenes infections at the pharyngeal level. Initially, we analyzed bacterial adhesion to FaDu hypopharyngeal carcinoma cells and the ability to antagonize S. pyogenes on FaDu cell layers and HaCat keratinocytes. Due to its promising adhesive and antagonistic features, we studied the dairy strain Lactobacillus helveticus MIMLh5, also through in vitro immunological experiments. First, we performed quantification of several cytokines and measurement of NF-κB activation in FaDu cells. MIMLh5 efficiently reduced the induction of interleukin-6 (IL-6), IL-8, and tumor necrosis factor alpha (TNF-α), in a dose-dependent manner. After stimulation of cells with IL-1β, active NF-κB was still markedly lowered. Nevertheless, we observed an increased secretion of IL-6, gamma interferon (IFN-γ), and granulocyte-macrophage colony-stimulating factor (GM-CSF) under these conditions. These effects were associated with the ability of MIMLh5 to enhance the expression of the heat shock protein coding gene hsp70. In addition, MIMLh5 increased the GM-CSF/G-CSF ratio. This is compatible with a switch of the immune response toward a TH1 pathway, as supported by our observation that MIMLh5, once in contact with bone marrow-derived dendritic cells, triggered the secretion of TNF-α and IL-2. In conclusion, we propose MIMLh5 as a potential probiotic bacterium for the human pharynx, with promising antagonistic and immunomodulatory properties.

Hydrogen production from glycerol using halophilic fermentative bacteria

Glycerol-based hydrogen production by the halophilic bacteria Halanaerobium saccharolyticum subspecies saccharolyticum and senegalensis was studied as batch experiments. The main metabolites of glycerol fermentation of both strains were hydrogen, carbon dioxide, and acetate. Subspecies saccharolyticum also produced 1,3-propanediol (1,3-PD), butyrate, and ethanol. The highest hydrogen yields were achieved with 2.5g/l glycerol and 150g/l salt at pH 7.4 (subsp. saccharolyticum, yield 0.6mol/mol glycerol) and at pH 7.0 (subsp. senegalensis, yield 1.6mol/mol glycerol). The hydrogen yield of subsp. senegalensis has potential for practical applications after scale-up and bioprocess optimizations and metabolic engineering after genome-wide sequencing could be applied to improve the yield of subsp. saccharolyticum.

Oral bacteria as potential probiotics for the pharyngeal mucosa

The research described here was aimed at the selection of oral bacteria that displayed properties compatible with their potential use as probiotics for the pharyngeal mucosa. We included in the study 56 bacteria newly isolated from the pharynges of healthy donors, which were identified at the intraspecies level and characterized in vitro for their probiotic potential. The experiments led us to select two potential probiotic bacterial strains (Streptococcus salivarius RS1 and ST3) and to compare them with the prototype oral probiotic S. salivarius strain K12. All three strains efficiently bound to FaDu human epithelial pharyngeal cells and thereby antagonized Streptococcus pyogenes adhesion and growth. All were sensitive to a variety of antibiotics routinely used for the control of upper respiratory tract infections. Immunological in vitro testing on a FaDu layer revealed different responses to RS1, ST3, and K12. RS1 and ST3 modulated NF-kappaB activation and biased proinflammatory cytokines at baseline and after interleukin-1beta (IL-1beta) induction. In conclusion, we suggest that the selected commensal streptococci represent potential pharyngeal probiotic candidates. They could display a good degree of adaptation to the host and possess potential immunomodulatory and anti-inflammatory properties.

Implication of an outer surface lipoprotein in adhesion of Bifidobacterium bifidum to Caco-2 cells

We found that the human intestinal isolate Bifidobacterium bifidum MIMBb75 strongly adhered to Caco-2 cells. Proteinase K and lithium chloride treatments showed that proteins play a key role in MIMBb75 adhesion to Caco-2 cells. By studying the cell wall-associated proteins, we identified a surface protein, which we labeled BopA. We purified the protein chromatographically and found that it functioned as an adhesion promoter on Caco-2 cells. In silico analysis of the gene coding for this protein and globomycin experiments showed that BopA is a cysteine-anchored lipoprotein expressed as a precursor polypeptide. A database search indicated that BopA appears to function biologically as an oligopeptide/tripeptide-solute-binding protein in the ABC transport system. We discovered a protein corresponding to BopA and its gene in eight other highly adherent B. bifidum strains. Finally, we found that B. bifidum MIMBb75 and BopA affected the production of interleukin-8 in Caco-2 epithelial cells. BopA is the first protein described to date to be directly involved in the adhesion of bifidobacteria to Caco-2 cells and to show immunomodulatory activity.

Molecular characterization of Bifidobacterium longum biovar longum NAL8 plasmids and construction of a novel replicon screening system

In this study, we performed molecular characterization and sequence analysis of three plasmids from the human intestinal isolate Bifidobacterium longum biovar longum NAL8 and developed a novel vector screening system. Plasmids pNAL8H (10 kb) and pNAL8M (4.9 kb) show close sequence similarity to and the same gene organization as the already characterized B. longum plasmids. The B. longum plasmid pNAC1 was identified as being most closely related to pNAL8L (3.5 kb). However, DNA sequence analysis suggested that direct repeat-rich sites could have promoted several recombination events to diversify the two plasmid molecules. We verified the likely rolling circle replication of plasmid pNAL8L and studied the phylogenetic relationship in all the Bifidobacterium plasmids fully sequenced to date based on in silico comparative sequence analysis of their replication proteins and iteron regions. Our transformation experiments confirmed that the ColE1 replication origin from high-copy-number pUC vectors could interfere with the replication apparatus of Bifidobacterium plasmids and give rise to false positive clones. As a result, we developed a system suitable for avoiding possible interference by other functional replication modules on the vector and for screening functional replicons from wild-type plasmids.

Intracellular redox equilibrium and growth phase affect the performance of luciferase-based biosensors

Light emission from the bacterial luciferase operon has been variously exploited during last two decades. The use of convenient inducible promoters has granted significant degrees of specificity to whole cell-based assays for high-throughput screening and environmental monitoring. Nevertheless, unexplained unspecific responses have been repeatedly reported. Here, we show that the impairment of the intracellular biochemical equilibrium interferes with the luminescence produced by Escherichia coli and Staphylococcus aureus strains carrying the lux operon under constitutive or inducible control. Compounds as trimethoprim and methotrexate, by indirectly inducing NADPH accumulation, enhance light emission. Conversely, molecules driving the cell toward an oxidized state, as dimethyl sulfoxide, inhibit luminescence. These findings fit into the accepted biochemical pathway for bioluminescence, where NADPH and reducing equivalents are necessary for the production of luciferase substrates, although they do not directly take part into the light-emitting reaction. Moreover, we investigated the influence of induction timing upon the bioluminescence response from inducible reporter systems and demonstrated a correlation between the emitted light and the growth phase at which induction is performed. Our results provide explanations for some unspecific responses recorded so far in whole cell-based luminescent biosensors and emphasize the intrinsic limitations of this kind of reporting system.

Bioluminescence-based bioassays for rapid detection of nisin in food

We have developed a method for determining ultralow amounts of nisin in food samples that is based on luminescent biosensor bacteria. Modified bacterial luciferase operon luxABCDE was placed under control of the nisin-inducible nisA promoter in plasmid pNZ8048, and the construct was transformed into Lactococcus lactis strains NZ9800 and NZ9000. The nisRK genes of these strains allow them to sense nisin and relay the signal to initiate transcription from nisA promoter. The resulting luminescence can be directly measured from living bacteria without the addition of exogenous substrates. Induction leads to detectable luminescence within ten minutes. Lyophilization of the biosensor cells produced viable and inducible sensor elements that can be utilized as freshly cultivated cells for rapid detection of nisin. The linear dose-response relationship perceived in the assay facilitates quantification of nisin in samples. The sensitivity of the nisin bioassay was 0.1 pg/ml in pure solution and 3 pg/ml in milk, exceeding the performance of all previously reported methods.

Staphylococcus aureus adheres to human intestinal mucus but can be displaced by certain lactic acid bacteria

There is increasing evidence that Staphylococcus aureus may colonize the intestinal tract, especially among hospitalized patients. As Staph. aureus has been found to be associated with certain gastrointestinal diseases, it has become important to study whether this bacterium can colonize the intestinal tract and if so, whether it is possible to prevent colonization. Adhesion is the first step in colonization; this study shows that Staph. aureus adheres to mucus from resected human intestinal tissue. Certain lactic acid bacteria (LAB), mainly commercial probiotics, were able to reduce adhesion and viability of adherent Staph. aureus. In displacement assays the amount of adherent Staph. aureus in human intestinal mucus was reduced 39-44% by Lactobacillus rhamnosus GG, Lactococcus lactis subsp. lactis and Propionibacterium freudenreichii subsp. shermanii. Moreover, adherent Lactobacillus reuteri, Lc. lactis and P. freudenreichii reduced viability of adherent Staph. aureus by 27-36%, depending on the strain, after 2 h incubation. This was probably due to the production of organic acids and hydrogen peroxide and possibly in the case of L. reuteri to the production of reuterin. This study shows for the first time that Staph. aureus can adhere to human intestinal mucus and adherent bacteria can be displaced and killed by certain LAB strains via in situ production of antimicrobial substances.

Whole Cell Strategies Based on lux Genes for High Throughput Applications Toward New Antimicrobials

The discovery/development of novel drug candidates has witnessed dramatic changes over the last two decades. Old methods to identify lead compounds are not suitable to screen wide libraries generated by combinatorial chemistry techniques. High throughput screening (HTS) has become irreplaceable and hundreds of different approaches have been described. Assays based on purified components are flanked by whole cell-based assays, in which reporter genes are used to monitor, directly or indirectly, the influence of a chemical over the metabolism of living cells. The most convenient and widely used reporters for real-time measurements are luciferases, light emitting enzymes from evolutionarily distant organisms. Autofluorescent proteins have been also extensively employed, but proved to be more suitable for end-point measurements, in situ applications - such as the localization of fusion proteins in specific subcellular compartments - or environmental studies on microbial populations. The trend toward miniaturization and the technical advances in detection and liquid handling systems will allow to reach an ultra high throughput screening (uHTS), with 100,000 of compounds routinely screened each day. Here we show how similar approaches may be applied also to the search for new and potent antimicrobial agents.

Bioluminescent yeast assays for detecting estrogenic and androgenic activity in different matrices

In this paper we describe the construction and use of a set of bioluminescent yeast strains for the detection of compounds that can affect androgen or estrogen receptor mediated hormonal signalling. The set includes Saccharomyces cerevisiae strains expressing human androgen receptor (AR), estrogen receptor alpha (ERalpha) or estrogen receptor beta (ERbeta), along with firefly luciferase controlled by a respective hormone responsive promoter. A constitutively luminescent strain was included in the set for determining the cytotoxicity of the sample. Yeast cells were incubated with pure chemicals or complex samples for 2.5 h, after which the signal could be detected from the cell-sample mixture after simply adding the D-luciferin substrate. The assays could be completed in one day and they required no cell lysis or centrifugation steps, which makes them suitable for high-throughput analysis of samples. Due to a short incubation time the assays are directly applicable to different sample matrices, requiring no pretreatment of the samples. The assays were used to assess the hormonal activity in moisturizing lotions as an example of a complex sample matrix known to contain endocrine disrupting chemicals. Six out of eight tested moisturisers showed high estrogenic activity, whereas no androgenic activity was observed in the samples.

A new recombinant cell-based bioluminescent assay for sensitive androgen-like compound detection

A public concern is continuously arising about the presence of natural and anthropogenic compounds which affect human health by modulating normal endocrine functions. These substances, defined as endocrine disrupting compounds (EDC) represent an heterogeneous class of molecules either steroidal or not, sharing the ability of interfering with the endocrine system via nuclear receptor signaling pathways. Therefore there is an urgent need for high throughput screening systems able to detect EDCs and evaluate their biological activity. However, little attention has been dedicated to the development of assays for androgen-like compounds. The present work describes the development and optimization of a new rapid and sensitive bioluminescent yeast-based bioassay for androgen-like compounds in a 96-well microplate format. The bioassay is based on recombinant Saccharomyces cerevisiae cells modified to express human androgen receptor (hAR) and containing the sequence androgen response element (ARE) which drives the expression of Photinus pyralis luciferase, used as reporter gene. A recombinant yeast strain constitutively expressing luciferase was used as external control to correct the light signal accordingly to cell viability and sample matrix aspecific effects. The bioassay responds to testosterone as reference androgen in a concentration-dependent manner from 0.05 to 1000 nM allowing an accurate and precise quantitative evaluation in aqueous environmental samples down to 10(-11)mol/L. Other known androgen-like compounds exhibit similar dose-response behavior, thus permitting the use of the bioassay for an overall detection of androgen-like effect in environmental samples.

Adhesion of bacteria to resected human colonic tissue: quantitative analysis of bacterial adhesion and viability

Adhesion to the intestinal mucosa is considered to be one of the main selection criteria of lactic acid bacteria for probiotic use. Adhesive probiotics are, for example, considered to provide better antagonism against pathogenic bacteria when compared to non-adhesive strains. Here a new model is described for studying adhesion and interaction of probiotic and pathogenic bacteria in the intestinal mucus in which the intestinal microbiota is present. The model is based on the use of human intestinal tissue, fluorescent-tagged bacteria and confocal laser scanning microscopy (CLSM) in adhesion measurements as well as human intestinal mucus and bioluminescent-tagged bacteria in viability measurements. Use of CLSM enabled, for the first time, real-time three-dimensional observations of live probiotic bacteria in their natural environment, the intestinal mucosa. When the real-time measurement of bacterial adhesion was combined with the real-time sensitive measurement of bacterial viability, it could be studied whether or not the adherent pathogens were alive. The model was used to study the interaction between Lactobacillus rhamnosus GG and Salmonella enterica serovar Typhimurium. We show that L. rhamnosus GG did not affect the adhesion or the viability of S. enterica serovar Typhimurium. Instead S. enterica serovar Typhimurium was shown to decrease the adhesion of L. rhamnosus GG in displacement assays. Moreover, the method is suitable for studies in which the interaction of two or more bacteria is examined in an environment in which other bacteria are present.

Quantification of streptavidin adsorption in microtitration wells

Streptavidin-coated microtitration plates have an important role as a solid phase in clinical diagnostics. We have designed techniques for evaluating quantitative and functional aspects of streptavidin adsorbed in microtitration wells. The theoretical monolayer adsorption capacity was modeled based on the molecular dimensions of the protein. Adsorbed streptavidin was quantified by direct labeling of protein with terbium chelate and with a sensitive bicinchoninic acid-based protein assay. A new small molecular weight (1037Da) reporter molecule, a europium-labeled biotin (Eu-biotin), was synthesized and used for monitoring adsorption and for determination of biotin-binding capacities of the streptavidin-coated wells. The theoretical monolayer adsorption of streptavidin yielded 6.20 pmol/cm(2) (370 ng) and consequently the theoretical adsorption capacity of a C12-format microtitration well (200 microl liquid, coated area 1.54 cm(2)) was 9.55 pmol/well (570 ng). Adsorption properties of streptavidin from two suppliers were tested, one of which yielded 350-380 ng/well while the other yielded over 500 ng/well. The biotin binding capacities were about 11 and 14 pmol/well, respectively. We managed to quantify surface-adsorbed streptavidin with sensitive fluorescence and protein measurement methods in the microtitration well. The new Eu-biotin reporter molecule enabled an exact and convenient determination of the biotin-binding capacities of streptavidin surfaces.

Measurement of bacterial adhesion—in vitro evaluation of different methods

The adhesion of bacteria to host tissue is the first step in pathogenesis. Similarly, bacterial adhesion to inanimate surfaces is the first step in formation of biofilms-a real problem in industrial processes and medical devices. Various agents capable of blocking the adhesion of bacteria to surfaces have been identified, such as probiotics, which are supposed to prevent the adhesion of pathogenic bacteria to the intestinal mucosa. Although measurement of bacterial adhesion is important itself, especially when agents used to prevent adhesion are developed, a relative small number of techniques can be used in the measurement of adhesion. These techniques are not well validated and there is lack of studies where those methods are compared to each other. Here we have compared different commonly used methods to measure adhesion of bacteria; radioactive labelling, fluorescence tagging, and staining of bacteria. The methods were used to measure the adhesion of Escherichia coli and Salmonella enterica serovar Typhimurium to intestinal mucus. Moreover, selected probiotic strains were used to study whether probiotics or the adhesion method used affected the results. As a result, we show that the best reproducibility and sensitivity were obtained using radioactive labelling. With other methods, the sensitivity was too low due to poorly adhering bacteria and low signal-to-background ratio.

Development of a Bioluminescence Resonance Energy-Transfer Assay for Estrogen-Like Compound in Vivo Monitoring

A new bioluminescence resonance energy transfer (BRET) homogeneous assay to evaluate the presence of estrogen-like compounds has been developed and optimized. The assay is based on the direct evaluation of estrogen alphareceptor (ERalpha) homodimerization as a result of estrogen-like compound binding. ERalpha monomer was genetically fused either to Renilla luciferase (Rluc) or to enhanced yellow fluorescent protein (EYFP). In the presence of estrogens, ERalpha dimerization brings Rluc and EYFP molecules close enough for an energy transfer. An in vitro BRET assay was first developed using purified fusion proteins (ERalpha-Rluc and ERalpha-EYFP) expressed in Escherichia coli to evaluate and optimize the analytical performances of the assay in the presence of 17-beta estradiol. The "in vivo" BRET quantitative assay was then developed by coexpressing the two fusion proteins in live HepG2 cells. The assay can be performed in 96-well microplate format with a 30-min incubation and allows detection with adequate accuracy and precision of as low as 1 nM of 17-beta estradiol. This new "in vivo" BRET assay allows evaluating the estrogen-like activity and synthetic xenoestrogens from biological and environmental samples.

Discarding multidrug resistance inducers, the possible role of a biosensing reporter in antimicrobial discovery

The aim of the present work was to determine whether the luminescence-based reporter plasmid pQacLux could be applied to drug discovery in order to discard compounds with defined properties. Non-pathogenic Staphylococcus aureus RN4220 cells bearing pQacLux were incubated with different concentrations of a disinfectant of common use in hospitals. The in vivo light emission response of the plasmid to the given stimuli was then quantified and compared to a negative control for the construction of dose-response curves. The selected disinfectant provided a convenient model for the activity of quaternary ammonium compounds. In spite of the use of a raw model solution, the system revealed high levels of sensitivity. According to the results obtained, pQacLux could be conveniently used in the first steps of drug development in order to discard all possible multidrug resistance inducers.

A cell-free biosensor for the detection of transcriptional inducers using firefly luciferase as a reporter

A cell-free biosensor for the detection of transcription induction by specific small-molecule ligands is presented. As model systems, tetracycline and mercury-inducible promoters were used containing firefly luciferase as reporter gene. Escherichia coli S30 extract was prepared and used for coupled transcription-translation reactions. By using purified Tet repressor and MerR regulatory proteins, we could study repressor-operator interactions for optimizing the relative concentrations of each component. Previously, detection of tetracycline and mercury using similar transcriptional regulation in whole living cells has been carried out. As compared to whole-cell biosensors, our results showed better sensitivity for the detection of tetracycline and the toxic effect of mercury was avoided in the cell-free system. Also, as the system omits cell cultivation and bacterial membranes as molecule passage inhibitors, it is possible to carry out assays in much shorter times and without the use of genetically modified organisms.

Rapid screening method for the detection of antimicrobial substances

Bioluminescence is phenomenon where living organisms produce light and this production is directly dependent on metabolic activity of the organism. Genes encoding enzymes, luciferases, responsible for light production can be cloned into indicator strains, thus allowing sensitive detection of antimicrobial activity. This study utilized bacterial luciferase genes cloned into Staphylococcus aureus, Escherichia coli and Salmonella enterica serovar Typhimurium indicator strains and showed that the detection of antimicrobial activity can be obtained already in 2 h without laborious plate counting and overnight incubation. Indicator strains used in the study harboured luxAB genes responsible of producing light as well as luxCDE genes for synthesis of long-chain fatty aldehyde as substrate for light production. As a consequence, no exogenous aldehyde addition was needed allowing stable light production. Furthermore, the method was used for the detection of antimicrobial activity from lactic acid bacteria after the effect of organic acids was eliminated.

Monitoring promoter activity in a single bacterial cell by using green and red fluorescent proteins

We investigated the possibility of monitoring promoter activity with flow cytometry by using green fluorescent protein (GFPmut2) and red fluorescent protein (drFP583) in a single bacterial cell. The drFP583 was used as an intrinsic marker of the bacterial cells, because it was expressed constantly in Escherichia coli MC1061 strain. The GFPmut2 expressed under the control of the Hg(2+) ion inducible mer promoter/operator, was used to study promoter activity. Over 75% of the cells were positive for red and green fluorescence in flow cytometric analysis. The average green fluorescence of the whole population increased from 6.7 to 1700 when the mercury concentration was increased from 0 to 1 x 10(-4) M, while the red fluorescence was unaffected by the mercury concentration. These results show that gfpmut2 and drFP583 could be expressed under different promoters in one bacterial cell and measured independently with a flow cytometer.