Two-colour fluorescence fluorimetric analysis for direct quantification of bacteria and its application in monitoring bacterial growth in cellulose degradation systems

Preparation of xylooligosaccharides from rice husks and their structural characterization, antioxidant activity, and probiotic properties

Rice husks are rich in xylan, which can be hydrolyzed by xylanase to form xylooligosaccharides (XOS). XOS are a functional oligosaccharide such as improving gut microbiota and antioxidant properties. In this study, the structure and functional characteristics of XOS were studied. The optimal xylanase hydrolysis conditions through response surface methodology (RSM) were: xylanase dosage of 3000 U/g, hydrolysis time of 3 h, hydrolysis temperature of 50 °C. Under this condition, the yield of XOS was 150.9 mg/g. The TG-DTG curve showed that XOS began to decompose at around 200 °C. When the concentration of XOS reached 1.0 g/L, the clearance rate of DPPH reached 65.76 %, and the scavenging rate of OH reached 62.10 %, while the clearance rate of ABTS free radicals reached 97.70 %, which was equivalent to the clearance rate of VC. XOS had a proliferative effect on four probiotics: Lactobacillus plantarum, Lactobacillus brucelli, Lactobacillus acidophilus, and Lactobacillus rhamnosus. However, the further experiments are needed to explore the improvement effect of XOS on human gut microbiota, laying a foundation for the effective utilization of XOS. XOS have a wide range of sources, low price, and broad development prospects. The reasonable utilization of XOS can bring greater economic benefits.

Porphyrin-BODIPY Dyad: Enhancing Photodynamic Inactivation via Antenna Effect

A porphyrin-BODIPY dyad (P-BDP) was obtained through covalent bonding, featuring a two-segment design comprising a light-harvesting antenna system connected to an energy acceptor unit. The absorption spectrum of P-BDP resulted from an overlap of the individual spectra of its constituent parts, with the fluorescence emission of the BODIPY unit experiencing significant quenching (96 %) due to the presence of the porphyrin unit. Spectroscopic, computational, and redox investigations revealed a competition between photoinduced energy and electron transfer processes. The dyad demonstrated the capability to sensitize both singlet molecular oxygen and superoxide radical anions. Additionally, P-BDP effectively induced the photooxidation of L-tryptophan. In suspensions of Staphylococcus aureus cells, the dyad led to a reduction of over 3.5 log (99.99 %) in cell survival following 30 min of irradiation with green light. Photodynamic inactivation caused by P-BDP was also extended to the individual bacterium level, focusing on bacterial cells adhered to a surface. This dyad successfully achieved the total elimination of the bacteria upon 20 min of irradiation. Therefore, P-BDP presents an interesting photosensitizing structure that takes advantage of the light-harvesting antenna properties of the BODIPY unit combined with porphyrin, offering potential to enhance photoinactivation of bacteria.

A novel nanoparticle-based fluorescent sandwich immunoassay for specific detection of Salmonella Typhimurium

The diseases caused by foodborne pathogens have a serious impact on human health and social stability. Conventional detection methods can involve long assay times and complex pretreatment steps, making them unsuitable for rapid, large-scale analysis of food samples. We constructed a novel nano-fluorescence sandwich immunosorbent immunoassay (nano-FSIA) to rapidly detect Salmonella Typhimurium in food, based on strong covalent binding between streptavidin and biotin. We used antibodies coupled to large particle-size fluorescent microspheres as fluorescent probes for direct quantitative analysis of S. typhimurium in milk. The optimized parameters were determined, and specificity and sensitivity were validated in phosphate-buffered saline (PBS) and milk. The results demonstrated a wide dynamic detection range for S. typhimurium (103-108 colony forming units [CFU]/mL), with the limit of detection in PBS and milk at 234 and 346 CFU/mL, respectively. The results of nano-FSIA were consistent with those of plate counts and enzyme-linked immunosorbent assays, providing an effective and promising single-bacterium counting method for the rapid detection of Salmonella.

Enhancement of liposomal properties of thyme essential oil using lysozyme modification: Physicochemical, storage, and antibacterial properties

Thyme essential oil (TEO) is a natural food antimicrobial agent derived of spice, but suffers from volatility and poor water solubility, which problem can be effectively solved by the encapsulation of liposomes. On this basis, a safe and common natural antibacterial protein, LYZ was used to modify the TEO liposomes (TEO-lips) for gaining better properties. 2.5 mg/mL TEO and 0.05 % LYZ/S100 mass ratio were the best formula for the preparation of LYZ-TEO-lips. After LYZ modification, the particle size and PDI increased, and the zeta potential decreased slightly. The modification of LYZ not only improves the thermal stability of TEO-Lips, weakens the influence of acid and salt ions on liposomes, but also improves the antibacterial properties of TEO-Lips. In brief, LYZ has the potential to improve the overall properties of liposomes and can provide a reference for the development of antimicrobial liposomes.

Combination of direct boiling and glass beads increases the purity and accuracy of bacterial DNA extraction

Extraction of DNA is a key step in molecular biology experiments and important for counting tiny microbial individuals. Direct boiling and mechanical cell lysis like glass beads are two independent physical extraction methods, thus crossing the barriers of thresholds of magnitude in popular reagent kits or traditional spread plate method when non-equilibrium phenomenon is ongoing. The two approaches above were combined to generate a new one. In three typical microbial species, direct boiling with glass beads significantly increased the purity of DNA solution compared with some other methods (p < 0.05). The qPCR results of them were closer to direct microscopy counting than some other methods. Therefore, it provides a new choice in extracting bacterial DNA for specific circumstances.

An optimized workflow to measure bacterial predation in microplates

The predatory bacterium Bdellovibrio bacteriovorus invades and proliferates inside other bacteria by non-binary division. Here we describe a fluorescence-based technique for the immediate evaluation of predator density independently of plaque formation, an optimized setup to monitor predation in microplates, and the CuRveR package to quantify both prey killing and predator proliferation dynamics. This protocol allows to assess the impact of mutations or chemicals on predation. CuRveR also constitutes a user-friendly tool to analyze growth or decay data unrelated to predation.

For complete details on the use and execution of this profile, please refer to Kaljević et al., 2021.

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A protocol for routine culturing of Bdellovibrio bacteriovorus predatory bacteria

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A quick fluorescence-based technique to obtain predator cells numbers

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An automated assay of prey killing and predator proliferation in microplates

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The CuRveR package to extract prey decay and predator growth parameters

Ultra-Rapid Drug Susceptibility Testing for Klebsiella pneumoniae Clinical Isolates in 60 Min by SYBR Green I/Propidium Iodide Viability Assay

Background

We aimed to optimize and validate the drug susceptibility test (DST) assay by SYBR Green I/PI (SG-PI) method using a panel of 89 Klebsiella pneumoniae clinical isolates in comparison with the conventional DST method to three most important antibiotics used for treatment of this bacterial infection, including imipenem, cefmetazole, and gentamicin.

Methods

By staining with SYBR Green I and PI dyes, green fluorescence and red fluorescence, which linearly correlated with the percentages of live and dead or membrane damaged cells, respectively, were used to produce two standard curves to calculate the relative cell membrane impermeable rates for each log and stationary phase cultures. Stationary phase K. pneumoniae cells were used in imipenem and cefmetazole SG-PI DST assay whereas log phase cells were used in the gentamicin assay. The conventional broth microdilution method was used as a gold standard for DST for comparison.

Results

Data showed that after antibiotic treatment for 30–60 min, the antibiotic-resistant K. pneumoniae strains had significantly higher numbers of surviving cells than the susceptible strains at different concentrations of imipenem, cefmetazole, and gentamicin, where the average relative membrane impermeable rates were 88.5, 92.5, and 103.8% for resistant clinical strains, respectively, and 9.1, 49.3, and 71.5% for susceptible strains, respectively. Overall, the total concordances between the ultra-rapid SG-PI method and conventional minimal inhibitory concentration assay in diagnosing imipenem, cefmetazole and gentamicin resistance were high and were 96.6% (86/89), 95.4% (83/87), and 95.5% (85/89), respectively.

Conclusion

We demonstrate that our novel SG-PI assay can accurately and stably detect resistance to different antibiotics in clinical isolates of K. pneumoniae in an ultra-fast manner in 60–90 min.

Rapid Determination of Antibiotic Resistance in Klebsiella pneumoniae by a Novel Antibiotic Susceptibility Testing Method Using SYBR Green I and Propidium Iodide Double Staining

Due to the broad-spectrum antibiotic usage and empirical treatments, the pathogenic bacterium, Klebsiella pneumoniae, has shown extremely high detection rates at hospitals with an increasing antibiotic resistance. Therefore, rapid detection of the antibiotic resistance is urgently required and essential for effective treatments. In this study, we evaluated the performance of a newly developed method for ultra-rapid detection of antibiotic resistance in 30–60 min in K. pneumoniae by using the SYBR Green I and propidium iodide (PI) staining. A total of 100 clinical isolates were tested for antibiotic resistance using four different antibiotics (ceftriaxone, cefepime, meropenem, and ciprofloxacin). The results showed that the SYBR Green I/PI rapid antibiotic susceptibility test (AST) could reliably detect antibiotic resistance to the four drugs in 60 min, and the results were highly concordant with the conventional AST (i.e., Kirby-Bauer method and broth microdilution method) for detection of ceftriaxone, cefepime, meropenem, and ciprofloxacin resistance with a high accuracy of 99, 96, 96, and 93%, respectively. Therefore, the rapid AST established in our study helps to enable targeted therapy to save lives and reduce the empirical use of antibiotics and ultimately the health and economic burdens of antibiotic resistance.

Magnetic Nanoplatforms for in Situ Modification of Macromolecules: Synthesis, Characterization, and Photoinactivating Power of Cationic Nanoiman-Porphyrin Conjugates

A nanoplatform concept was developed to synthesize accessible photoactive magnetic nanoparticles (MNPs) of Fe₃O₄ coated with silica. This approach was based on the covalent binding of 5,10,15,20-tetrakis(pentafluorophenyl)porphyrin (TPPF₂₀) to aminopropyl-grafted MNPs by nucleophilic aromatic substitution reaction (S_NAr) to obtain conjugate MNP-P1. After in situ modification, the remaining pentafluorophenyl groups of TPPF₂₀ attached to MNPs were substituted by dimethylaminoethoxy groups to form MNP-P2. The basic amine group of these conjugates can be protonated in aqueous media. In addition, MNP-P1 and MNP-P2 were intrinsically charged to produce cationic conjugates MNP⁺-P1 and MNP⁺-P2⁺ by methylation. All of them were easily purified by magnetic decantation in high yields. The average size of the MNPs was ∼15 nm, and the main difference between these conjugates was the greater coating with positive charges of MNP⁺-P2⁺, as shown by the zeta potential values. Absorption spectra exhibited the Soret and Q bands characteristic of TPPF₂₀ linked to MNPs. Furthermore, these conjugates showed red fluorescence emission of porphyrin with quantum yields of 0.011-0.036. The photodynamic effect sensitized by the conjugates indicated the efficient formation of singlet molecular oxygen in different media, reaching quantum yield values of 0.17-0.34 in N,N-dimethylformamide. The photodynamic activity of the conjugates was evaluated to inactivate the Gram-positive bacteria Staphylococcus aureus, the Gram-negative bacteria Escherichia coli, and the yeast Candida albicans. The modified cationic MNP⁺-P2⁺ was the most effective conjugate for photodynamic inactivation (PDI) of microorganisms. Binding of this conjugate to bacteria and photoinactivation capability was checked by means of fluorescence microscopy. Also, sustainable use by recycling was determined after three PDI treatments. Therefore, this methodology is a suitable scaffold for the in situ modification of conjugates, and in particular, MNP⁺-P2⁺ represents a useful photodynamic active material to eradicate microorganisms.

Determination of live and dead Komagataeibacter xylinus cells and first attempt at precise control of inoculation in nanocellulose production

The timely enumeration of cells of nanocellulose-producing bacteria is challenging due to their unique growth properties. To better understand the metabolism of the bacteria and better control the concentration of living cells during cultivation, a prompt cell counting technology is crucial and urgently required. In this work, two fluorescent dyes, the asymmetrical anthocyanidin dye SYBR Green I (SG) and propidium iodide (PI), were first combined for Komagataeibacter xylinus species to determine live/dead bacterial cells quantitatively and promptly. The number of live and dead K. xylinus cells determined using an epifluorescence microscope corresponded well to the results obtained using a fluorescence microplate reader. The R² values were 0.9986 and 0.9920, respectively, and were similar to those obtained with the LIVE/DEAD^® BacLight^TM commercial kit. SG/PI double-staining showed proper efficiency in distinguishing live/dead cells for the K. xylinus strain (R²  = 0.9898). The technology was applied to standardize four different K. xylinus strains, and the initial cell concentration of the strains was precisely controlled (no significant difference among the strains, P> 0.05). The cellulose yield per live cell was calculated, and significant differences (P < 0.05) were found among the four strains in the following order: DHU-ATCC-1> DHU-ZCY-1> DHU-ZGD-1> ATCC 23770. The study shows (i) the application of the SG/PI staining to standardizing inocula for bacterial cellulose production so that a more accurate comparison can be made between different strains, and (ii) the lower cost of using SG rather than the SYTO 9 of the commercially available LIVE/DEAD^® BacLight^TM kit.

A microfluidic biosensor for online and sensitive detection of Salmonella typhimurium using fluorescence labeling and smartphone video processing

Early screening of foodborne pathogens is a key to ensure food safety. In this study, we developed a microfluidic biosensor for online and sensitive detection of Salmonella based on immunomagnetic separation, fluorescence labeling and smartphone video processing. First, the immune magnetic nanoparticles were used to specifically separate and efficiently concentrate the target bacteria and the magnetic bacteria were formed. Then, the magnetic bacteria were labeled with the immune fluorescent microspheres and the fluorescent bacteria were formed. Finally, the fluorescent bacteria were continuously injected into the microfluidic chip on the smartphone-based fluorescent microscopic system, and the fluorescent spots were online counted using the smartphone App based on inter-frame difference algorithm to obtain the amount of the target bacteria. Under the optimal conditions, this proposed biosensor was able to quantitatively detect Salmonella typhimurium ranging from 1.4 × 10² to 1.4 × 10⁶ CFU/mL, and its lower detection limit was 58 CFU/mL. This biosensor could be extended for detection of multiple foodborne pathogens using different fluorescent materials.

Near real-time enumeration of live and dead bacteria using a fibre-based spectroscopic device

A rapid, cost-effective and easy method that allows on-site determination of the concentration of live and dead bacterial cells using a fibre-based spectroscopic device (the optrode system) is proposed and demonstrated. Identification of live and dead bacteria was achieved by using the commercially available dyes SYTO 9 and propidium iodide, and fluorescence spectra were measured by the optrode. Three spectral processing methods were evaluated for their effectiveness in predicting the original bacterial concentration in the samples: principal components regression (PCR), partial least squares regression (PLSR) and support vector regression (SVR). Without any sample pre-concentration, PCR achieved the most reliable results. It was able to quantify live bacteria from 108 down to 106.2 bacteria/mL and showed the potential to detect as low as 105.7 bacteria/mL. Meanwhile, enumeration of dead bacteria using PCR was achieved between 108 and 107 bacteria/mL. The general procedures described in this article can be applied or modified for the enumeration of bacteria within populations stained with fluorescent dyes. The optrode is a promising device for the enumeration of live and dead bacterial populations particularly where rapid, on-site measurement and analysis is required.

Bead-Based Flow-Cytometric Cell Counting of Live and Dead Bacteria

Flow cytometry (FCM) is based on the detection of scattered light and fluorescence to identify cells with characteristics of interest. Many flow cytometers cannot precisely control the flow through its interrogation point and hence the volume and concentration of the sample cannot be immediately obtained. Here we describe the optimization and evaluation of a bead-based method for absolute cell counting applicable to basic flow cytometers without specialized counting features. Prior to the application of this method to an unknown concentration of a species of bacteria, a calibration experiment should be completed to characterize limits of detection and range of linearity with respect to the plate count method. To demonstrate the calibration process, mixtures of Escherichia coli or Staphylococcus aureus with proportions of live and dead cells ranging from 0% to 100% were prepared. These samples were stained using nucleic acid-binding dyes, and 6 μm reference beads were added (LIVE/DEAD^® BacLight kit). The calibration samples were analyzed using bead-based FCM as well as the agar plate count method, and the results from both methods were compared.

Simulated wastewater reduced Klebsiella michiganensis strain LH-2 viability and corresponding antibiotic resistance gene abundance in bio-electrochemical reactors

A previous study revealed that the electrolytic stimulation process in bio-electrochemical reactors (BER) can accelerate growth of sulfadiazine (SDZ) antibiotic resistant bacteria (ARB) in nutrient broth medium. However, the influence of different medium nutrient richness on the fate of ARB and the relative abundance of their corresponding antibiotic resistance genes (ARGs) in this process is unknown. Specifically, it is not clear if the fate of ARB in minimal nutrition simulated wastewater is the same as in nutrient broth under electrolytic stimulation. Therefore, in this study, nutrient broth medium and the simulated wastewater were compared to identify differences in the relative abundance of Klebsiella michiganensis LH-2 ARGs in response to the electrolytic stimulation process, as well as the fate of the strain in simulated wastewater. Lower biomass, specific growth rates and viable bacterial counts were obtained in response to the application of increasing current to simulated wastewater medium. Furthermore, the percentage of ARB lethality, which was reflected by flow cytometry analysis, increased with current in the medium. A significant positive correlation of sul genes and intI gene relative abundance versus current was also observed in nutrient broth. However, a significant negative correlation was observed in simulated wastewater because of the higher metabolic burden, which may have led to decreased ARB viability. Further investigation showed that the decrease in ARGs abundance was responsible for decreased strain tolerance to SDZ in simulated wastewater. These results reveal that minimal nutrition simulated wastewater may reduce ARB and ARGs propagation in BER.

Effects ofdirect current on Klebsiella spp. viability and corresponding resistance gene expression in simulative bio-electrochemical reactors

The fate of antibiotic-resistant bacteria (ARB) and associated antibiotic-resistant gene (ARG) expression under electrolytic stimulation in bio-electrochemical reactors (BERs) was unknown. In this study, sulfadiazine resistant bacteria (Klebsiella spp.), which were isolated from a BER, were subjected to constant direct current (DC) stimulation in a simulated BER. With an increase of the current from 7 to 28 mA, it was found that lactic dehydrogenase (LDH) showed a 1.03-, 1.21-, 1.34-, and 1.46-fold value compared with the control at 48 h, indicating that the cell membrane permeability had increased. Since the adenosine triphosphate (ATP) concentration increased with the current, the specific growth rate of Klebsiella spp. increased (R = 0.98). The viable count of Klebsiella spp. reached a maximum at 19 mA and then decreased. The percentage of ARB lethality, which was reflected by flow cytometry analysis, increased from 18% (7 mA) to 37.8% (28 mA) at 48 h. Reactive oxygen species (ROS) produced from the electrolysis of water were greater with the increasing current (R = 0.94), which may be responsible for the high lethality rate of Klebsiella spp.. Scanning electronic microscope results showed that electrolytic stimulation changed the cell surface morphology with some cell disruption. An upregulation of sulII and int1 expression was observed. A significant correlation between int1 and the current (R = 0.97) were observed. Taken together, BERs possess potential risks in accelerating ARB multiplication and promoting ARG expression.

Data for discriminating dead/live bacteria in homogenous cell suspensions and the effect of insoluble substrates on turbidimetric measurements

Estimation of bacterial growth by rapid traditional methods such as spectrophometric measurements at 600 nm (OD600) is not applicable for cultures containing insoluble particles in the growth media. Colony counts are the only suitable alternative but these are laborious and not high-throughput. The data presented in this article is related to the research article entitled “Two-colour fluorescence fluorimetric analysis for direct quantification of bacteria and its application in monitoring bacterial growth in cellulose degradation systems” (Duedu and French, 2017) [1]. This data article presents original primary data describing the discrimination of dead/live bacteria in homogenous cell suspensions and how the presence of insoluble substrates affect the turbidity of the suspensions.