Multiparametric flow cytometry and cell sorting for the assessment of viable, injured, and dead bifidobacterium cells during bile salt stress

Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects

Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.

A streamlined workflow for a fast and cost-effective count of tyndallized probiotics using flow cytometry

The use of dead probiotics and their cellular metabolites seems to exhibit immunomodulatory and anti-inflammatory properties, providing protection against pathogens. These inanimate microorganisms, often referred to as tyndallized or heat-killed bacteria, are a new class of probiotics employed in clinical practice. Safety concerns regarding the extensive use of live microbial cells have increased interest in inactivated bacteria, as they could eliminate shelf-life problems and reduce the risks of microbial translocation and infection. Culture-dependent methods are not suitable for the quality assessment of these products, and alternative methods are needed for their quantification. To date, bacterial counting chambers and microscopy have been used for tyndallized bacteria enumeration, but no alternative validated methods are now available for commercial release. The aim of the present study is to design a new method for the qualitative and quantitative determination of tyndallized bacterial cells using flow cytometric technology. Using a live/dead viability assay based on two nucleic acid stains, thiazole orange (TO) and propidium iodide (PI), we optimized a workflow to evaluate bacterial viability beyond the reproduction capacity that provides information about the structural properties and metabolic activities of probiotics on FACSVerse without using beads as a reference. The data obtained in this study represent the first analytical application that works effectively both on viable and non-viable cells. The results provided consistent evidence, and different samples were analyzed using the same staining protocol and acquisition settings. No significant discrepancies were highlighted between the declared specification of commercial strain and the analytical data obtained. For the first time, flow cytometry was used for counting tyndallized bacterial cells as a quality control assessment in probiotic production. This aspect becomes important if applied to medical devices where we cannot boast metabolic but only mechanical activities.

Probiotics and Paraprobiotics: Effects on Microbiota-Gut-Brain Axis and Their Consequent Potential in Neuropsychiatric Therapy

Neuropsychiatric disorders are clinical conditions that affect cognitive function and emotional stability, often resulting from damage or disease in the central nervous system (CNS). These disorders are a worldwide concern, impacting approximately 12.5% of the global population. The gut microbiota has been linked to neurological development and function, implicating its involvement in neuropsychiatric conditions. Due to their interaction with gut microbial communities, probiotics offer a natural alternative to traditional treatments such as therapeutic drugs and interventions for alleviating neuropsychiatric symptoms. Introduced by Metchnikoff in the early 1900s, probiotics are live microorganisms that provide various health benefits, including improved digestion, enhanced sleep quality, and reduced mental problems. However, concerns about their safety, particularly in immunocompromised patients, warrant further investigation; this has led to the concept of "paraprobiotics", inactivated forms of beneficial microorganisms that offer a safer alternative. This review begins by exploring different methods of inactivation, each targeting specific cellular components like DNA or proteins. The choice of inactivation method is crucial, as the health benefits may vary depending on the conditions employed for inactivation. The subsequent sections focus on the potential mechanisms of action and specific applications of probiotics and paraprobiotics in neuropsychiatric therapy. Probiotics and paraprobiotics interact with gut microbes, modulating the gut microbial composition and alleviating gut dysbiosis. The resulting neuropsychiatric benefits primarily stem from the gut-brain axis, a bidirectional communication channel involving various pathways discussed in the review. While further research is needed, probiotics and paraprobiotics are promising therapeutic agents for the management of neuropsychiatric disorders.

Convergence of flow cytometry and bacteriology. Current and future applications: a focus on food and clinical microbiology

Since its development in the 1960s, flow cytometry (FCM) was quickly revealed a powerful tool to analyse cell populations in medical studies, yet, for many years, was almost exclusively used to analyse eukaryotic cells. Instrument and methodological limitations to distinguish genuine bacterial signals from the background, among other limitations, have hampered FCM applications in bacteriology. In recent years, thanks to the continuous development of FCM instruments and methods with a higher discriminatory capacity to detect low-size particles, FCM has emerged as an appealing technique to advance the study of microbes, with important applications in research, clinical and industrial settings. The capacity to rapidly enumerate and classify individual bacterial cells based on viability facilitates the monitoring of bacterial presence in foodstuffs or clinical samples, reducing the time needed to detect contamination or infectious processes. Besides, FCM has stood out as a valuable tool to advance the study of complex microbial communities, or microbiomes, that are very relevant in the context of human health, as well as to understand the interaction of bacterial and host cells. This review highlights current developments in, and future applications of, FCM in bacteriology, with a focus on those related to food and clinical microbiology.

Detection of Glycolytically Active Lacticaseibacillus paracasei Strain Shirota by Flow Cytometry Targeting the Efflux Activity of Fluorescent Dye: a Potential Tool for Quality Assessment of Probiotic Cells in Milk Products

The rapid and accurate detection of viable probiotic cells in dairy products is important for assessing product quality in manufacturing. Flow cytometry is widely used for the rapid analysis of bacterial cells. However, further investigation is needed into the optimum property to use it for assessing cell viability. Here, we proposed using the efflux activity of a fluorescent dye, carboxyfluorescein (CF), as an indicator of cell viability. CF is generated from 5(6)-carboxyfluorescein diacetate as a result of cleavage by intracellular esterase. It generally accumulates in the cell, but certain bacterial species are known to extrude it. We found here that the probiotic strain Lacticaseibacillus paracasei strain Shirota (LcS) also extruded CF in the presence of energy sources, such as glucose. To investigate the mechanism of its CF-efflux activity, we screened CF-efflux-negative mutants from a random mutagenesis LcS library and examined the whole genome for genes responsible for CF efflux. We identified a base substitution in the pfkA gene in the glycolytic pathway, and we demonstrated that intact pfkA was essential for CF efflux, indicating that CF-efflux-positive cells must have uncompromised glycolytic activity. We also confirmed that there was a good correlation between the rate of CF-efflux-positive cells and that of colony-forming cells of LcS in a fermented milk product, whereas other properties, such as esterase activity and cell membrane integrity, lost their correlation with the colony-forming activity after long storage. We propose that CF-efflux activity could be an appropriate indicator of cell viability in certain probiotic strains. IMPORTANCE To our knowledge, this is the first report to demonstrate that CF efflux requires uncompromised glycolytic activity in certain lactic acid bacteria. Compared with the cell properties currently widely used for cell viability assessment, such as intracellular esterase activity and membrane integrity, CF-efflux activity enables the accurate detection of culturable cells, especially in products stored for long periods at cold temperatures. These results indicate strongly that CF-efflux activity can be an adequate cell-viability indicator and that flow cytometric quantification could be an alternative to conventional CFU counting. Our findings should be especially informative for dairy/probiotic product manufacturing.

Sublethally injured microorganisms in food processing and preservation: Quantification, formation, detection, resuscitation and adaption

Sublethally injured state has been recognized as a survival strategy for microorganisms suffering from stressful environments. Injured cells fail to grow on selective media but can normally grow on nonselective media. Numerous microorganism species can form sublethal injury in various food matrices during processing and preservation with different techniques. Injury rate was commonly used to evaluate sublethal injury, but mathematical models for the quantification and interpretation of sublethally injured microbial cells still require further study. Injured cells can repair themselves and regain viability on selective media under favorable conditions when stress is removed. Conventional culture methods might underestimate microbial counts or present a false negative result due to the presence of injured cells. Although the structural and functional components may be affected, the injured cells pose a great threat to food safety. This work comprehensively reviewed the quantification, formation, detection, resuscitation and adaption of sublethally injured microbial cells. Food processing techniques, microbial species, strains and food matrix all significantly affect the formation of sublethally injured cells. Culture-based methods, molecular biological methods, fluorescent staining and infrared spectroscopy have been developed to detect the injured cells. Cell membrane is often repaired first during resuscitation of injured cells, meanwhile, temperature, pH, media and additives remarkably influence the resuscitation. The adaption of injured cells negatively affects the microbial inactivation during food processing.

Stress Response in Bifidobacteria

Bifidobacteria naturally inhabit diverse environments, including the gastrointestinal tracts of humans and animals. Members of the genus are of considerable scientific interest due to their beneficial effects on health and, hence, their potential to be used as probiotics. By definition, probiotic cells need to be viable despite being exposed to several stressors in the course of their production, storage, and administration. Examples of common stressors encountered by probiotic bifidobacteria include oxygen, acid, and bile salts. As bifidobacteria are highly heterogenous in terms of their tolerance to these stressors, poor stability and/or robustness can hamper the industrial-scale production and commercialization of many strains. Therefore, interest in the stress physiology of bifidobacteria has intensified in recent decades, and many studies have been established to obtain insights into the molecular mechanisms underlying their stability and robustness. By complementing traditional methodologies, omics technologies have opened new avenues for enhancing the understanding of the defense mechanisms of bifidobacteria against stress. In this review, we summarize and evaluate the current knowledge on the multilayered responses of bifidobacteria to stressors, including the most recent insights and hypotheses. We address the prevailing stressors that may affect the cell viability during production and use as probiotics. Besides phenotypic effects, molecular mechanisms that have been found to underlie the stress response are described. We further discuss strategies that can be applied to improve the stability of probiotic bifidobacteria and highlight knowledge gaps that should be addressed in future studies.

The identification of Pseudomonas aeruginosa persisters using flow cytometry

Pseudomonas aeruginosa persisters are a rare and poorly characterized subpopulation of cells that are responsible for many recurrent infections. The lack of knowledge on the mechanisms that lead to persister cell development is mainly a result of the difficulty in isolating and characterizing this rare population. Flow cytometry is an ideal method for identifying such subpopulations because it allows for high-content single-cell analysis. However, there are fewer established protocols for bacterial flow cytometry compared to mammalian cell work. Herein, we describe and propose a flow cytometry protocol to identify and isolate P. aeruginosa persister cells. Additionally, we show that the percentage of potential persister cells increases with increasing antibiotic concentrations above the MIC.

A rapid method for the assessment of the vitality of microorganisms using flow cytometry

Cultivability, viability and vitality make it possible to characterize the behavior of a cellular population. Vitality was assessed using the kinetic parameters of specific metabolisms depending on whether the strains were used, for example, for the acidification of lactic acid bacteria or for CO₂ production in fermenting yeasts. However, these methods are time-consuming. We developed a cytometric descriptor based on the energy-dependent extrusion of carboxyfluorescein from cells, subsequent to carboxyfluorescein diacetate staining, and compared it to the measurements of metabolic activities of various bacteria and yeasts. For all of the microorganisms tested, the cytometric descriptor ΔFI₁₅ was well correlated with the results of the metabolic measurements and, moreover, has the advantage of being easier and faster to use than metabolic methods. It can be very useful for evaluating the vitality of the starters before inoculation in industrial processes. This article is protected by copyright. All rights reserved.

Assessing the Levisticum officinale Koch. essential oil as a novel preservative for stored chia seeds (Salvia hispanica L.) with emphasis on probable mechanism of action

The present study was undertaken to explore the inhibitory effect of Levisticum officinale Koch. essential oil (L_offEO) on the growth and aflatoxin B₁ secretion by Aspergillus flavus (AF-LHP-SH1, aflatoxigenic strain) causing deterioration of stored chia seeds (Salvia hispanica). The chemical profile analysis of L_offEO by GC-MS analysis revealed the presence of α-terpinyl acetate (26.03 %) as a major component followed by terpineol <1- > (24.03 %) and citronellal (24.03 %). Results on antifungal and antiaflatoxigenic activity indicated that L_offEO at 2.0 and 1.75 μL/mL caused complete inhibition of growth and aflatoxin B₁ production, respectively. Antifungal toxicity of L_offEO was strongly correlated with the inhibition of ergosterol content, leakage of cellular ions, and disintegration of membrane permeability. Reduction in cellular methylglyoxal by L_offEO indicated a novel antiaflatoxigenic mechanism of action. The L_offEO showed moderate free radical quenching activity in DPPH assay (IC₅₀ = 26.10 μL/mL) and exhibited remarkable inhibitory efficacy against lipid peroxidation of chia seeds. In addition, L_offEO presented strong in situ antiaflatoxigenic efficacy, and exhibited non-phytotoxic nature, acceptable sensory characteristics, and favorable safety profile (LD₅₀ = 19786.59 μL/kg), which recommends its practical utilization as a novel and safe preservative to improve the shelf life of stored chia seeds from fungal infestation and aflatoxin B₁ contamination.

Rapid detection and enumeration of aerobic mesophiles in raw foods using dielectrophoresis

The concept of dielectrophoresis (DEP), which involves the movement of neutral particles by induced polarization in nonuniform electric fields, has been exploited in various biological applications. However, only a few studies have investigated the use of DEP for detecting and enumerating microorganisms in foodstuffs. Therefore, we aimed to evaluate the accuracy and efficiency of a DEP-based method for enumerating viable bacteria in three raw foods: freshly cut lettuce, chicken breast, and minced pork. The DEP separation of bacterial cells was conducted at 20 V of output voltage and 6000 to 9000 kHZ of frequency with sample conductivity of 30-70 μS/cm. The accuracy and validity of the DEP method for enumerating viable bacteria were compared with those of the conventional culture method; no significant variation was observed. We found a high correlation between the data obtained using DEP and the conventional aerobic plate count culture method, with a high coefficient of determination (R2 > 0.90) regardless of the food product; the difference in cell count data between both methods was within 1.0 log CFU/mL. Moreover, we evaluated the efficiency of the DEP method for enumerating bacterial cells in chicken breasts subjected to either freezing or heat treatment. After thermal treatment at 55 °C and 60 °C, the viable cell counts determined via the DEP method were found to be lower than those obtained using the conventional culture method, which implies that the DEP method may not be suitable for the direct detection of injured cells. In addition to its high accuracy and efficiency, the DEP method enables the determination of viable cell counts within 30 min, compared to 48 h required for the conventional culture method. In conclusion, the DEP method may be a potential alternative tool for rapid determination of viable bacteria in a variety of foodstuffs.

A Possible Flow Cytometry-Based Viability and Vitality Assessment Protocol for Pathogenic Vibrio cholerae O1 and O139 Postexposure to Simulated Gastric Fluid

During the intake of contaminated water, for diarrheal disease to occur, Vibrio cholerae must survive through the bactericidal digestive secretion of gastric fluid during passage through the stomach. Determining the viability of these bacteria is challenging, with the standard cultivation methods for viability being time-consuming and unable to culture cells that may still function accordingly. This study assessed the use of enzyme action and membrane integrity as alternatives for determining vitality and viability, respectively, in gastric acid-stressed pathogenic Vibrio cholerae O1 and O139, using fluorescent probes thiazole orange (TO) for viability based on membrane integrity, carboxyfluorescein diacetate (CFDA) with acetoxymethyl ester (AM) for vitality based on metabolic activity, and propidium iodide (PI) for cell death/damage due to loss of membrane integrity, with flow cytometry. Simulated gastric fluid-treated bacterial cells were labelled with blends of TO+PI and CFDA-AM+PI, and these stained cells were separated into heterologous populations based on their fluorescence signal. The gastric acid exposed cells presented with high green fluorescence signals after staining with the metabolic probe CFDA-AM, which indicated intact (live) cells due to being metabolically active, whereas when the same cells were stained with the DNA probe (TO), these appeared to be in a “stressed state” due to loss of membrane integrity. Damaged cells (dead cells) showed high red fluorescence levels after staining with PI probe. The use of flow cytometry with fluorescent probes is a favorable method for evaluating the vitality and viability of bacteria when cells are labelled with a combination of CFDA-AM+PI.

Factors that influence clinical efficacy of live biotherapeutic products

Traditional probiotics are increasingly being used in a medical context. The use of these products as drugs is considerably different from the traditional use as food or food supplements, as, obviously, the target population is different (diseased versus healthy or at risk population). Besides the target population, also the regulatory context is different, mainly with respect to production, administration regime and type of clinical studies required. In this paper we will, besides the regulatory differences, focus on aspects that may impact the efficacy of a live biotherapeutic product (drug), especially in a clinical setting. The impact of the dosage seems to depend on the strain and the application and may follow some rationale. In contrast, information on the impact of the time of administration or diet, is often still lacking. The matrix and the use of protective measures may clearly have an impact on the survival and efficacy of the strain.

Sporopollenin Exine Microcapsules as Potential Intestinal Delivery System of Probiotics

Despite several decades of research into encapsulation of bacteria, most of the proposed technologies are in the form of immobilized cultures. In this work, sporopollenin exine capsules (SECs) opened, using silica particles which act as pressing micro-probes, and loaded with Lactobacillus casei (L. casei) cells, are described for the first time. The proposed encapsulation provided ≈30× higher encapsulation yield (30.87%), compared to direct compression of SECs (0.99%). Encapsulated L. casei cells show 1.21- and 2.25-folds higher viability compared to free cells, in in vitro simulated fasted and fed media representing the human gastrointestinal (GI) tract, respectively. Encapsulated L. casei can proliferate inside the SECs, generating enough pressure to cause the SECs to burst and release the viable and metabolically active cells. The noticeable difference with the application of the SECs as a means of encapsulation is that the SECs may act as a bioreactor and provide time for the encapsulated cells to multiply thousands of times before being released, following the SEC's burst. The unique advantages of SECs alongside the proposed encapsulation method, demonstrates the potential application of SECs as delivery system of probiotics to the distal part of the human GI tract.

An approach to increase the success rate of cultivation of soil bacteria based on fluorescence-activated cell sorting

Soil microbiota are considered a source of undiscovered bioactive compounds, yet cultivation of most bacteria within a sample remains generally unsuccessful. Two main reasons behind the unculturability of bacteria are the presence of cells in a viable but not culturable state (such as dormant cells) and the failure to provide the necessary growth requirements in vitro (leading to the classification of some bacterial taxa as yet-to-be-cultured). The present work focuses on the development of a single procedure that helps distinguish between both phenomena of unculturability based on viability staining coupled with flow cytometry and fluorescence-activated cell sorting. In the selected soil sample, the success rate of cultured bacteria was doubled by selecting viable and metabolically active bacteria. It was determined that most of the uncultured fraction was not dormant or dead but likely required different growth conditions. It was also determined that the staining process introduced changes in the taxonomic composition of the outgrown bacterial biomass, which should be considered for further developments. This research shows the potential of flow cytometry and fluorescence-activated cell sorting applied to soil samples to improve the success rate of bacterial cultivation by estimating the proportion of dormant and yet-to-be-cultured bacteria and by directly excluding dormant cells from being inoculated into growth media.

Densely Populated Water Droplets in Heavy-Oil Seeps

Most of the microbial degradation in oil reservoirs is believed to take place at the oil-water transition zone (OWTZ). However, a recent study indicates that there is microbial life enclosed in microliter-sized water droplets dispersed in heavy oil of Pitch Lake in Trinidad and Tobago. This life in oil suggests that microbial degradation of oil also takes place in water pockets in the oil-bearing rock of an oil leg independent of the OWTZ. However, it is unknown whether microbial life in water droplets dispersed in oil is a generic property of oil reservoirs rather than an exotic exception. Hence, we took samples from three heavy-oil seeps, Pitch Lake (Trinidad and Tobago), the La Brea Tar Pits (California, USA), and an oil seep on the McKittrick oil field (California, USA). All three tested oil seeps contained dispersed water droplets. Larger droplets between 1 and 10 μl revealed high cell densities of up to 10⁹ cells ml^-1 Testing for ATP content and LIVE/DEAD staining showed that these populations consist of active and viable microbial cells with an average of 60% membrane-intact cells and ATP concentrations comparable to those of other subsurface ecosystems. Microbial community analyses based on 16S rRNA gene amplicon sequencing revealed the presence of known anaerobic oil-degrading microorganisms. Surprisingly, the community analyses showed similarities between all three oil seeps, revealing common OTUs, although the sampling sites were thousands of kilometers apart. Our results indicate that small water inclusions are densely populated microhabitats in heavy oil and possibly a generic trait of degraded-oil reservoirs.IMPORTANCE Our results confirmed that small water droplets in oil are densely populated microhabitats containing active microbial communities. Since these microhabitats occurred in three tested oil seeps which are located thousands of kilometers away from each other, such populated water droplets might be a generic trait of biodegraded oil reservoirs and might be involved in the overall oil degradation process. Microbial degradation might thus also take place in water pockets in the oil-bearing oil legs of the reservoir rock rather than only at the oil-water transition zone.

Fluorescence-Activated Cell Sorting Using the D-Root Device and Optimization for Scarce and/or Non-Accessible Root Cell Populations

Fluorescence-activated cell sorting (FACS) is a technique used to isolate specific cell populations based on characteristics detected by flow cytometry. FACS has been broadly used in transcriptomic analyses of individual cell types during development or under different environmental conditions. Different protoplast extraction protocols are available for plant roots; however, they were designed for accessible cell populations, which normally were grown in the presence of light, a non-natural and stressful environment for roots. Here, we report a protocol using FACS to isolate root protoplasts from Arabidopsis green fluorescent protein (GFP)-marked lines using the minimum number of enzymes necessary for an optimal yield, and with the root system grown in darkness in the D-Root device. This device mimics natural conditions as the shoot grows in the presence of light while the roots grow in darkness. In addition, we optimized this protocol for specific patterns of scarce cell types inside more differentiated tissues using the mCherry fluorescent protein. We provide detailed experimental protocols for effective protoplasting, subsequent purification through FACS, and RNA extraction. Using this RNA, we generated cDNA and sequencing libraries, proving that our methods can be used for genome-wide transcriptomic analyses of any cell-type from roots grown in darkness.

Effect of salinity on mature wastewater treatment biofilm microbial community assembly and metabolite characteristics

The response mechanism of wastewater treatment biofilms to salt stress has not yet been fully established. The aim of this study was to reveal the comprehensive biological effects of salinity on biofilm microbial community and metabonomic characteristics. The study assessed performance at a range of sodium chloride (NaCl) concentrations of 0.6, 14 and 20 g/L. Biofilm coverage rate decreased significantly with increasing NaCl concentrations. High NaCl concentrations resulted in more compact and smoother biofilm morphologies. NaCl concentrations affected bacterial community variation at the class and genus level, with Gammaproteobacteria being the most dominant Proteobacteria, exhibiting NaCl tolerance at concentrations ranging from 0 to 20 g/L. Also, NaCl sensitive or tolerant species were identified, such as Pseudomonas and Planococcus, respectively. Dominant metabolites in wastewater treatment biofilms belonging to nucleotide, lipid, vitamin, amino acid and carbohydrate metabolism pathways decreased with increasing NaCl concentrations. High concentrations of NaCl regulated cell motility, transcription and membrane transport functions. In particular, the activity of ABC transporters were up-regulated at NaCl concentrations of 0.6 g/L and down-regulated at higher salinity concentrations. In addition, transcription machinery were inhibited under the stress of 14 g/L NaCl. These findings further our understanding of the short-term adaption mechanisms of wastewater treatment biofilms to high NaCl concentration environments.

Coordinated photodegradation and biodegradation of organic matter from macrophyte litter in shallow lake water: Dual role of solar irradiation

Eutrophication and climate warming cause macrophytes to spread rapidly in shallow lakes. The accumulation of excess decayed litter in lake water can improve the particulate organic matter content and lead to ecological deterioration. While decomposition of macrophyte litters in aquatic ecosystems is generally assumed to be biologically driven, photodegradation has been largely overlooked. In this study, the potential contribution of photodegradation to the decomposition of organic matter from macrophyte litter in a shallow lake was investigated under two types of light radiation: laboratory incubation light and natural solar radiation. Results showed that the combined photo- and biodegradation treatment removed more litter mass compared to solely photodegradation or biodegradation for over 108 days. More reactive oxygen species (ROS) were produced during litter degradation in lake water under the combined photo- and biodegradation treatments in comparison to other treatments. Removal efficiency of litter was doubled in the presence of ROS compared when ROS were captured. Additionally, NMR analysis revealed that lignin guaiacyl units were preferentially lost and the litter became more refractory under the combined photo oxidation and microbial degradation after 108 days. High-throughput sequencing analysis further indicated that solar irradiation stimulates the growth of bacteria (Treponema and Magnetospirillum) and fungi (Aspergillus) that have the ability to degrade aromatic compounds. Altogether, both ROS and specific microorganisms played important role in promoting litter degradation in lake water under light irradiation. Therefore, the role of solar radiation in particulate organic matter decomposition needs to be considered for a more accurate prediction of carbon dynamics in aquatic ecosystems.

A novel pharmaceutical approach for the analytical validation of probiotic bacterial count by flow cytometry

INTRODUCTION

Flow cytometry is a powerful and sensitive technique able to characterize single cells within a heterogeneous population. Different fluorescent dyes can be combined and used together to analyze a great variety of parameters simultaneously. In particular, flow-cytometry allows to measure viability and vitality of probiotics measuring their metabolic activity, fermentation capacity, acidification potential or oxygen uptake ability (Hayouni et al., 2008). To now, plate counting is considered the gold standard in microbiological technique for probiotic enumeration. However, this approach is limited to the detection of only those viable cells which are able to proliferate and form colonies on a solid medium but is not able to recognize not cultivable bacteria and nonviable cells.

AIM

The aim of the present study was to apply The International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) parameters for the validation of new analytical methods in microbiology. ICH requirements, which are commonly employed for the analysis of drugs and chemical analytes, have been here applied to live cells for the comparison between a flow-cytometric assay and the traditional plate count method for the quantification of viable probiotics bacteria.

METHODS AND RESULTS

Combining specific viability dyes such as thiazole orange (TO) and propidium iodide (PI), probiotic counts of Lactobacillus and Bifidobacterium species were carried out using a FACS Verse (BD Biosciences) cytometer. Analyses were conducted in parallel with the traditional plate count, on specific media. Raw data were analyzed using the FACSuite software (BD Biosciences) and then elaborated with the statistical software Neolicy (VWR International). Results indicated that flow cytometry provides very similar results in cell counting if compared to classical microbiology approaches, showing better performances (ICH parameters) than the traditional plate count method.

CONCLUSIONS

This work demonstrated the analytical ICH validation of probiotic counts in food supplement products using a robust flow cytometric approach able to enumerate and to assess bacteria viability with stronger results in comparison to the traditional plate count.

Flow Cytometry to Assess the Counts and Physiological State of Cronobacter sakazakii Cells after Heat Exposure

Cronobacter sakazakii is an opportunistic pathogen that is associated with outbreaks of neonatal necrotizing enterocolitis, septicaemia, and meningitis. Reconstituted powdered infant formulae is the most common vehicle of infection. The aim of the present study is to gain insight into the physiological states of C. sakazakii cells using flow cytometry to detect the compromised cells, which are viable but non-culturable using plate-based methods, and to evaluate the impact of milk heat treatments on those populations. Dead-cell suspensions as well as heat-treated and non-heat-treated cell suspensions were used. After 60 or 65 °C treatments, the number of compromised cells increased as a result of cells with compromised membranes shifting from the heat-treated suspension. These temperatures were not effective at killing all bacteria but were effective at compromising their membranes. Thus, mild heat treatments are not enough to guarantee the safety of powered infant formulae. Flow cytometry was capable of detecting C. sakazakii’s compromised cells that cannot be detected with classical plate count methods; thus, it could be used as a screening test to decrease the risk derived from the presence of pathogenic viable but non-culturable cells in this food that is intended for newborns’ nutrition.

Development of omics-based protocols for the microbiological characterization of multi-strain formulations marketed as probiotics: the case of VSL#3

The growing commercial interest in multi-strain formulations marketed as probiotics has not been accompanied by an equal increase in the evaluation of quality levels of these biotechnological products. The multi-strain product VSL#3 was used as a model to setup a microbiological characterization that could be extended to other formulations with high complexity. Shotgun metagenomics by deep Illumina sequencing was applied to DNA isolated from the commercial VSL#3 product to confirm strains identity safety and composition. Single-cell analysis was used to evaluate the cell viability, and β-galactosidase and urease activity have been used as marker to monitor the reproducibility of the production process. Similarly, these lots were characterized in detail by a metaproteomics approach for which a robust protein extraction protocol was combined with advanced mass spectrometry. The results identified over 1600 protein groups belonging to all strains present in the VSL#3 formulation. Of interest, only 3.2 % proteins showed significant differences mainly related to small variations in strain abundance. The protocols developed in this study addressed several quality criteria that are relevant for marketed multi-strain products and these represent the first efforts to define the quality of complex probiotic formulations such as VSL#3.

Broad-Spectrum Antibacterial Effects of Human Adipose-Derived Stromal Cells

Introduction

Many pathological conditions may benefit from cell therapy using mesenchymal stromal cells, particularly from adipose tissue (ASCs). Cells may be grafted in an environment with a remnant polymicrobial component. The aim is to investigate the behavior of ASCs when brought in contact with a large panel of bacteria.

Materials and Methods

Carboxyfluorescein-labelled bacterial interaction with ASCs was followed by confocal time-lapse microscopy. Costaining with LAMP-1 was also analyzed. Viability of 4 gram-negative and 4 gram-positive bacterial strains after 6 h of coculture with ASCs was assessed by agar colony counting and by flow cytometry using SYTO-62®/propidium iodide (PI) for membrane permeabilization and DiOC6 for depolarization. A murine model of periodontitis was used to assess in vivo antibacterial capacities of ASCs.

Results

A significant increase of PI-positive events for all bacterial strains and an increase of the DiOC6 signal were obtained after contact with ASCs. The number of CFU was also significantly decreased for several bacterial strains. 0.4 μm transwell systems illustrated the necessary direct contact to induce maximal bacterial membrane damages. Some bacteria were observed into phagolysosomes, confirming macrophage-like properties of ASCs. In vivo, the bacterial load was significantly lower in the ASC-grafted side compared to the control.

Conclusion

Our results highlight for the first time a broad range of antibacterial actions of ASCs, by phagocytosis, secretion of oxygenated free radicals and antibacterial molecules. These data are in line with the development of new therapeutic strategies based on ASC transplantation, appropriated in immune-dysbiotic tissue context such as periodontitis or chronic wounds.

Inactivation of Escherichia coli O157:H7 by High Hydrostatic Pressure Combined with Gas Packaging

The inactivation of Escherichia coli O157:H7 (E. coli) in physiological saline and lotus roots by high hydrostatic pressure (HHP) in combination with CO₂ or N₂ was studied. Changes in the morphology, cellular structure, and membrane permeability of the cells in physiological saline after treatments were investigated using scanning electron microscopy, transmission electron microscopy, and flow cytometry, respectively. It was shown that after HHP treatments at 150–550 MPa, CO₂-packed E. coli cells had higher inactivation than the N₂-packed and vacuum-packed cells, and no significant difference was observed in the latter two groups. Further, both the morphology and intracellular structure of CO₂-packed E.coli cells were strongly destroyed by high hydrostatic pressure. However, serious damage to the intracellular structures occurred in only the N₂-packed E. coli cells. During HHP treatments, the presence of CO₂ caused more disruptions in the membrane of E. coli cells than in the N₂-packed and vacuum-packed cells. These results indicate that the combined treatment of HHP and CO₂ had a strong synergistic bactericidal effect, whereas N₂ did not have synergistic effects with HHP. Although these two combined treatments had different effects on the inactivation of E. coli cells, the inactivation mechanisms might be similar. During both treatments, E. coli cells were inactivated by cell damage induced to the cellular structure through the membrane components and the extracellular morphology, unlike the independent HHP treatment.

Trichoderma harzianum mitigates salt stress in cucumber via multiple responses

Trichoderma harzianum T-soybean plays an important role in controlling soybean root rot disease. However, the mechanism by which it improves plant tolerance to salt stress is not clear. In this study, we investigated the possible mechanism of T-soybean in mitigating the damage caused by salt stress in Cucumis sativus L plants. Our results suggest that T-soybean improved salt tolerance of cucumber seedlings by affecting the antioxidant enzymes including peroxidase (POD) (EC 1.11.1.6), polyphenol oxidase (PPO) (EC 1.14.18.1), phenylalanine ammonia-lyase (PAL) (EC 4.3.1.5), catalase (CAT) (EC 1.11.1.6), superoxide dismutase (SOD) (EC 1.15.1.1), ascorbate peroxidase (APX) (EC 1.11.1.11), and glutathione reductase (GR) (EC 1.6.4.2), by increasing the levels of proline, soluble sugars, soluble protein, ascorbic acid (AsA) and chlorophyll as well as improving root activity. Treatment with T-soybean improved the ratio of glutathione (GSH)/oxidized glutathione (GSSG) and AsA/dehydroascorbate (DHA), and up-regulated the expression of CsAPX and CsGR genes involved in the AsA-GSH cycle. In addition, treatment with T-soybean increased the K⁺ content and K⁺/Na⁺ ratio while decreased the Na⁺ concentration and ethylene level. In summary, the improved salt tolerance of cucumber plants may be due to multiple mechanisms of T-soybean, such as the increase in reactive oxygen species (ROS) scavenging, as well as maintaining osmotic balance and metabolic homeostasis under salt stress.

Physical insights of ultrasound-assisted ethanol production from composite feedstock of invasive weeds

Invasive weeds ubiquitously found in terrestrial and aquatic ecosystems form potential feedstock for lignocellulosic ethanol production. The present study has reported a bioprocess for production of ethanol using mixed feedstock of 8 invasive weeds found in India. The feedstock was subjected to pretreatment comprising dilute acid hydrolysis (for hydrolysis of hemicellulosic fraction), alkaline delignification and enzymatic hydrolysis of cellulosic fraction. Pentose-rich and hexose-rich hydrolyzates obtained from pretreatment were fermented separately using microbial cultures of S. cerevisiae and C. shehatae. Fermentation mixture was sonicated at 35 kHz at 10% duty cycle. The time profiles of total reducing sugars, ethanol and biomass was fitted to a kinetic model using Genetic Algorithm. Sonication boosted the kinetics of fermentation 2-fold. The net bioethanol yield of the process was ∼220 g/kg raw biomass (with contributions of 86.8 and 133 g/kg raw biomass from pentose and hexose fermentations, respectively). Comparative evaluation of parameters of kinetic model under control and test conditions revealed several beneficial influences of sonication on both pentose and hexose fermentation systems such as faster transport of nutrients, substrate and products across cell membrane, rise in Monod saturation constant for substrate with concurrent reduction in substrate inhibition, and reduction of energy requirements for cell maintenance. Flow cytometry analysis of native and ultrasound-treated cells revealed no adverse influence of sonication on cell viability.

Mechanistic investigations in biobutanol synthesis via ultrasound-assisted ABE fermentation using mixed feedstock of invasive weeds

This study reports an ultrasound-assisted Acetone-Butanol-Ethanol (ABE) fermentation process using Clostridium acetobutylicum MTCC 11,274 and mixed feedstock consisting of eight highly invasive weeds. Composite (pentose + hexose) hydrolyzate was fermented with sonication at 35 kHz and 10% duty cycle (test) and mechanical agitation at 150 rpm (control). Net solvent yield with sonication was 0.288 g/g raw biomass in 92 h against yield of 0.168 g/g raw biomass in 120 h with mechanical agitation. Butanol yield in test and control fermentation was 0.233 and 0.149 g/g total fermentable sugar, respectively. Substrate and metabolites profiles in test and control fermentation were analyzed using biokinetic model. Sonication enhanced kinetics of metabolic reactions with rise in substrate affinity of enzymes (reduced saturation constants) and greater resistance to substrate inhibition. Flow cytometry analysis of cells exposed to sonication revealed high cell viability with no adverse effect on physiology.

Exopolysaccharides May Increase Gastrointestinal Stress Tolerance of Lactobacillus reuteri

This study investigated a possible relationship between exopolysaccharides (EPS) production and the resistance to bile salts and low pH in intestinal strains of Lactobacillus reuteri. The strains displayed a mucoid phenotype, when grown in the presence of 10 % sucrose. Scanning electron microscopy (SEM) revealed strands of exopolysaccharide linking neighbouring cells. The strains (except L. reuteri B1/1) produced EPS in the range from 15.80 to 650.70 mg.l−1. The strains were tested for tolerance to bile salts (0.15; 0.3 %) and low pH (1.5—2.0—2.5—3.0). The survival rate, after the treatment with artificial gastric and intestinal juices, was determined by flow cytometric analysis. The strains of L. reuteri that produced 121—650 mg.l−1 of EPS showed a significantly higher tolerance (P < 0.001) to the gastric juice at pH 3 and 2.5, throughout the entire exposure time, in comparison to the strains that produced less than 20 mg.l−1 of EPS. L. reuteri L26, with the highest production of EPS, exhibited the highest survival rate (60 %) at pH 2 after the 120 minutes of in-cubation and was able to tolerate pH 1.5 for 30 minutes. Higher production of EPS significantly (P < 0.001) increased the strains’ tolerance against the intestinal juice in the presence of 0.15 and 0.3 % bile salts and was time dependent. L. reuteri L26 showed the highest tolerance (P < 0.001) against 0.3 % bile salts. This investigation revealed a positive correlation between the EPS production and the resistance of intestinal L. reuteri to the stress conditions of the gastrointestinal tract (GIT).

High phenol degradation capacity of a newly characterized Acinetobacter sp. SA01: Bacterial cell viability and membrane impairment in respect to the phenol toxicity

An efficient phenol-degrading bacterial strain, belonging to Acinetobacter genus, was isolated and selected to study the impact of different environmentally relevant phenol concentrations on the degradation process. The bacterial isolate, labeled as Acinetobacter sp. SA01 was able to degrade the maximum phenol concentration of 1 g/l during 60 h at optimum condition of pH 7, 30 °C and 180 rpm. Aeration and initial cell density, the two important factors, were carefully examined in the optimal growth conditions. The results showed that these two variables related proportionally with phenol degradation rate. Further investigations showed no effect of inoculum size on the enhancement of degradation of phenol at over 1 g/l. Flow cytometry (FCM) study was performed to find out the relationship between phenol-induced damages and phenol degradation process. Single staining using propidium iodide (PI) showed increased cell membrane permeability with an increase of phenol concentration, while single staining with carboxyfluorescein diacetate (cFDA) demonstrated a considerable reduction in esterase activity of the cells treated with phenol at more than 1 g/l. A detailed investigation of cellular viability using concurrent double staining of cFDA/PI revealed that the cell death increases in cells exposed to phenol at more than 1 g/l. The rate of cell death was low but noticeable in the presence of phenol concentration of 2 g/l, over time. Phenol at concentrations of 3 and 4 g/l caused strong toxicity in living cells of Acinetobacter sp. SA01. The plate count method and microscopy analysis of the cells treated with phenol at 1.5 and 2 g/l confirmed an apparent reduction in cell number over time. It was assumed that the phenol concentrations higher than 1 g/l have destructive effects on membrane integrity of Acinetobacter sp. SA01. Our results also revealed that the toxicity did not reduce by increasing initial cell density. Scanning electron microscopy (SEM) examination of bacterial cells revealed the surface morphological changes following exposure to phenol. The bacterial cells, with wizened appearance and wrinkled surface, were observed by exposing to phenol (1 g/l) at lag phase. A morphological change occurred in the mid-logarithmic phase as the bacterial cells demonstrated coccobacilli form as well as elongated filamentous shape. The wrinkled cell surface were totally disappeared in mid-stationary phase, suggesting that the complete degradation of phenol relieve the stress and direct bacterial cells toward possessing smoother cell membrane.

New Diketopyrrolopyrrole-Based Ratiometric Fluorescent Probe for Intracellular Esterase Detection and Discrimination of Live and Dead Cells in Different Fluorescence Channels

A new diketopyrrolopyrrole-based fluorescent probe (DPP-AM) was designed and synthesized for ratiometric detection of esterase and for imaging of live and dead cells in different modes. DPP-AM showed red fluorescence because of the intramolecular charge transfer (ICT) process from the DPP moiety to the pyridinium cation and gave remarkable ratio changes (about 70 folds), with the fluorescence changing from red to yellow, after treating with esterase because of the broken ICT process. Besides, the detection limit of DPP-AM toward esterase in vitro was 9.51 × 10^-5 U/mL. After pretreating with H₂O₂ and ultraviolet light radiation, the health status of TPC1 cells was successfully imaged. More importantly, DPP-AM showed yellow fluorescence in live cells and a red fluorescent signal in dead cells, indicating that DPP-AM has great potential applications for assessing esterase activity as well as for discriminating live and dead cells.

The use of fluorescent techniques in combination with flow cytometry for fast counting of Bifidobacterium longum ATCC BAA-2753 in BIFICO capsule

BIFICO is a main microecological drug that the main ingredient is Bifidobacterium longum ATCC BAA-2753. It's necessary to detect the number of Bifidobacterium longum ATCC BAA-2753 for quality control during the production of BIFICO. Plate count assay (PCA) is the most commonly used method for counting microbial cells. However, not all microorganisms can be counted by PCA. (e.g. uncultured microorganisms under specific growth conditions). In this study, a method of fluorescent techniques in combination with flow cytometry (FCM) was established for the counting of Bifidobacterium longum BAA-2753. Using SYTO9 and PI stain, flow cytometric analysis could easily differentiate live bacteria and dead bacteria. The number of live bacteria determined by FCM was about fourfold higher than that counted by PCA. Therefore, the FCM method could be a practical tool for the quality control of Bifidobacterium longum BAA-2753 in the industrial production of BIFICO.

Rapid assessment of viable but non-culturable Bacillus coagulans MTCC 5856 in commercial formulations using Flow cytometry

Accurate enumeration of bacterial count in probiotic formulation is imperative to ensure that the product adheres to regulatory standards and citation in consumer product label. Standard methods like plate count, can enumerate only replicating bacterial population under selected culture conditions. Viable but non culturable bacteria (VBNC) retain characteristics of living cells and can regain cultivability by a process known as resuscitation. This is a protective mechanism adapted by bacteria to evade stressful environmental conditions. B. coagulans MTCC 5856(LactoSpore®) is a probiotic endospore which can survive for decades in hostile environments without dividing. In the present study, we explored the use of flow cytometry to enumerate the viable count of B. coagulans MTCC 5856 under acidic and alkaline conditions, high temperature and in commercial formulations like compressed tablets and capsules. Flow cytometry (FCM) was comparable to plate count method when the spores were counted at physiological conditions. We show that VBNC state is induced in B. coagulans MTCC 5856by high temperature and acidic pH. The cells get resuscitated under physiological conditions and FCM was sensitive to detect the VBNC spores. Flow cytometry showed excellent ability to assess the viable spore count in commercial probiotic formulations of B. coagulans MTCC 5856. The results establish Flow cytometry as a reliable method to count viable bacteria in commercial probiotic preparations. Sporulation as well as existence as VBNC could contribute to the extreme stability of B. coagulans MTCC 5856.

Flow cytometry: a versatile technology for specific quantification and viability assessment of micro-organisms in multistrain probiotic products

AIMS

Classical microbiology techniques are the gold standard for probiotic enumeration. However, these techniques are limited by parameters of time, specificity and incapacity to detect viable but nonculturable (VBNC) micro-organisms and nonviable cells. The aim of the study was to evaluate flow cytometry as a novel method for the specific quantification of viable and nonviable probiotics in multistrain products.

METHODS AND RESULTS

Custom polyclonal antibodies were produced against five probiotic strains from different species (Bifidobacterium bifidum R0071, Bifidobacterium longum ssp. infantis R0033, Bifidobacterium longum ssp. longum R0175, Lactobacillus helveticus R0052 and Lactobacillus rhamnosus R0011). Evaluation of specificity confirmed that all antibodies were specific at least at the subspecies level. A flow cytometry method combining specific antibodies and viability assessment with SYTO^® 24 and propidium iodide was applied to quantify these strains in three commercial products. Analyses were conducted on two flow cytometry instruments by two operators and compared with classical microbiology using selective media. Results indicated that flow cytometry provides higher cell counts than classical microbiology (P < 0·05) in 73% of cases highlighting the possible presence of VBNC. Equivalent performances (repeatability and reproducibility) were obtained for both methods.

CONCLUSIONS

This study showed that flow cytometry methods can be applied to probiotic enumeration and viability assessment. Combination with polyclonal antibodies can achieve sufficient specificity to differentiate closely related strains.

SIGNIFICANCE AND IMPACT OF THE STUDY

Flow cytometry provides absolute and specific quantification of viable and nonviable probiotic strains in a very short time (<2 h) compared with classical techniques (>48 h), bringing efficient tools for research and development and quality control.

Shear treatment of starter culture medium improves separation behavior of Streptococcus thermophilus cells

A central step in the production of starter cultures is the separation of the cells from the fermentation medium, which is usually achieved by disk centrifuges. In case of microorganisms which produce exopolysaccharides (e.g., various strains of lactic acid bacteria), the properties of the respective exopolysaccharides may interfere with this separation step. By using six strains of Streptococcus thermophilus the hypothesis was tested that a shear treatment of the fermented culture medium improves subsequent cell separation markedly. Depending on the type of exopolysaccharides (freely present in the medium, or as capsules around the cells) an energy input of up to 2.5 kJ/mL generated with an Ultra-Turrax affected cell chain length of the strains and viscosity of fermentation medium differently. For bacteria producing capsular exopolysaccharides, space- and time-resolved centrifugation experiments revealed an increase of sedimentation velocity after shear treatment. In general, viability of the microorganisms, detected by flow cytometry measurements and fermentation experiments, was not affected by the shearing procedure. The results therefore indicate that strain-targeted shearing is helpful to improve the separability of cells from the fermented media.

Flow cytometric characterization of bacterial abundance and physiological status in a nitrifying-denitrifying activated sludge system treating landfill leachate

Flow cytometry has recently been presented as a research tool in the assessment of the viability/activity of activated sludge from municipal wastewater treatment plants, but it has not put in practice for industrial biotreatments yet. In this study, for the first time ever, the reliability and significance of the multiparameter flow cytometry applied to the biological nitrification-denitrification treatment of leachate have been evaluated. Using a double staining procedure (cFDA/PI), the viable, damaged, and dead subpopulations were determined, and the results were compared to those obtained with conventional methods, such as nitrogen and oxygen uptake rates or plate counting. Flow cytometry showed that viable cells represented approximately 47% of the total population, whereas active cells accounted for 90%. For both sludge from nitrification and denitrification processes, with less than 1% of them being also culturable in plate. Either flow cytometry or uptake rates revealed that health status of sludge remained constant throughout the biotreatment, which is consistent with the high recirculation rates. Under anaerobic starvation conditions, physiological status of sludge remained constant as well as specific oxygen and denitrification rates. Nevertheless, both the culturability in plate and the nitrification rate significantly decreased. These findings proved that multiparameter flow cytometry is a useful tool for the assessment of the viability and activity of sludge from a nitrification-denitrification biotreatment process. These results gathered all the bacterial communities in the sludge, so the decay in minority populations, such as nitrifying bacteria, requires the use of a complementary technique to evaluate specific activities.

Physiological Responses of Salinity-Stressed Vibrio sp. and the Effect on the Biofilm Formation on a Nanofiltration Membrane

This study evaluated the effects of salinity on the physiological characteristics of Vibrio sp. B2 and biofilm formation on nanofiltration (NF) membrane coupons used in the high recovery seawater desalination process. The test conditions were at 0.6, 1.2, and 2.4 M sodium chloride (NaCl), equivalent to salinity of seawater, brine at 50% and 75% water recovery, respectively. High salinity inhibited the cell growth rate but increased the viability and bacterial membrane integrity. In addition, protein and eDNA concentrations of salinity-stressed bacteria were increased at 1.2 and 2.4 M NaCl. In particular, protein concentration was linearly correlated with the NaCl concentration. Similarly, less biofilm formation on the NF membrane coupon (without permeation flux) was observed by the salinity-stressed bacteria; however, the production of extracellular polymeric substances (EPS) was significantly increased as compared to control, and protein was an influential factor for biofilm formation. This study shows that salinity-stressed bacteria have a high potential to cause biofouling on membrane surface as the bacteria still maintain the cell activity and overproduce EPS. The potential of biofilm formation by the salinity-stressed bacteria has not been reported. Therefore, the findings are important to understand the mechanisms of membrane biofouling in a high salinity environment.

Changes of the Bacterial Abundance and Communities in Shallow Ice Cores from Dunde and Muztagata Glaciers, Western China

In this study, six bacterial community structures were analyzed from the Dunde ice core (9.5-m-long) using 16S rRNA gene cloning library technology. Compared to the Muztagata mountain ice core (37-m-long), the Dunde ice core has different dominant community structures, with five genus-related groups Blastococcus sp./Propionibacterium, Cryobacterium-related., Flavobacterium sp., Pedobacter sp., and Polaromas sp. that are frequently found in the six tested ice layers from 1990 to 2000. Live and total microbial density patterns were examined and related to the dynamics of physical-chemical parameters, mineral particle concentrations, and stable isotopic ratios in the precipitations collected from both Muztagata and Dunde ice cores. The Muztagata ice core revealed seasonal response patterns for both live and total cell density, with high cell density occurring in the warming spring and summer months indicated by the proxy value of the stable isotopic ratios. Seasonal analysis of live cell density for the Dunde ice core was not successful due to the limitations of sampling resolution. Both ice cores showed that the cell density peaks were frequently associated with high concentrations of particles. A comparison of microbial communities in the Dunde and Muztagata glaciers showed that similar taxonomic members exist in the related ice cores, but the composition of the prevalent genus-related groups is largely different between the two geographically different glaciers. This indicates that the micro-biogeography associated with geographic differences was mainly influenced by a few dominant taxonomic groups.

Application of flow cytometry to wine microorganisms

Flow cytometry (FCM) is a powerful technique allowing detection and enumeration of microbial populations in food and during food process. Thanks to the fluorescent dyes used and specific probes, FCM provides information about cell physiological state and allows enumeration of a microorganism in a mixed culture. Thus, this technique is increasingly used to quantify pathogen, spoilage microorganisms and microorganisms of interest. Since one decade, FCM applications to the wine field increase greatly to determine population and physiological state of microorganisms performing alcoholic and malolactic fermentations. Wine spoilage microorganisms were also studied. In this review we briefly describe FCM principles. Next, a deep revision concerning enumeration of wine microorganisms by FCM is presented including the fluorescent dyes used and techniques allowing a yeast and bacteria species specific enumeration. Then, the last chapter is dedicated to fluorescent dyes which are used to date in fluorescent microscopy but applicable in FCM. This chapter also describes other interesting "future" techniques which could be applied to study the wine microorganisms. Thus, this review seeks to highlight the main advantages of the flow cytometry applied to wine microbiology.