Specific detection of Pseudomonas spp. in milk by fluorescence in situ hybridization using ribosomal RNA directed probes

The multidrug-resistant Pseudomonas fluorescens strain: a hidden threat in boar semen preservation

Although the bacterial composition of boar ejaculate has been extensively studied, the bacterial composition of extended boar semen is often overlooked, despite the potential risks these microorganisms may pose to the long-term preservation of extended boar semen at 15-17°C. In this study, we characterized the bacterial community composition of extended semen and discovered that Pseudomonas spp. was the dominant flora. The dominant strains were further isolated and identified as a potential new species in the Pseudomonas fluorescens group and named GXZC strain, which had adverse effects on sperm quality and was better adapted to growth at 17°C. Antimicrobial susceptibility testing showed that the GXZC strain was resistant to all commonly used veterinary antibiotics. Whole-genome sequencing (WGS) and genome annotation revealed the large genetic structure and function [7,253,751 base pairs and 6,790 coding sequences (CDSs)]. Comparative genomic analysis with the closest type strains showed that the GXZC strain predicted more diversity of intrinsic and acquired resistance genes to multi-antimicrobial agents. Taken together, our study highlights a problem associated with the long-term storage of extended boar semen caused by a P. fluorescens group strain with unique biological characteristics. It is essential to develop a new antibacterial solution for the long-term preservation of boar semen.

Application of flow cytometry for rapid bacterial enumeration and cells physiological state detection to predict acidification capacity of natural whey starters

Natural whey starter cultures are undefined microbial communities mainly consisting of thermophilic lactic acid bacteria (LAB). The technological pressure that shapes the natural whey starter community before and during the back-slopping procedure can impact the amount and viability of the different thermophilic LAB. Traditional culture-dependent analytical methods are useful for evaluating natural whey cultures based on plate enumeration with various culture media and are commonly used as self-control procedures in dairy items. These methods have high variability and require days to obtain results. As the dairy industry has been searching for a solution to this problem for a long time, researchers must explore alternative methods for the technological evaluation of natural whey and assessment of the health status of the thermophilic acidifying bacteria community in the cheesemaking process. The flow cytometry approach has been considered an alternative to classical methods in this work sector. This study compared bacterial enumeration by plate counting and flow cytometry on natural whey samples. Flow cytometry results showed positive agreement with a tendency to overestimate, linearity, and correlation with plate counting. Other parameters have also been introduced for evaluating a natural whey starter, measuring the physiological state of the cells. Specifically, cell-wall damage and metabolic activity were also evaluated, allowing us to quantify the number of cells even in sub-optimal physiological conditions.

Toehold switch based biosensors for sensing the highly trafficked rosewood Dalbergia maritima

Nucleic acid sensing is a 3 decades old but still challenging area of application for different biological sub-domains, from pathogen detection to single cell transcriptomics analysis. The many applications of nucleic acid detection and identification are mostly carried out by PCR techniques, sequencing, and their derivatives used at large scale. However, these methods’ limitations on speed, cost, complexity and specificity have motivated the development of innovative detection methods among which nucleic acid biosensing technologies seem promising. Toehold switches are a particular class of RNA sensing devices relying on a conformational switch of secondary structure induced by the pairing of the detected trigger RNA with a de novo designed synthetic sensing mRNA molecule. Here we describe a streamlined methodology enabling the development of such a sensor for the RNA-mediated detection of an endangered plant species in a cell-free reaction system. We applied this methodology to help identify the rosewood Dalbergia maritima, a highly trafficked wood, whose protection is limited by the capacity of the authorities to distinguish protected logs from other unprotected but related species. The streamlined pipeline presented in this work is a versatile framework enabling cheap and rapid development of new sensors for custom RNA detection.

Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review

As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.

Flow-FISH as a Tool for Studying Bacteria, Fungi and Viruses

Many techniques are currently in use to study microbes. These can be aimed at detecting, identifying, and characterizing bacterial, fungal, and viral species. One technique that is suitable for high-throughput analysis is flow cytometry-based fluorescence in situ hybridization, or Flow-FISH. This technique employs (fluorescently labeled) probes directed against DNA or (m)RNA, for instance targeting a gene or microorganism of interest and provides information on a single-cell level. Furthermore, by combining Flow-FISH with antibody-based protein detection, proteins of interest can be measured simultaneously with genetic material. Additionally, depending on the type of Flow-FISH assay, Flow-FISH can also be multiplexed, allowing for the simultaneous measurement of multiple gene targets and/or microorganisms. Together, this allows for, e.g., single-cell gene expression analysis or identification of (sub)strains in mixed cultures. Flow-FISH has been used in mammalian cells but has also been extensively employed to study diverse microbial species. Here, the use of Flow-FISH for studying microorganisms is reviewed. Specifically, the detection of (intracellular) pathogens, studying microorganism biology and disease pathogenesis, and identification of bacterial, fungal, and viral strains in mixed cultures is discussed, with a particular focus on the viruses EBV, HIV-1, and SARS-CoV-2.

A Milk Foodomics Investigation into the Effect of Pseudomonas fluorescens Growth under Cold Chain Conditions

Pseudomonas fluorescens is a psychrotrophic species associated with milk spoilage because of its lipolytic and proteolytic activities. Consequently, monitoring P. fluorescens or its antecedent activity in milk is critical to preventing quality defects of the product and minimizing food waste. Therefore, in this study, untargeted metabolomics and peptidomics were used to identify the changes in milk related to P. fluorescens activity by simulating the low-temperature conditions usually found in milk during the cold chain. Both unsupervised and supervised multivariate statistical approaches showed a clear effect caused by the P. fluorescens inoculation on milk samples. Our results showed that the levels of phosphatidylglycerophosphates and glycerophospholipids were directly related to the level of contamination. In addition, our metabolomic approach allowed us to detect lipid and protein degradation products that were directly correlated with the degradative metabolism of P. fluorescens. Peptidomics corroborated the proteolytic propensity of P. fluorescens-contaminated milk, but with lower sensitivity. The results obtained from this study provide insights into the alterations related to P. fluorescens 39 contamination, both pre and post heat treatment. This approach could represent a potential tool to retrospectively understand the actual quality of milk under cold chain storage conditions, either before or after heat treatments.

Microbiota Associated with Different Developmental Stages of the Dry Rot Fungus Serpula lacrymans

The dry rot fungus Serpula lacrymans causes significant structural damage by decaying construction timber, resulting in costly restoration procedures. Dry rot fungi decompose cellulose and hemicellulose and are often accompanied by a succession of bacteria and other fungi. Bacterial-fungal interactions (BFI) have a considerable impact on all the partners, ranging from antagonistic to beneficial relationships. Using a cultivation-based approach, we show that S. lacrymans has many co-existing, mainly Gram-positive, bacteria and demonstrate differences in the communities associated with distinct fungal parts. Bacteria isolated from the fruiting bodies and mycelia were dominated by Firmicutes, while bacteria isolated from rhizomorphs were dominated by Proteobacteria. Actinobacteria and Bacteroidetes were less abundant. Fluorescence in situ hybridization (FISH) analysis revealed that bacteria were not present biofilm-like, but occurred as independent cells scattered across and within tissues, sometimes also attached to fungal spores. In co-culture, some bacterial isolates caused growth inhibition of S. lacrymans, and vice versa, and some induced fungal pigment production. It was found that 25% of the isolates could degrade pectin, 43% xylan, 17% carboxymethylcellulose, and 66% were able to depolymerize starch. Our results provide first insights for a better understanding of the holobiont S. lacrymans and give hints that bacteria influence the behavior of S. lacrymans in culture.

Pseudomonas spp.: Are Food Grade Organic Acids Efficient against These Spoilage Microorganisms in Fresh Cheeses?

Psychrotolerant Pseudomonas spp. are among the most common spoilage agents in fresh, soft and semi-soft cheeses; therefore, hurdles inhibiting their growth are in strong demand by producers. This study aimed to establish Minimal Inhibiting Concentrations (MICs) of lactic and acetic acid towards P. fluorescens and to evaluate the efficacy of a cheese surface treatment with these two organic acids. MICs were determined in Brain Heart Infusion broth at 30 °C: the inhibition was achieved at a concentration of 49.96 mM and 44.40 mM of acetic and lactic acid, respectively. Two series of inhibition tests were performed on fresh “Primo sale” cheese, inoculated with P. brenneri MGM3, then dipped into different acid solutions (acetic acid: 49.96, 99.92 and 149.88 mM; lactic acid: 44.40, 88.80 and 133.20 mM) and stored at 6 °C. P. brenneri MGM3 were enumerated, including a control series. A significantly lower growth was revealed at the highest concentrations tested, both for acetic (p < 0.01) and lactic acid (p < 0.05) if compared to control samples. A conditioning of “Primo sale” surface with organic acid solutions could be a useful hurdle for Pseudomonas inhibition and shelf-life extension; it should be applied in combination with other mild interventions to fight spoilage and maintain the original product characteristics.

Identification and Visualization of a Distinct Microbiome in Ocular Surface Conjunctival Tissue

Purpose

Knowledge of whether microorganisms reside in protected niches of the conjunctiva is potentially significant in terms of minimizing risks of contact lens inflammation/infection and endophthalmitis. We define if and how microbial communities from limbal and forniceal conjunctival tissue differ from those on the conjunctival surface.

Methods

Human limbal and forniceal conjunctival tissue was obtained from 23 patients undergoing pterygium surgery and analyzed with data from a recent study of conjunctival surface swabs (n = 45). Microbial communities were analyzed by extracting total DNA from tissue samples and surface swabs and sequencing the 16S rRNA gene using the Illumina MiSeq platform. Sequences were quality filtered, clustered into operational taxonomic units (OTUs) at 97% similarity. OTUs associated with blank extraction and sampling negative controls were removed before analysis. Fluorescent in situ hybridization (FISH) was performed on cyrosections of limbal and forniceal conjunctival tissue.

Results

There was a significant difference in bacterial community structure between the conjunctival surface and fornix (P = 0.001) and limbus (P = 0.001) tissue. No difference was found in bacterial communities between the limbus and fornix (P = 0.764). Fornix and limbal samples were dominated by OTUs classified to the genus Pseudomonas (relative abundance 79.9%), which were found only in low relative abundances on conjunctival surfaces (6.3%). Application of FISH showed the presence of Pseudomonas in the forniceal tissue sample.

Conclusions

There is a discrete tissue-associated microbiome in freshly-collected human limbal and fornix tissue, which is different from the microbial community structure and composition of the ocular surface microbiome.

Apportioning bacterial carbon source utilization in soil using 14 C isotope analysis of FISH-targeted bacterial populations sorted by fluorescence activated cell sorting (FACS): 14 C-FISH-FACS

An unresolved need in microbial ecology is methodology to enable quantitative analysis of in situ microbial substrate carbon use at the population level. Here, we evaluated if a novel combination of radiocarbon-labelled substrate tracing, fluorescence in situ hybridisation (FISH) and fluorescence-activated cell sorting (FACS) to sort the FISH-targeted population for quantification of incorporated radioactivity (¹⁴ C-FISH-FACS) can address this need. Our test scenario used FISH probe PSE1284 targeting Pseudomonas spp. (and some Burkholderia spp.) and salicylic acid added to rhizosphere soil. We examined salicylic acid-¹⁴ C fate (mineralized, cell-incorporated, extractable and non-extractable) and mass balance (0-24 h) and show that the PSE1284 population captured ∼ 50% of the Nycodenz extracted biomass ¹⁴ C. Analysis of the taxonomic distribution of the salicylic acid biodegradation trait suggested that PSE1284 population success was not due to conservation of this trait but due to competitiveness for the added carbon. Adding 50KBq of ¹⁴ C sample^-1 enabled detection of ¹⁴ C in the sorted population at ∼ 60-600 times background; a sensitivity which demonstrates potential extension to analysis of rarer/less active populations. Given its sensitivity and compatibility with obtaining a C mass balance, ¹⁴ C-FISH-FACS allows quantitative dissection of C flow within the microbial biomass that has hitherto not been achieved.

Identification of pathogens in mastitis milk samples with fluorescent in situ hybridization

Traditionally, the bacteriological examination of mastitis milk samples is performed by culture followed by biochemical tests on the cultured bacteria to allow identification of the causative pathogen. Depending on the species involved, this classic identification is time-consuming compared to other techniques such as fluorescent in situ hybridization (FISH), a culture-independent method that utilizes oligonucleotides (labeled with a fluorophore) that are specific to a string of target DNA/RNA. In the current study, the applicability of FISH was evaluated for the detection of mastitis pathogens directly in milk samples. To remove interfering lipids and proteins from mastitis milk samples prior to FISH, a previously published enzymatic treatment with savinase was evaluated. FISH was performed using oligonucleotides specific for Staphylococcus aureus, Streptococcus agalactiae, Streptococcus uberis, Enterococcus faecalis, Enterococcus faecium, Escherichia coli, and Trueperella (Arcanobacterium) pyogenes. The enzymatic pretreatment and the sensitivity of FISH were evaluated using spiked whole milk samples and mastitis milk samples with bacterial loads of less than 10(3) up to 10(8) colony-forming units (CFU)/ml. Bacteria were reliably detected in milk samples with bacterial numbers of 10(6) CFU/ml or higher. However, bacteria present in numbers below 10(6) CFU/ml were not detectable in all cases. The ability of FISH to identify mastitis-causing pathogens directly in milk samples, and therefore earlier than classical culture methods, can supplement the classic diagnostic procedures for mastitis milk samples.

No seasonal effect on culturable pseudomonads in fresh milks from cattle herds

Freshly drawn raw milk from 37 single herds on farms manufacturing raw cow cheese under the Protected Designation of Origin (PDO) label were sampled over 13 mo for pseudomonad counts. Coliforms, somatic cells, and coagulase-positive staphylococci were counted and total fat and protein contents measured. For pseudomonad counts, the overall mean value was 3.60×10(3) cfu/mL. We observed very high variation between different producers and within the same producers (average standard deviation 1.30×10(4) cfu/mL), but we did not detect a seasonal effect. The only statistical correlation with other milk quality parameters was with coliforms. A survey of milking practices and milking machine sanitation together with environmental and milk sampling for pseudomonad counts in 7 cheese workshops showed that no real negligence or error could be imputed to producers. The main problems were the presence of non-aeruginosa pseudomonads in potable water and a few isolated failures during the cleaning and rinsing phases of sanitation.

Pseudomonas fluorescens induces strain-dependent and strain-independent host plant responses in defense networks, primary metabolism, photosynthesis, and fitness

Colonization of plants by nonpathogenic Pseudomonas fluorescens strains can confer enhanced defense capacity against a broad spectrum of pathogens. Few studies, however, have linked defense pathway regulation to primary metabolism and physiology. In this study, physiological data, metabolites, and transcript profiles are integrated to elucidate how molecular networks initiated at the root-microbe interface influence shoot metabolism and whole-plant performance. Experiments with Arabidopsis thaliana were performed using the newly identified P. fluorescens GM30 or P. fluorescens Pf-5 strains. Co-expression networks indicated that Pf-5 and GM30 induced a subnetwork specific to roots enriched for genes participating in RNA regulation, protein degradation, and hormonal metabolism. In contrast, only GM30 induced a subnetwork enriched for calcium signaling, sugar and nutrient signaling, and auxin metabolism, suggesting strain dependence in network architecture. In addition, one subnetwork present in shoots was enriched for genes in secondary metabolism, photosynthetic light reactions, and hormone metabolism. Metabolite analysis indicated that this network initiated changes in carbohydrate and amino acid metabolism. Consistent with this, we observed strain-specific responses in tryptophan and phenylalanine abundance. Both strains reduced host plant carbon gain and fitness, yet provided a clear fitness benefit when plants were challenged with the pathogen P. syringae DC3000.

Denitrification likely catalyzed by endobionts in an allogromiid foraminifer

Nitrogen can be a limiting macronutrient for carbon uptake by the marine biosphere. The process of denitrification (conversion of nitrate to gaseous compounds, including N(2) (nitrogen gas)) removes bioavailable nitrogen, particularly in marine sediments, making it a key factor in the marine nitrogen budget. Benthic foraminifera reportedly perform complete denitrification, a process previously considered nearly exclusively performed by bacteria and archaea. If the ability to denitrify is widespread among these diverse and abundant protists, a paradigm shift is required for biogeochemistry and marine microbial ecology. However, to date, the mechanisms of foraminiferal denitrification are unclear, and it is possible that the ability to perform complete denitrification is because of the symbiont metabolism in some foraminiferal species. Using sequence analysis and GeneFISH, we show that for a symbiont-bearing foraminifer, the potential for denitrification resides in the endobionts. Results also identify the endobionts as denitrifying pseudomonads and show that the allogromiid accumulates nitrate intracellularly, presumably for use in denitrification. Endobionts have been observed within many foraminiferal species, and in the case of associations with denitrifying bacteria, may provide fitness for survival in anoxic conditions. These associations may have been a driving force for early foraminiferal diversification, which is thought to have occurred in the Neoproterozoic era when anoxia was widespread.

Detection of Helicobacter pylori in raw bovine milk by fluorescence in situ hybridization (FISH)

The transmission pathways of Helicobacter pylori in humans have not been fully elucidated. Research in the last decade has proposed that foodborne transmission, among others, may be a plausible route of human infection. Owing to the organism's fastidious growth characteristics and its ability to convert to viable, yet unculturable states upon exposure to stress conditions, the detection of H. pylori in foods via culture-dependent methods has been proven to be laborious, difficult and in most cases unsuccessful. Hence, nucleic acid-based methods have been proposed as alternative methods but, to date, only PCR-based methods have been reported in the literature. In the current study, fluorescence in situ hybridization (FISH) was used for the detection of H. pylori in raw, bulk-tank bovine milk. After repeated milk centrifugation and washing steps, the bacterial flora of raw milk was subjected to fixation and permeabilization and H. pylori detection was conducted by FISH after hybridization with an H. pylori-specific 16S rRNA-directed fluorescent oligonucleotide probe. Using this protocol, H. pylori was detected in four out of the twenty (20%) raw milk samples examined. The data presented in this manuscript indicate that FISH can serve as an alternative molecular method for screening raw bovine milk for the presence of H. pylori.

DNA signature-based approaches for bacterial detection and identification

During the late eighties, environmental microbiologists realized the potential of the polymerase chain reaction (PCR) for the design of innovative approaches to study microbial communities or to detect and identify microorganisms in diverse and complex environments. In contrast to long-established methods of cultivation-based microbial identification, PCR-based techniques allow for the identification of microorganisms regardless of their culturability. A large number of reports have been published that describe PCR-inspired methods, frequently complemented by sequencing or hybridization profiling, to infer taxonomic and clonal microbial diversity or to detect and identify microorganisms using taxa-specific genomic markers. Typing methods have been particularly useful for microbial ecology-driven studies; however, they are not suitable for diagnostic purposes, such as the detection of specific species, strains or clones. Recently, comprehensive reviews have been written describing the panoply of typing methods available and describing their advantages and limitations; however, molecular approaches for bacterial detection and identification were either not considered or only vaguely discussed. This review focuses on DNA-based methods for bacterial detection and identification, highlighting strategies for selecting taxa-specific loci and emphasizing the molecular techniques and emerging technological solutions for increasing the detection specificity and sensitivity. The massive and increasing number of available bacterial sequences in databases, together with already employed bioinformatics tools, hold promise of more reliable, fast and cost-effective methods for bacterial identification in a wide range of samples in coming years. This tendency will foster the validation and certification of these methods and their routine implementation by certified diagnostic laboratories.

Composition of bacterial communities associated with natural and laboratory populations of Asobara tabida infected with Wolbachia

Asobara tabida wasps are fly endoparasitoids that naturally harbor three Wolbachia strains, which induce cytoplasmic incompatibility and control oogenesis. To investigate whether other bacteria play a role in wasp biology, we surveyed the bacterial communities of wild A. tabida populations originating from different regions of France and of laboratory colonies using PCR-denaturing gradient gel electrophoresis and culture methods. Proteobacteria and Firmicutes were found to be the main phyla represented in these populations. Among these were several cultured and uncultured representatives of the genera Acetobacter, Acidomonas, Bacillus, Brevibacillus, Duganella, Herbaspirillum, Pseudomonas, Staphylococcus, and Streptococcus. In addition to Wolbachia, wild individuals harbored Rickettsia, which tended to be lost when insects were reared in the laboratory. The antibiotic treatment used to generate wasp sublines singly infected with Wolbachia also affected the overall bacterial composition, with most fingerprint sequences being characteristic of the family Enterobacteriaceae. We also screened for potentially heritable endosymbionts by PCR and fluorescence in situ hybridization in stable laboratory lines, with only Wolbachia being consistently found in wasp ovaries.

Peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) assay for specific detection of Mycobacterium immunogenum and DNA-FISH assay for analysis of pseudomonads in metalworking fluids and sputum

Specific and rapid detection and quantification of mycobacteria in contaminated metalworking fluid (MWF) are problematic due to complexity of the matrix and heavy background co-occurring microflora. Furthermore, cross-reactivity among neighboring species of Mycobacterium makes species differentiation difficult for this genus. Here, we report for the first time a species-specific peptide nucleic acid-fluorescence in situ hybridization (PNA-FISH) method for Mycobacterium immunogenum, a non-tuberculous Mycobacterium species prevalent in MWF and implicated in occupational lung disease hypersensitivity pneumonitis and pseudo-outbreaks. A novel species-specific 14-bp PNA probe was designed for M. immunogenum based on its 16S rRNA gene sequence and was validated for specificity, by testing against a panel of other phylogenetically closely related rapidly growing mycobacteria and representative species of gram-positive, gram-negative, and acid fast organisms. In addition, a DNA-FISH protocol was optimized for co-detection of Pseudomonas, the most predominantly co-occurring genus in contaminated MWF. Reliable quantification for both the test organisms was achieved at or above a cell density of 10(3)cellsml(-1), a recognized minimum limit for microscopic quantification. The mycobacterial PNA-FISH assay was successfully adapted to human sputum demonstrating its potential for clinical diagnostic applications in addition to industrial MWF monitoring, to assess MWF-associated exposures and pseudo-outbreaks.

Microbial populations analysis and field application of biofilter for the removal of volatile-sulfur compounds from swine wastewater treatment system

A biofilter packed with granular activated carbon (GAC) was applied to eliminate volatile-sulfur compounds (VSC) emitted from solid-liquid separation tank in swine wastewater treatment system. Hydrogen sulfide, methanethiol, dimethyl disulfide, and dimethyl sulfide were effectively reduced to 96-100% at gas residence times of 13-30s. Elemental sulfur and sulfate are their primary oxidation metabolites. Regarding odor, an average of 86% reduction was achieved at short residence time (13s). In addition, bioaerosol emissions could also be effectively reduced by 90% with the biofilter. Advantages of the system include low moisture demand, low pressure drop, and high biofilm stability. Further characterization of bacterial populations of the activated carbon samples using the fluorescent in situ hybridization (FISH) technique revealed that Pseudomonas sp. remained the predominant community (56-70%) after long-term evaluation of 415 days.

Culturable psychrotrophic bacterial communities in raw milk and their proteolytic and lipolytic traits

During cold storage after milk collection, psychrotrophic bacterial populations dominate the microflora, and their extracellular enzymes, mainly proteases and lipases, contribute to the spoilage of dairy products. The diversity, dynamics, and enzymatic traits of culturable psychrotrophs in raw milk from four farms were investigated over a 10-month period. About 20% of the isolates were found to be novel species, indicating that there is still much to be learned about culturable psychrotrophs in raw milk. The psychrotrophic isolates were identified and classified in seven classes. Three classes were predominant, with high species richness (18 to 21 species per class) in different seasons of the year: Gammaproteobacteria in spring and winter, Bacilli in summer, and Actinobacteria in autumn. The four minor classes were Alphaproteobacteria, Betaproteobacteria, Flavobacteria, and Sphingobacteria. The dominant classes were found in all four dairies, although every dairy had its own unique "bacterial profile." Most but not all bacterial isolates had either lipolytic or both lipolytic and proteolytic activities. Only a few isolates showed proteolytic activity alone. The dominant genera, Pseudomonas and Acinetobacter (Gammaproteobacteria), showed mainly lipolytic activity, Microbacterium (Actinobacteria) was highly lipolytic and proteolytic, and the lactic acid bacteria (Lactococcus and Leuconostoc) displayed very minor enzymatic ability. Hence, the composition of psychrotrophic bacterial flora in raw milk has an important role in the determination of milk quality. Monitoring the dominant psychrotrophic species responsible for the production of heat-stable proteolytic and lipolytic enzymes offers a sensitive and efficient tool for maintaining better milk quality in the milk industry.

Quantification ofLeuconostocpopulations in mixed dairy starter cultures using fluorescencein situhybridization

AIMS

Development of a rapid method to identify and quantify Leuconostoc populations in mesophilic starter cultures.

METHODS AND RESULTS

16S rRNA-targeted oligonucleotide probes were used in a whole cell in situ hybridization assay for the identification of the genus Leuconostoc and an undescribed Leuconostoc ribospecies. The probes were fluorescently labelled and used to quantify the Leuconostoc populations in five different mixed starter cultures.

CONCLUSIONS

There was a good correlation between the results obtained using fluorescence in situ hybridization (FISH) with that of standard plate counting methods.

SIGNIFICANCE AND IMPACT OF THE STUDY

To develop a FISH method capable of identifying and quantifying the Leuconostoc population in starter cultures within 1 day.

Simple detection of small amounts of Pseudomonas cells in milk by using a microfluidic device

AIMS

Flow cytometry offers rapid and reliable analyses of bacteria in milk. However, a flow cytometer is relatively expensive and operation is rather complicated for an unskilled operator. We applied flow cytometry using a microfluidic device (on-chip flow cytometry) in detection of small amounts of milk-spoiling bacteria.

METHODS AND RESULTS

Pseudomonas cells in milk were in situ hybridized with Cy5-labelled probe specific for Pseudomonas spp. under optimized condition. Numbers of Pseudomonas cells in the stationary phase and in the starved state determined by on-chip flow cytometry were compared with those determined by conventional plate counting, and on-chip flow cytometry detected targeted cells in milk that were undetectable as colony forming units(CFU) on Standards Methods Agar.

CONCLUSIONS

The contamination in milk with fewer than 10 CFU ml(-1) of targeted cells in starved state was detectable with simple procedure (0.5 h milk-clearing, 1 h fixation, 2 h hybridization and 0.5 h on-chip flow cytometry following 12 h enrichment of cells).

SIGNIFICANCE AND IMPACT OF THE STUDY

On-chip flow cytometry following fluorescence in situ hybridization could be applicable to simple detection of milk-spoiling bacteria.

Application of FISH technology for microbiological analysis: current state and prospects

In order to identify and quantify the microorganisms present in a certain ecosystem, it has become necessary to develop molecular methods avoiding cultivation, which allows to characterize only the countable part of the microorganisms in the sample, therefore losing the information related to the microbial component which presents a vitality condition, although it cannot duplicate in culture medium. In this context, one of the most used techniques is fluorescence in situ hybridization (FISH) with ribosomal RNA targeted oligonucleotide probes. Owing to its speed and sensitivity, this technique is considered a powerful tool for phylogenetic, ecological, diagnostic and environmental studies in microbiology. Through the use of species-specific probes, it is possible to identify different microorganisms in complex microbial communities, thus providing a solid support to the understanding of inter-species interaction. The knowledge of the composition and distribution of microorganisms in natural habitats can be interesting for ecological reasons in microbial ecology, and for safety and technological aspects in food microbiology. Methodological aspects, use of different probes and applications of FISH to microbial ecosystems are presented in this review.

Biofilm formation and biocides sensitivity of Pseudomonas marginalis isolated from a maple sap collection system

The susceptibility of planktonic and biofilm cells of Pseudomonas marginalis toward four commonly used biocides at different temperatures (15 and 30 degrees C) and biofilm growth times (24 and 48 h) was assessed. Using the MBEC biofilm device, biofilm production in maple sap was shown to be highly reproducible for each set of conditions tested. Biofilm formation was influenced by growth temperature and time. A temperature of 15 degrees C and incubation time of 24 h yielded fewer CFU per peg and showed fewer adhered cells and typical biofilm structures, based on scanning electron microscopy observations as compared with other conditions. Minimal biofilm eradication concentration values for P. marginalis were significantly greater (P. < 0.001) than were MBCs for planktonic cells and for every biocide tested, with the exception of minimal biofilm eradication concentration values for peracetic acid at 15 degrees C and 24 h. Sodium hypochlorite and peracetic acid sanitizers were able to eliminate P. marginalis biofilms at lower concentrations as compared with hydrogen peroxide- and quaternary ammonium-based sanitizers (P < 0.001). According to the results obtained, sodium hypochlorite and peracetic acid sanitizers would be more appropriate for maple sap collection system sanitation.

Simultaneous enumeration of viable Enterobacteriaceae and Pseudomonas spp. within three hours by multicolor fluorescence in situ hybridization with vital staining

A new means of rapidly and simultaneously counting viable phylogenetically different bacteria was developed. The cyanine dimer dye, BOBO-3 that selectively stains bacteria with damaged membranes were used to evaluate bacterial viability based on membrane integrity. Viable Enterobacteriaceae and Pseudomonas spp. could be selectively detected within three hours using multicolor fluorescence in situ hybridization (FISH) following BOBO-3 staining (BOBO3-FISH).

Numbers and locations of native bacteria on field-grown wheat roots quantified by fluorescence in situ hybridization (FISH)

Native bacteria, Pseudomonas and filamentous bacteria were quantified and localized on wheat roots grown in the field using fluorescence in situ hybridization (FISH). Seminal roots were sampled through the season from unploughed soil in a conservation farming system. Such soils are spatially heterogeneous, and many roots grow slowly through hard soil with cracks and pores containing dead roots remnant from previous crops. Root and rhizosphere morphology, and contact with soil particles were preserved, and autofluorescence was avoided by observing sections in the far-red with Cy5 and Cy5.5 fluorochromes. Spatial analyses showed that bacteria were embedded in a stable matrix (biofilm) within 11 microm of the root surface (range 2-30 microm) and were clustered on 40% of roots. Half the clusters co-located with axial grooves between epidermal cells, soil particles, cap cells or root hairs; the other half were not associated with visible features. Across all wheat roots, although variable, bacteria averaged 15.4 x 10(5) cells per mm(3) rhizosphere, and of these, Pseudomonas and filaments comprised 10% and 4%, respectively, with minor effects of sample time, and no effect of plant age. Root caps were most heavily colonized by bacteria along roots, and elongation zones least heavily colonized. Pseudomonas varied little with root development and were 17% of bacteria on the elongation zone. Filamentous bacteria were not found on the elongation zone. The most significant factor to rhizosphere populations along a wheat root, however, was contact with dead root remnants, where Pseudomonas were reduced but filaments increased to 57% of bacteria (P < 0.001). This corresponded with analyses of root remnants showing they were heavily colonized by bacteria, with 48% filaments (P < 0.001) and 1.4%Pseudomonas (P = 0.014). Efforts to manage rhizosphere bacteria for sustainable agricultural systems should continue to focus on root cap and mucilage chemistry, and remnant roots as sources of beneficial bacteria.

Enumeration of respiring Pseudomonas spp. in milk within 6 hours by fluorescence in situ hybridization following formazan reduction

Respiring Pseudomonas spp. in milk were quantified within 6 h by fluorescence in situ hybridization (FISH) with vital staining. FISH with an oligonucleotide probe based on 16S rRNA sequences was used for the specific detection of Pseudomonas spp. at the single cell level. 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) was used to estimate bacterial respiratory activity. The numbers of respiring Pseudomonas cells as determined by FISH with CTC staining (CTC-FISH) were almost the same or higher than the numbers of CFU as determined by the conventional culture method.

A flow cytometric technique for quantification and differentiation of bacteria in bulk tank milk

AIMS

The present study describes a flow cytometric technique for quantification and differentiation of bacteria in bulk tank milk according to the main cause of elevated counts.

METHODS AND RESULTS

A total of 75 Danish bulk tank milk samples exceeding the grading level of 3.0 x 10(4) CFU ml(-1) were examined by both flow cytometry and traditional microbiological analyses. The correlation coefficient (r) between the two methods was 0.71. For the differential analyses of the dominant bacterial populations four different parameters were used to give a species-characteristic pattern. The four parameters were as follows: staining with Oregon Green conjugated wheat germ agglutinin that binds to the cell wall of bacteria, staining with hexidium iodide that binds to all bacterial DNA, the flow cytometric forward scatter and the flow cytometric side scatter. Three regions in the flow cytometric plot were defined: region 1 includes bacteria mainly associated with poor hygiene, region 2 includes psychrotrophic hygiene bacteria and region 3 includes bacteria mainly related to mastitis. The ability of the flow cytometric technique to predict the main cause of elevated bacterial counts on routine samples was examined. Comparing these results with results obtained by traditional microbiological analyses for identification showed that for 81% of the samples the two techniques agreed on the main cause of an elevated bacterial count.

CONCLUSIONS

The ability of the presented flow cytometric technique to enumerate and differentiate bacteria in bulk tank milk according to the main cause of elevated counts was demonstrated.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study described the first step in development of a technique suitable for routine analyses of bulk tank milk samples. A technique indicating the main cause of an elevated count will enable the farmer to eliminate the contamination source within a short time limit.

Alteration of raw-milk cheese by Pseudomonas spp.: monitoring the sources of contamination using fluorescence spectroscopy and metabolic profiling

Thirty Pseudomonas spp. strains isolated from milk, water, cheese centre and cheese surface in two traditional workshops manufacturing raw milk St. Nectaire cheese were characterised by fluorescence spectroscopy and Biolog metabolic profiling. Factorial discriminant analysis (FDA) of the two data sets revealed clear linkages between groups of isolates. In the first workshop, milk could be incriminated as the sole source of cheese contamination. In the second one, milk and cheese centre isolates were found similar but surface cheese contaminants could be linked to a secondary contamination originating from water. Thus, it is possible to characterise, differentiate and trace Pseudomonas spp. strains using the fluorescence and metabolic profiling techniques. In addition, the two data sets were found highly correlated by canonical correlation analysis (CCA). Fluorescence spectroscopy however showed several advantages because of its low cost and processing speed.