Applications and challenges for single-bacteria analysis by flow cytometry

Flow cytometry (FCM) is a powerful technique for single-bacteria analysis via simultaneous light-scattering and fluorescence measurements. By offering high-throughput, quantitative, and multiparameter analysis at the single-cell level, FCM has gained an increased popularity in microbiological research, food safety monitoring, water quality control, and clinical diagnosis. Here we will review the recent applications of flow cytometry in areas such as (1) total bacterial cell count, (2) bacterial viability analysis, (3) specific bacterial detection and identification, (4) characterization of physiological changes under environmental perturbations, and (5) biological function studies. Nevertheless, despite these widespread applications, challenges still remain for the detection of small sizes of bacteria and biochemical features that cannot be brightly stained via fluorescence. Recent improvement in FCM instrumentation will be discussed, and particularly the development of high sensitivity flow cytometry for advanced analysis of single bacterial cells will be highlighted.     

Biosensors for the analysis of food- and waterborne pathogens and their toxins

Biosensors are devices which combine a biochemical recognition element with a physical transducer. There are various types of biosensors, including electrochemical, acoustical, and optical sensors. Biosensors are used for medical applications and for environmental testing. Although biosensors are not commonly used for food microbial analysis, they have great potential for the detection of microbial pathogens and their toxins in food. They enable fast or real-time detection, portability, and multipathogen detection for both field and laboratory analysis. Several applications have been developed for microbial analysis of food pathogens, including E. coli O157:H7, Staphylococcus aureus, Salmonella, and Listeria monocytogenes, as well as various microbial toxins such as staphylococcal enterotoxins and mycotoxins. Biosensors have several potential advantages over other methods of analysis, including sensitivity in the range of ng/mL for microbial toxins and <100 colony-forming units/mL for bacteria. Fast or real-time detection can provide almost immediate interactive information about the sample tested, enabling users to take corrective measures before consumption or further contamination can occur. Miniaturization of biosensors enables biosensor integration into various food production equipment and machinery. Potential uses of biosensors for food microbiology include online process microbial monitoring to provide real-time information in food production and analysis of microbial pathogens and their toxins in finished food. Biosensors can also be integrated into Hazard Analysis and Critical Control Point programs, enabling critical microbial analysis of the entire food manufacturing process. In this review, the main biosensor approaches, technologies, instrumentation, and applications for food microbial analysis are described.     

Rapid detection of single cell bacteria as a novel approach in food microbiology

Solid-phase cytometry (SPC) is a novel technique that allows rapid detection of bacteria at the single cell level, without the need for a growth phase. After filtration of the sample, the retained microorganisms are fluorescently labeled on the membrane filter and automatically counted by a laser scanning device. Each fluorescent spot can be visually inspected with an epifluorescence microscope connected to the ChemScan by a computer-driven moving stage. Depending on the fluorogenic labels used, information on the identity and the physiological status of the microorganisms can be obtained within a few hours. Although SPC was originally recommended for the determination of the total viable microbial count in water and other liquid samples, it may also be a promising technique for the detection and enumeration of bacteria in food samples, provided they can be isolated from the unfilterable matrix. The short detection time inherent in this approach is a considerable advantage over conventional plate counting, especially for slow-growing microorganisms. The basic principles of SPC are discussed as well as its potential for the detection of Mycobacterium paratuberculosis, a model example of a slow-growing bacterium in milk.     

High-performance liquid chromatography of microbial acid metabolites

The use of high-performance liquid chromatography with a cation-exchange column and effluent monitoring at 210 nm has been evaluated for the profiling of selected microbial metabolites including aliphatic, dicarboxylic, and phenolic acids, as an adjunct to the identification of selected bacteria, detection of bacterial metabolites in foods, and the monitoring of industrial microbial fermentations. Advantages of the technique include the simultaneous profiling of different classes of organic acids without derivatization. Most applications require only qualitative or semi-quantitative data. For others, data are given on the day-to-day reproducibility for several acids.     

Coupling of enzymatic and immunoassay steps to detect E. coli: a new, highly sensitive tandem technique for the analysis of low levels of bacteria

A tandem technique for the detection of very low levels E. coli within about 2 h is demonstrated. The technique couples the widely employed microbial enzymatic detection methods with an immunoassay step. The bacterial marker enzyme, E. coli β-D-galactosidase, was used in conjunction with synthetic enzyme substrates to produce products that could be measured with a highly sensitive enzyme-labelled immunosorbent assay (ELISA). The commercially available 4-methylumbelliferyl-β-D-galactoside and a newly prepared substrate, 4-methylcoumarin-3-propionate-7-O-β-D-galactoside, were used with an ELISA for 7-hydroxy-4-methylcoumarin to demonstrate the detection of low levels of E. coli. The 2 h test indicates that a few viable bacteria cells could be detected by the tandem procedure. The end point of the test is an ELISA with colorimetric measurement step. The novel approach retains the essential features of the microbial enzymatic detection procedures and provides a highly sensitive detection system that can be used for rapid screening or quantification of viable microbial cells in water samples. The tandem test is generic for commonly employed glycosidases and other marker enzymes for which 4-methylumbillerone substrates are available.     

Immunomagnetic separation using carbonyl iron powder and flow cytometry for rapid detection of <Emphasis Type="Italic">Flavobacterium psychrophilum</Emphasis>

Bacterial cold water disease, caused by Flavobacterium psychrophilum, is a serious problem in the aquaculture industry worldwide. Several methods to prevent and treat cold water disease have been studied. Although detection at the early stage of F. psychrophilum infection is very important for the prevention and treatment of cold water disease, an effective detection method has not yet been developed. The use of flow cytometry (FCM) for the rapid determination of bacterial cell numbers with high sensitivity is beginning to attract attention. Immunomagnetic separation (IMS) has also been used to detect F. psychrophilum. The purpose of the present study was to develop a method to quickly determine the number of bacterial cells by combining the FCM and IMS methods. Because samples can be more effectively concentrated using smaller magnetic beads and stronger magnetism, we used carbonyl iron powder as the magnetic beads for the IMS. The detection level of F. psychrophilum using FCM combined with IMS was 5 orders lower than that using FCM without IMS. The values determined using FCM combined with IMS strongly correlated with those obtained using the colony-counting method, in the range of approximately 10–10⁸ colony-forming units per milliliter. One FCM assay could be completed within 60 s and the total assay time, including sample preparation, was less than 2 h. The combined method of FCM with IMS developed in this study can be used reliably for the rapid detection of F. psychrophilum.     

<Emphasis Type="Italic">Gluconobacter</Emphasis> sp. cells for manufacturing of effective electrochemical biosensors and biofuel cells

Gluconobacter oxydans bacteria exhibit a unique metabolism for quick and incomplete oxidation of a wide range of different compounds (aldoses, ketoses, mono- and poly-alcohols, etc.). Such biotransformation efficiency with simple biomass production led to the industrial applications of these bacteria in the production of several important commodities. Their respiratory activity can also be successfully studied and used in the field of bioelectrochemistry. The main aim of this review is to present various strategies to improve selectivity of assays using intact/treated cells of G. oxydans, to introduce the application of G. oxydans-based biosensors in selective monitoring of analytes during biotransformation processes and to provide information about utilizable sugars in fermentation media or in biological oxygen demand value determination. The final part of the review describes potential application of G. oxydans cells in the generation of electricity from complex fuels within microbial fuel cells by advanced direct electron transfer route between bacterial cells and electrodes.     

Probiotics—Interactions with Bile Acids and Impact on Cholesterol Metabolism

The use of probiotics, alone or in interaction with bile acids, is a modern strategy in the prevention and treatment of hypercholesterolemia. Numerous mechanisms for hypocholesterolemic effect of probiotics have been hypothesized, based mostly on in vitro evidence. Interaction with bile acids through reaction of deconjugation catalyzed by bile salt hydrolase enzymes (BSH) is considered as the main mechanism of cholesterol-lowering effects of probiotic bacteria, but it has been reported that microbial BSH activity could be potentially detrimental to the human host. There are several approaches for prevention of possible side effects associated with BSH activity, which at the same time increase the viability of probiotics in the intestines and also in food matrices. The aim of our study was to summarize present knowledge of probiotics??bile acids interactions, with special reference to cholesterol-lowering mechanisms of probiotics, and to report novel biotechnological approaches for increasing the pharmacological benefits of probiotics.     

Rapid analysis of Gram-positive bacteria in water via membrane filtration coupled with nanoprobe-based MALDI-MS

Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is challenging when it is directly applied to identify bacteria in water. This study demonstrates a rapid, sensitive, and selective technique for detection of Gram-positive bacteria in water. It involves a combination of membrane filtration (MF) and vancomycin-conjugated magnetite nanoparticles (VNPs) to selectively separate and concentrate Gram-positive bacteria in tap water and reservoir water, followed by rapid analysis of the isolates using whole-cell MALDI-MS. VNPs specifically recognize cells of Gram-positive bacteria, which serves as a basis for affinity capture of target Gram-positive bacteria. A two-step procedure of surface modification of bare magnetite nanoparticles was applied to synthesize VNPs. MF prior to VNP-based magnetic separation can effectively increase the enrichment factor and detection sensitivity and reduce time-consuming culture steps and the matrix effect for analysis of bacteria in MALDI-MS. The enrichment factor for the MF-VNP technique is about 6 × 10⁴. A variety of bacteria, including Staphylococcus aureus, Bacillus subtilis, Bacillus cereus, and Enterococcus faecium, were successfully analyzed from aqueous solutions and their mixtures with Gram-negative bacteria. The optimal conditions of the VNP/MALDI-MS technique, including selection of the MALDI matrix, the choice of cell-washing solution, and the VNP concentration, were also investigated. The capture efficiencies of Gram-positive bacteria with VNPs were 26.7–33.3%. The mass variations of characteristic peaks of the captured bacteria were within ±5 Da, which indicated good reproducibility of the proposed technique. The technique was applied to detect Gram-positive bacteria in tap water and reservoir water with an analysis time of around 2 h. The detection limit for Bacillus cereus, Enterococcus faecium, and Staphylococcus aureus was 5 × 10² cfu/ml for 2.0-l water samples.     

Evaluation of the surface affinity of water in three biochars using fast field cycling NMR relaxometry

Many soil functions depend on the interaction of water with soil. The affinity of water for soils can be altered by applying soil amendments like stone meal, manure, or biochar (a carbonaceous material obtained by pyrolysis of biomasses). In fact, the addition of hydrophobic biochar to soil may increase soil repellency, reduce water‐adsorbing capacity, inhibit microbial activity, alter soil filter, buffer, storage, and transformation functions. For this reason, it is of paramount importance to monitor water affinity for biochar surface (also referred to as ‘wettability’) in order to better address its applications in soil systems. In this study, we propose the use of fast field cycling NMR relaxometry technique with the application of a new mathematical model for data interpretation, as a valid alternative to the traditional contact angle (CA) measurements for biochar wettability evaluation. Either NMR or CA results revealed the same wettability trend for the biochars studied here. The advantage of NMR relaxometry over CA measurements lies in the possibility to obtain at the microscopic level a variety of different information in only one shot. In fact, while CA provides only wettability evaluation, NMR relaxometry also allows achievement of the mechanisms for water molecular dynamics on biochar surface, thereby leading to the possibility to understand better, in future research, the role of biochar in increasing soil quality and plant nutrition. Copyright © 2016 John Wiley & Sons, Ltd.     

Cell‐Laden Hydrogels for Multikingdom 3D Printing

Living materials are created through the embedding of live, whole cells into a matrix that can house and sustain the viability of the encapsulated cells. Through the immobilization of these cells, their bioactivity can be harnessed for applications such as bioreactors for the production of high‐value chemicals. While the interest in living materials is growing, many existing materials lack robust structure and are difficult to pattern. Furthermore, many living materials employ only one type of microorganism, or microbial consortia with little control over the arrangement of the various cell types. In this work, a Pluronic F127‐based hydrogel system is characterized for the encapsulation of algae, yeast, and bacteria to create living materials. This hydrogel system is also demonstrated to be an excellent material for additive manufacturing in the form of direct write 3D‐printing to spatially arrange the cells within a single printed construct. These living materials allow for the development of incredibly complex, immobilized consortia, and the results detailed herein further enhance the understanding of how cells behave within living material matrices. The utilization of these materials allows for interesting applications of multikingdom microbial cultures in immobilized bioreactor or biosensing technologies.     

Industrial applications of instrumental neutron activation analysis

Neutron activation analysis is shown as a useful diagnostic technique in semiconductor industry. A better acceptance of the method for applications in industry has been achieved through a specialized analytical service. Its main application is the characterization of high purity silicon in all stages of production. Irradiation of large sample volumes allowes a very sensitive detection of impurities in silicon with detection limits down to 10^–16 g/g. Other applications discussed are the analysis of silicon carbide, quartz, pure water and titanium. Special techniques described are autoradiography, depth profiling and surface analysis. In semiconductor process technology NAA was used to monitor contamination of silicon wafers.     

Process analysis using ion mobility spectrometry

Ion mobility spectrometry, originally used to detect chemical warfare agents, explosives and illegal drugs, is now frequently applied in the field of process analytics. The method combines both high sensitivity (detection limits down to the ng to pg per liter and ppb_v/ppt_v ranges) and relatively low technical expenditure with a high-speed data acquisition. In this paper, the working principles of IMS are summarized with respect to the advantages and disadvantages of the technique. Different ionization techniques, sample introduction methods and preseparation methods are considered. Proven applications of different types of ion mobility spectrometer (IMS) used at ISAS will be discussed in detail: monitoring of gas insulated substations, contamination in water, odoration of natural gas, human breath composition and metabolites of bacteria. The example applications discussed relate to purity (gas insulated substations), ecology (contamination of water resources), plants and person safety (odoration of natural gas), food quality control (molds and bacteria) and human health (breath analysis).     

Staying alive: new perspectives on cell immobilization for biosensing purposes

Intact living cells, because of their simplicity of use and their ability to provide highly valuable functional information, are well suited to biosensing applications. Cells can be genetically engineered by introduction of reporter proteins, modified to achieve analyte selectivity for their sensing capabilities, and connected to a transducer to obtain whole-cell biosensors. These bioanalytical features are increasingly attracting attention in the pharmaceutical, environmental, medical, and industrial fields. Whole-cell biosensors based on different recognition elements and transduction mechanisms have been also incorporated into portable devices and, with recent advances in micro and nanofabrication and microfluidics technology, miniaturized to achieve single-cell level analysis. Cell immobilization, widely used in, for example, microbial biofermentors or bioremediation systems, is now emerging as an appealing way of integrating whole-cell biosensors into devices, to maintain long-term cell viability, to increase the reproducibility of the cell’s response, and to avoid the spread of genetically modified cells into the environment, the latter being very important when devices are used for analysis in the field. A plethora of materials and functionalized surfaces have been proposed for immobilization of microbial or mammalian cells, each one having peculiar advantages and limitations. This critical review highlights and discusses recent trends, together with selected bioanalytical applications of immobilized viable cells. In particular the review focuses on some aspects that seem to hold great promise for future applications of immobilized cells, spanning from microbial biosensors to microbial biofilms, cell microarrays, and single-cell analysis.     

High resolution applications of laser-induced breakdown spectroscopy for environmental and forensic applications

Laser-induced breakdown spectroscopy (LIBS) has been used in the elemental analysis for a variety of environmental samples and as a proof of concept for a host of forensic applications. In the first application, LIBS was used for the rapid detection of carbon from a number of different soil types. In this application, a major breakthrough was achieved by using a multivariate analytical approach that has brought us closer towards a “universal calibration curve”. In a second application, it has been demonstrated that LIBS in combination with multivariate analysis can be employed to analyze the chemical composition of annual tree growth rings and correlate them to external parameters such as changes in climate, forest fires, and disturbances involving human activity. The objectives of using this technology in fire scar determinations are: 1) To determine the characteristic spectra of wood exposed to forest fires and 2) To examine the viability of this technique for detecting fire occurrences in stems that did not develop fire scars. These examples demonstrate that LIBS-based techniques are inherently well suited for diverse environmental applications. LIBS was also applied to a variety of proof of concept forensic applications such as the analysis of cremains (human cremation remains) and elemental composition analysis of prosthetic implants.     

Classification of the biological material with use of FTIR spectroscopy and statistical analysis

Rapid detection and discrimination of dangerous biological materials such as bacteria and their spores has become a security aim of considerable importance. Various analytical methods, including FTIR spectroscopy combined with statistical analysis have been used to identify vegetative bacteria, bacterial spores and background interferants. The present work discusses the application of FTIR technique performed in reflectance mode using Horizontal Attenuated Total Reflectance accessory (HATR) to the discrimination of biological materials. In comparison with transmission technique the HATR is more rapid and do not require the sample destruction, simultaneously giving similar absorbance bands. HATR-FTIR results combined with statistical analysis PCA and HCA demonstrate that this combination provides novel and accurate microbial identification technique.     

Fast determination of paracetamol and its hydrolytic degradation product p-aminophenol by capillary and microchip electrophoresis with contactless conductivity detection

Paracetamol (PAC) is one of the most extensively used analgesics and antipyretic drugs to treat mild and moderate pain. P-aminophenol (PAP), the main hydrolytic degradation product of PAC, can be found in environmental water. Recently, CE has been developed for the detection of a wide variety of chemical substances. The purpose of this study is to develop a simple and fast method for the detection and separation of PAC and its main hydrolysis product PAP using CE and microchip electrophoresis with capacitively coupled contactless conductivity detection. The determination of these compounds using microchip electrophoresis with capacitively coupled contactless conductivity detection is being reported for the first time. The separation was run for all analytes using a BGE (20 mM β-alanine, pH 11) containing 14% (v/v) methanol. The RSDs obtained for migration time were less than 4%, and RSDs obtained for peak area were less than 7%. The detection limits (S/N = 3) that were achieved ranged from 0.3 to 0.6 mg/L without sample preconcentration. The presented method showed rapid analysis time (less than 1 min), high efficiency and precision, low cost, and a significant decrease in the consumption of reagents. The microchip system has proved to be an excellent analytical technique for fast and reliable environmental applications.     

An easily-automated assay for the physiological state quantification of Pseudomonas sp. M18

In order to foreknow poorly performing cultures before wasting energy to scale them to large cultures, industrial microbial fermentation can greatly benefit from knowledge of the physiological state of cells. The method currently proposed is an easily automated physiological state determination method. We have designed one universal rRNA-specific probe for bacteria and developed novel signal probe hybridization (SPH) assay featuring no RNA extraction and no PCR amplification steps necessary to quantify the physiological state of microbial cells. The microbial cell was lysed with sonication and SDS. Signal probes were applied to hybridize and protect the rRNA target. S1 nuclease was then applied to remove the excessive signal probes, the single-stranded RNA and the mismatch RNA/DNA hybrids. The remaining signal probe was captured with a corresponding capture probe immobilized on a microplate and quantified with a horseradish peroxidase-conjugated color reaction. We then systemically optimized our assay. Results showed that the cell limit of detection (LOD) and the cell limit of quantification (LOQ) were 2.64 × 10⁴ cells and 9.86 × 10⁴ cells per well of microplate, respectively. The limit of detection (LOD) and the limit of quantification (LOQ) of signal probe were 49.0 fM and 344.0 fM respectively. Using this technique, we quantified the 16S rRNA levels during the fermentation process of Pseudomonas sp. M18. Our results indicate that the 16S rRNA levels can directly inform us about the physiological state of microbial cells. This technique has great potential for application to the microbial fermentation industry.