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Butterworth SJ, Barton F, Lloyd JR. Extremophilic microbial metabolism and radioactive waste disposal. Extremophiles 2023; 27:27. [PMID: 37839067 PMCID: PMC10577106 DOI: 10.1007/s00792-023-01312-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 09/12/2023] [Indexed: 10/17/2023]
Abstract
Decades of nuclear activities have left a legacy of hazardous radioactive waste, which must be isolated from the biosphere for over 100,000 years. The preferred option for safe waste disposal is a deep subsurface geological disposal facility (GDF). Due to the very long geological timescales required, and the complexity of materials to be disposed of (including a wide range of nutrients and electron donors/acceptors) microbial activity will likely play a pivotal role in the safe operation of these mega-facilities. A GDF environment provides many metabolic challenges to microbes that may inhabit the facility, including high temperature, pressure, radiation, alkalinity, and salinity, depending on the specific disposal concept employed. However, as our understanding of the boundaries of life is continuously challenged and expanded by the discovery of novel extremophiles in Earth's most inhospitable environments, it is becoming clear that microorganisms must be considered in GDF safety cases to ensure accurate predictions of long-term performance. This review explores extremophilic adaptations and how this knowledge can be applied to challenge our current assumptions on microbial activity in GDF environments. We conclude that regardless of concept, a GDF will consist of multiple extremes and it is of high importance to understand the limits of polyextremophiles under realistic environmental conditions.
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Affiliation(s)
- Sarah Jane Butterworth
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK
| | - Franky Barton
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
| | - Jonathan Richard Lloyd
- Department of Earth and Environmental Sciences, Research Centre for Radwaste Disposal and Williamson Research Centre, The University of Manchester, Manchester, UK.
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2
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Pavić D, Grbin D, Blagajac A, Ćurko J, Fiket Ž, Bielen A. Impact of nutrients and trace elements on freshwater microbial communities in Croatia: identifying bacterial bioindicator taxa. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-28179-4. [PMID: 37328727 DOI: 10.1007/s11356-023-28179-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/05/2023] [Indexed: 06/18/2023]
Abstract
Since aquatic microbial communities promptly respond to environmental changes, it is now evident that they can complement traditional taxa such as fish, macroinvertebrates and algae as bioindicators of water quality. The aim of this study was to correlate the physico-chemical parameters of water with the microbial community structure and the occurrence of putative bioindicator taxa. Thirty-five water samples were collected throughout Croatia and their physico-chemical parameters, including the concentration of trace elements using the high-resolution inductively coupled plasma mass spectrometry (HR-ICP-MS), and the composition of the microbial communities by high-throughput sequencing of the 16S rRNA marker gene, were analysed in parallel. Partial least squares regression (PLS-R) modelling revealed that a number of microbial taxa were positively correlated with some of the water parameters. For example, some taxa from the phylum Proteobacteria were positively correlated with the ion content of the water (e.g. Erythrobacter, Rhodobacteraceae, Alteromonadaceae), while some Firmicutes taxa, such as the well-known faecal indicators Enterococcus and Clostridium, were correlated with nutrient content (ammonium and total phosphorus). Among the trace elements, uranium was positively correlated with a highest number of microbial taxa. The results obtained will aid in development of protocols for eDNA-based biological assessment of water quality.
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Affiliation(s)
- Dora Pavić
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Dorotea Grbin
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Amalija Blagajac
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Josip Ćurko
- Department of Food Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia
| | - Željka Fiket
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Ana Bielen
- Department of Biochemical Engineering, Faculty of Food Technology and Biotechnology, University of Zagreb, Zagreb, Croatia.
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3
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Wang M, Bai Z, Liu S, Liu Y, Wang Z, Zhou G, Gong X, Jiang Y, Sui Z. Accurate quantification of total bacteria in raw milk by flow cytometry using membrane potential as a key viability parameter. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.114315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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4
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Yap M, O’Sullivan O, O’Toole PW, Cotter PD. Development of sequencing-based methodologies to distinguish viable from non-viable cells in a bovine milk matrix: A pilot study. Front Microbiol 2022; 13:1036643. [PMID: 36466696 PMCID: PMC9713316 DOI: 10.3389/fmicb.2022.1036643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 10/28/2022] [Indexed: 04/22/2024] Open
Abstract
Although high-throughput DNA sequencing-based methods have been of great value for determining the composition of microbial communities in various environments, there is the potential for inaccuracies arising from the sequencing of DNA from dead microorganisms. In this pilot study, we compared different sequencing-based methods to assess their relative accuracy with respect to distinguishing between viable and non-viable cells, using a live and heat-inactivated model community spiked into bovine milk. The methods used were shotgun metagenomics with and without propidium monoazide (PMA) treatment, RNA-based 16S rRNA sequencing and metatranscriptomics. The results showed that methods were generally accurate, though significant differences were found depending on the library types and sequencing technologies. Different molecular targets were the basis for variations in the results generated using different library types, while differences in the derived composition data from Oxford Nanopore Technologies-and Illumina-based sequencing likely reflect a combination of different sequencing depths, error rates and bioinformatics pipelines. Although PMA was successfully applied in this study, further optimisation is required before it can be applied in a more universal context for complex microbiomes. Overall, these methods show promise and represent another important step towards the ultimate establishment of approaches that can be applied to accurately identify live microorganisms in milk and other food niches.
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Affiliation(s)
- Min Yap
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- School of Microbiology, University College Cork, Cork, Ireland
| | - Orla O’Sullivan
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul W. O’Toole
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, Cork, Ireland
| | - Paul D. Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, Ireland
- APC Microbiome Ireland, Cork, Ireland
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5
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Pyo SH, Sayed M, Örn OE, Amorrortu Gallo J, Fernandez Ros N, Hatti-Kaul R. A facile process for adipic acid production in high yield by oxidation of 1,6-hexanediol using the resting cells of Gluconobacter oxydans. Microb Cell Fact 2022; 21:223. [PMID: 36307807 PMCID: PMC9617331 DOI: 10.1186/s12934-022-01947-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/13/2022] [Indexed: 11/26/2022] Open
Abstract
Background Adipic acid (AA) is one of the most important industrial chemicals used mainly for the production of Nylon 6,6 but also for making polyurethanes, plasticizers, and unsaturated polyester resins, and more recently as a component in the biodegradable polyester poly(butylene adipate terephthalate) (PBAT). The main route for AA production utilizes benzene as feedstock and generates copious amounts of the greenhouse gas NO2. Hence, alternative clean production routes for AA from renewable bio-based feedstock are drawing increasing attention. We have earlier reported the potential of Gluconobacter oxydans cells to oxidize 1,6-hexanediol, a potentially biobased diol to AA. Results The present report involves a study on the effect of different parameters on the microbial transformation of 1,6-hexanediol to adipic acid, and subsequently testing the process on a larger lab scale for achieving maximal conversion and yield. Comparison of three wild-type strains of G. oxydans DSM50049, DSM2003, and DSM2343 for the whole-cell biotransformation of 10 g/L 1,6-hexanediol to adipic acid in batch mode at pH 7 and 30 °C led to the selection of G. oxydans DSM50049, which showed 100% conversion of the substrate with over 99% yield of adipic acid in 30 h. An increase in the concentrations of the substrate decreased the degree of conversion, while the product up to 25 g/L in batch and 40 g/L in fed-batch showed no inhibition on the conversion. Moreover, controlling the pH of the reaction at 5–5.5 was required for the cascade oxidation reactions to work. Cell recycling for the biotransformation resulted in a significant decrease in activity during the third cycle. Meanwhile, the fed-batch mode of transformation by intermittent addition of 1,6-hexanediol (30 g in total) in 1 L scale resulted in complete conversion with over 99% yield of adipic acid (approximately 37 g/L). The product was recovered in a pure form using downstream steps without the use of any solvent. Conclusion A facile, efficient microbial process for oxidation of 1,6-hexanediol to adipic acid, having potential for scale up was demonstrated. The entire process is performed in aqueous medium at ambient temperatures with minimal greenhouse gas emissions. The enzymes involved in catalyzing the oxidation steps are currently being identified. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01947-6.
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Affiliation(s)
- Sang-Hyun Pyo
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, 22100, Lund, Sweden.
| | - Mahmoud Sayed
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, 22100, Lund, Sweden.,Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, 83523, Egypt
| | - Oliver Englund Örn
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, 22100, Lund, Sweden
| | - Jorge Amorrortu Gallo
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, 22100, Lund, Sweden
| | - Nídia Fernandez Ros
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, 22100, Lund, Sweden
| | - Rajni Hatti-Kaul
- Division of Biotechnology, Department of Chemistry, Center for Chemistry and Chemical Engineering, Lund University, 22100, Lund, Sweden
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Debata S, Kherani NA, Panda SK, Singh DP. Light-driven microrobots: capture and transport of bacteria and microparticles in a fluid medium. J Mater Chem B 2022; 10:8235-8243. [PMID: 36129102 DOI: 10.1039/d2tb01367c] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design of simple microrobotic systems with capabilities to address various applications like cargo transportation, as well as biological sample capture and manipulation in an individual unit, provides a novel route for designing advanced multifunctional microscale systems. Here, we demonstrate a facile approach to fabricate such multifunctional and fully controlled light-driven microrobots. The microrobots are titanium dioxide-silica Janus particles that are propelled in aqueous hydroquinone/benzoquinone fuel when illuminated by low-intensity UV light. The application of light provides control over the speed as well as activity of the microrobots. When modified with additional thin film coatings of nickel and gold, the microrobots exhibit the capturing and transportation of silica microparticles and E. coli bacteria. While transporting, they also show guided swimming under an external uniform magnetic field, which is interesting for deciding their moving path or the start/end positions. The fluorescent dye-based live/dead tests confirm that in the microrobot system almost no bacteria were harmed during the capturing or transportation. The simplistic design and steerable swimming with the ability to capture and transport are the important features of the microrobots. These features make them an ideal candidate for in vitro or lab-on-a-chip based studies, e.g., drug delivery, bacterial sensing, cell treatment, etc., where the capturing and transport of microscopic entities play a crucial role.
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Affiliation(s)
- Srikanta Debata
- Department of Physics, IIT Bhilai, GEC Campus, Sejbahar, Raipur, Chattisgarh, 492015, India.
| | - Nomaan Alam Kherani
- Department of EECS, IIT Bhilai, GEC Campus, Sejbahar, Raipur, Chattisgarh, 492015, India
| | - Suvendu Kumar Panda
- Department of Physics, IIT Bhilai, GEC Campus, Sejbahar, Raipur, Chattisgarh, 492015, India.
| | - Dhruv Pratap Singh
- Department of Physics, IIT Bhilai, GEC Campus, Sejbahar, Raipur, Chattisgarh, 492015, India.
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Combining microscopy assays of bacteria-surface interactions to better evaluate antimicrobial polymer coatings. Appl Environ Microbiol 2022; 88:e0224121. [PMID: 35108075 DOI: 10.1128/aem.02241-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Validation of the antimicrobial performance of contact-killing polymer surfaces through experimental determination of bacterial adhesion or viability is essential for their targeted development and application. However, there is not yet a consensus on a single most appropriate evaluation method or procedure. Combining and benchmarking previously reported assays could reduce the significant variation and misinterpretation of efficacy data obtained from different methods. In this work, we systematically investigated the response of bacteria cells to anti-adhesive and antiseptic polymer coatings by combining (i) bulk solution-based, (ii) thin-film spacer-based and (iii) direct contact assays. In addition, we evaluated the studied assays using a five-point scoring framework that highlights key areas for improvement. Our data suggest that combined microscopy assays provide a more comprehensive representation of antimicrobial performance, thereby helping to identify effective types of antibacterial polymer coatings. Importance We present and evaluate a combination of methods for validating the efficacy of antimicrobial surfaces. Antimicrobial surfaces/coatings based on contact-killing components can be instrumental to functionalise a wide range of products. However, there is not yet a consensus on a single, most appropriate method to evaluate their performance. By combining three microscopy methods, we were able to discern contact killing effects at the single cell level that were not detectable by conventional bulk microbiological analyses. The developed approach is considered advantageous for the future targeted development of robust and sustainable antimicrobial surfaces.
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Lindivat M, Bratbak G, Larsen A, Hess-Erga OK, Hoell IA. Flow Cytometric Analysis of Bacterial Protein Synthesis: Monitoring Vitality After Water Treatment. Front Microbiol 2021; 12:772651. [PMID: 34956134 PMCID: PMC8702973 DOI: 10.3389/fmicb.2021.772651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 11/12/2021] [Indexed: 11/13/2022] Open
Abstract
Bacterial vitality after water disinfection treatment was investigated using bio-orthogonal non-canonical amino acid tagging (BONCAT) and flow cytometry (FCM). Protein synthesis activity and DNA integrity (BONCAT–SYBR Green) was monitored in Escherichia coli monocultures and in natural marine samples after UV irradiation (from 25 to 200 mJ/cm2) and heat treatment (from 15 to 45 min at 55°C). UV irradiation of E. coli caused DNA degradation followed by the decrease in protein synthesis within a period of 24 h. Heat treatment affected both DNA integrity and protein synthesis immediately, with an increased effect over time. Results from the BONCAT method were compared with results from well-known methods such as plate counts (focusing on growth) and LIVE/DEAD™ BacLight™ (focusing on membrane permeability). The methods differed somewhat with respect to vitality levels detected in bacteria after the treatments, but the results were complementary and revealed that cells maintained metabolic activity and membrane integrity despite loss of cell division. Similarly, analysis of protein synthesis in marine bacteria with BONCAT displayed residual activity despite inability to grow or reproduce. Background controls (time zero blanks) prepared using different fixatives (formaldehyde, isopropanol, and acetic acid) and several different bacterial strains revealed that the BONCAT protocol still resulted in labeled, i.e., apparently active, cells. The reason for this is unclear and needs further investigation to be understood. Our results show that BONCAT and FCM can detect, enumerate, and differentiate bacterial cells after physical water treatments such as UV irradiation and heating. The method is reliable to enumerate and explore vitality of single cells, and a great advantage with BONCAT is that all proteins synthesized within cells are analyzed, compared to assays targeting specific elements such as enzyme activity.
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Affiliation(s)
- Mathilde Lindivat
- Faculty of Engineering and Science, Institute of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Haugesund, Norway
| | - Gunnar Bratbak
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Aud Larsen
- Department of Biological Sciences, University of Bergen, Bergen, Norway.,NORCE Environment, NORCE Norwegian Research Center AS, Bergen, Norway
| | | | - Ingunn Alne Hoell
- Faculty of Engineering and Science, Institute of Safety, Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Haugesund, Norway
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Legrand T, Wos‐Oxley M, Wynne J, Weyrich L, Oxley A. Dead or alive: microbial viability treatment reveals both active and inactive bacterial constituents in the fish gut microbiota. J Appl Microbiol 2021; 131:2528-2538. [PMID: 33945191 PMCID: PMC8596808 DOI: 10.1111/jam.15113] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/22/2021] [Accepted: 04/17/2021] [Indexed: 12/26/2022]
Abstract
AIMS This study evaluated the microbial viability of fish gut microbiota in both digesta (faecal) and mucosal samples using a modified propidium monoazide (PMA) protocol, followed by 16S ribosomal RNA (rRNA) gene sequencing. METHODS AND RESULTS Digesta and gut mucosal samples from farmed yellowtail kingfish (Seriola lalandi) were collected and a modified PMA treatment was applied prior to DNA extraction to differentiate both active and nonviable microbial cells in the samples. All samples were then sequenced using a standard 16S rRNA approach. The digesta and mucosal samples contained significantly different bacterial communities, with a higher diversity observed in digesta samples. In addition, PMA treatment significantly reduced the microbial diversity and richness of digesta and mucosal samples and depleted bacterial constituents typically considered to be important within fish, such as Lactobacillales and Clostridales taxa. CONCLUSIONS These findings suggest that important bacterial members may not be active in the fish gut microbiota. In particular, several beneficial lactic acid bacteria (LAB) were identified as nonviable bacterial cells, potentially influencing the functional potential of the fish microbiota. SIGNIFICANCE AND IMPACTS OF THE STUDY Standardizing the methods for characterizing the fish microbiota are paramount in order to compare studies. In this study, we showed that both sample type and PMA treatment influence the bacterial communities found in the fish gut microbiota. Our findings also suggest that several microbes previously described in the fish gut may not be active constituents. As a result, these factors should be considered in future studies to better evaluate the active bacterial communities associated with the host.
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Affiliation(s)
- T.P.R.A. Legrand
- School of Biological SciencesThe University of AdelaideAdelaideSAAustralia
- CSIRO, Agriculture and FoodHobartTasAustralia
- South Australian Research and Development InstituteAquatic Sciences CentreWest BeachSAAustralia
| | - M.L. Wos‐Oxley
- College of Science and EngineeringFlinders UniversityAdelaideSAAustralia
| | - J.W. Wynne
- CSIRO, Agriculture and FoodHobartTasAustralia
| | - L.S. Weyrich
- School of Biological SciencesThe University of AdelaideAdelaideSAAustralia
- Department of Anthropology and Huck Institutes of Life SciencesThe Pennsylvania State UniversityUniversity ParkPAUSA
| | - A.P.A. Oxley
- Faculty of Science Engineering and Built EnvironmentSchool of Life and Environmental SciencesDeakin UniversityGeelongVic.Australia
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A Possible Flow Cytometry-Based Viability and Vitality Assessment Protocol for Pathogenic Vibrio cholerae O1 and O139 Postexposure to Simulated Gastric Fluid. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5551845. [PMID: 34212032 PMCID: PMC8208853 DOI: 10.1155/2021/5551845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 05/21/2021] [Accepted: 05/27/2021] [Indexed: 12/26/2022]
Abstract
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.
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How to Evaluate Non-Growing Cells-Current Strategies for Determining Antimicrobial Resistance of VBNC Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10020115. [PMID: 33530321 PMCID: PMC7912045 DOI: 10.3390/antibiotics10020115] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/19/2021] [Accepted: 01/22/2021] [Indexed: 12/17/2022] Open
Abstract
Thanks to the achievements in sanitation, hygiene practices, and antibiotics, we have considerably improved in our ongoing battle against pathogenic bacteria. However, with our increasing knowledge about the complex bacterial lifestyles and cycles and their plethora of defense mechanisms, it is clear that the fight is far from over. One of these resistance mechanisms that has received increasing attention is the ability to enter a dormancy state termed viable but non-culturable (VBNC). Bacteria that enter the VBNC state, either through unfavorable environmental conditions or through potentially lethal stress, lose their ability to grow on standard enrichment media, but show a drastically increased tolerance against antimicrobials including antibiotics. The inability to utilize traditional culture-based methods represents a considerable experimental hurdle to investigate their increased antimicrobial resistance and impedes the development and evaluation of effective treatments or interventions against bacteria in the VBNC state. Although experimental approaches were developed to detect and quantify VBNCs, only a few have been utilized for antimicrobial resistance screening and this review aims to provide an overview of possible methodological approaches.
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12
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Lindivat M, Larsen A, Hess-Erga OK, Bratbak G, Hoell IA. Bioorthogonal Non-canonical Amino Acid Tagging Combined With Flow Cytometry for Determination of Activity in Aquatic Microorganisms. Front Microbiol 2020; 11:1929. [PMID: 33013733 PMCID: PMC7461810 DOI: 10.3389/fmicb.2020.01929] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 07/22/2020] [Indexed: 11/13/2022] Open
Abstract
In this study, we have combined bioorthogonal non-canonical amino acid tagging (BONCAT) and flow cytometry (FCM) analysis, and we demonstrate the applicability of the method for marine prokaryotes. Enumeration of active marine bacteria was performed by combining the DNA stain SYBR Green with detection of protein production with BONCAT. After optimization of incubation condition and substrate concentration on monoculture of Escherichia coli, we applied and modified the method to natural marine samples. We found that between 10 and 30% of prokaryotes in natural communities were active. The method is replicable, fast, and allow high sample throughput when using FCM. We conclude that the combination of BONCAT and FCM is an alternative to current methods for quantifying active populations in aquatic environments.
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Affiliation(s)
- Mathilde Lindivat
- Faculty of Engineering and Science, Institute of Safety Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Haugesund, Norway
| | - Aud Larsen
- NORCE Environment, NORCE Norwegian Research Centre AS, Bergen, Norway.,Department of Biological Sciences, University of Bergen, Bergen, Norway
| | | | - Gunnar Bratbak
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Ingunn Alne Hoell
- Faculty of Engineering and Science, Institute of Safety Chemistry and Biomedical Laboratory Sciences, Western Norway University of Applied Sciences, Haugesund, Norway
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Maertens H, Demeyere K, De Reu K, Dewulf J, Vanhauteghem D, Van Coillie E, Meyer E. Effect of subinhibitory exposure to quaternary ammonium compounds on the ciprofloxacin susceptibility of Escherichia coli strains in animal husbandry. BMC Microbiol 2020; 20:155. [PMID: 32527225 PMCID: PMC7291530 DOI: 10.1186/s12866-020-01818-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 05/10/2020] [Indexed: 12/04/2022] Open
Abstract
BACKGROUND Quaternary ammonium compound based disinfectants are commonly used in pig and poultry husbandry to maintain farm hygiene. However, studies have shown that subinhibitory concentrations of these disinfectants may increase antibiotic resistance. Investigation of antibiotic susceptibility is usually assessed via the microbroth dilution method, although this conventional culture-based technique only provides information on the bacteriostatic activity of an antimicrobial agent. Therefore, experiments were performed to investigate the effect of prior benzalkonium chloride (BKC) exposure on the viability of subsequent ciprofloxacin (CIP) treated Escherichia coli. RESULTS Following CIP treatment, bacterial cell counts were significantly higher after exposure to a subinhibitory BKC concentration than without BKC exposure. The flow cytometric results suggested a BKC-dependent onset of membrane damage and loss of membrane potential. CONCLUSION Our results indicate a lower bactericidal effect of CIP treatment on BKC-exposed E. coli isolates compared to unexposed E. coli isolates.
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Affiliation(s)
- H Maertens
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - K Demeyere
- Veterinary Biochemistry Unit, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - K De Reu
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - J Dewulf
- Veterinary Epidemiology Unit, Department of Reproduction, Obstetrics and Herd Health, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - D Vanhauteghem
- Veterinary Biochemistry Unit, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium
| | - E Van Coillie
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Technology and Food Science Unit, Brusselsesteenweg 370, 9090, Melle, Belgium
| | - E Meyer
- Veterinary Biochemistry Unit, Department of Pharmacology, Toxicology and Biochemistry, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820, Merelbeke, Belgium.
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Koufakis E, Manouras T, Anastasiadis SH, Vamvakaki M. Film Properties and Antimicrobial Efficacy of Quaternized PDMAEMA Brushes: Short vs Long Alkyl Chain Length. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:3482-3493. [PMID: 32168453 DOI: 10.1021/acs.langmuir.9b03266] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Quaternized poly(2-(dimethylamino)ethyl methacrylate) (PDMAEMA) brushes bearing quaternary ammonium groups of different alkyl chain lengths (ACLs) were prepared and assessed as biocidal coatings. For the synthesis of the antimicrobial brushes, first well-defined PDMAEMA chains were grown by surface-initiated atom transfer radical polymerization on glass and silicon substrates. Next, the tertiary amine groups of the polymer brushes were modified via a quaternization reaction, using alkyl halides, to obtain the cationic polymers. The polymer films were characterized by Fourier-transform infrared spectroscopy, ellipsometry, atomic force microscopy, and water contact angle measurements. The effect of the ACL of the quaternary ammonium groups on the physicochemical properties of the films as well as the contact killing efficiency of the surfaces against representative Gram-positive and Gram-negative bacteria was investigated. A hydrophilic to hydrophobic transition of the surfaces and a significant decrease of the degree of quaternization of the DMAEMA moieties was found upon increasing the ACL of the quaternization agent above six carbon atoms, allowing the wettability, the thickness, and the pH-response of the brushes to be tuned via a facile postpolymerization, quaternization reaction. At the same time, antimicrobial tests revealed that the hydrophilic polymer brushes exhibited enhanced bactericidal activity against Escherichia coli and Bacillus cereus, whereas the hydrophobic surfaces showed a significant deterioration of the in vitro bactericidal performance. Our results elucidate the antimicrobial action of quaternized polymer brushes, dictating the appropriate choice of the ACL of the quaternization agent for the development of coatings that effectively inhibit biofilm formation on surfaces.
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Affiliation(s)
- Eleftherios Koufakis
- Foundation for Research and Technology - Hellas, Institute of Electronic Structure and Laser, 700 13 Heraklion, Crete, Greece
- Department of Materials Science and Technology, University of Crete, 700 13 Heraklion, Crete, Greece
| | - Theodore Manouras
- Foundation for Research and Technology - Hellas, Institute of Electronic Structure and Laser, 700 13 Heraklion, Crete, Greece
| | - Spiros H Anastasiadis
- Foundation for Research and Technology - Hellas, Institute of Electronic Structure and Laser, 700 13 Heraklion, Crete, Greece
- Department of Chemistry, University of Crete, 700 13 Heraklion, Crete, Greece
| | - Maria Vamvakaki
- Foundation for Research and Technology - Hellas, Institute of Electronic Structure and Laser, 700 13 Heraklion, Crete, Greece
- Department of Materials Science and Technology, University of Crete, 700 13 Heraklion, Crete, Greece
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Adu KT, Wilson R, Baker AL, Bowman J, Britz ML. Prolonged Heat Stress of Lactobacillus paracasei GCRL163 Improves Binding to Human Colorectal Adenocarcinoma HT-29 Cells and Modulates the Relative Abundance of Secreted and Cell Surface-Located Proteins. J Proteome Res 2020; 19:1824-1846. [PMID: 32108472 DOI: 10.1021/acs.jproteome.0c00107] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Lactobacillus casei group bacteria improve cheese ripening and may interact with host intestinal cells as probiotics, where surface proteins play a key role. Three complementary methods [trypsin shaving (TS), LiCl-sucrose (LS) extraction, and extracellular culture fluid precipitation] were used to analyze cell surface proteins of Lactobacillus paracasei GCRL163 by label-free quantitative proteomics after culture to the mid-exponential phase in bioreactors at pH 6.5 and temperatures of 30-45 °C. A total of 416 proteins, including 300 with transmembrane, cell wall anchoring, and secretory motifs and 116 cytoplasmic proteins, were quantified as surface proteins. Although LS caused significantly greater cell lysis as growth temperature increased, higher numbers of extracytoplasmic proteins were exclusively obtained by LS treatment. Together with the increased positive surface charge of cells cultured at supra-optimal temperatures, proteins including cell wall hydrolases Msp1/p75 and Msp2/p40, α-fucosidase AlfB, SecA, and a PspC-domain putative adhesin were upregulated in surface or secreted protein fractions, suggesting that cell adhesion may be altered. Prolonged heat stress (PHS) increased binding of L. paracasei GCRL163 to human colorectal adenocarcinoma HT-29 cells, relative to acid-stressed cells. This study demonstrates that PHS influences cell adhesion and relative abundance of proteins located on the surface, which may impact probiotic functionality, and the detected novel surface proteins likely linked to the cell cycle and envelope stress.
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Affiliation(s)
- Kayode T Adu
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Richard Wilson
- Central Science Laboratory, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Anthony L Baker
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - John Bowman
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
| | - Margaret L Britz
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tasmania 7001, Australia
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Antimicrobial Activity and Mechanism of Action of the Amaranthus tricolor Crude Extract against Staphylococcus aureus and Potential Application in Cooked Meat. Foods 2020; 9:foods9030359. [PMID: 32204560 PMCID: PMC7142881 DOI: 10.3390/foods9030359] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/11/2020] [Accepted: 03/17/2020] [Indexed: 01/21/2023] Open
Abstract
Amaranthus tricolor has been reported to contain some antimicrobial compounds, such as alkaloids, polyphenols, and terpenoids. However, its effect on Staphylococcus aureus has been less well researched. Therefore, this study was designed to evaluate the antimicrobial activity and possible mechanism of action of the Amaranthus tricolor crude extract (ATCE) against S. aureus and potential application in cooked meat. The antimicrobial activity against S. aureus was assessed by disk diffusion, minimum inhibitory concentration (MIC) determinations, and growth curve. The changes of bacterial membrane potential, intracellular pH (pHin), content of bacterial protein and DNA, and cell morphology were measured to indicate its antimicrobial mechanism of action. The effects of different concentrations of ATCE on bacterial counts, pH, and color of lean cooked pork during 6 d storage were assessed. The results showed that the diameter of inhibition zone (DIZ) and MIC of ATCE against S. aureus were 12.63 ± 0.34 to 12.94 ± 0.43 mm and 80 mg/mL, respectively. The mechanism of action of ATCE against S. aureus was associated with cell membrane depolarization, reduction of pHin, decrease of bacterial protein content, cleavage of cell DNA, and leakage of cytoplasm. Besides, ATCE resulted in a reduction of 1.02 log CFU/g from 3 log CFU/g in S. aureus-inoculated lean cooked pork. The pH values of lean cooked pork treated with ATCE did not show significant changes as the storage time increased, but there was a slight and significant decrease seen with the application of 1 and 2 MIC of ATCE. After treating with ATCE, the color of lean cooked pork showed less lightness (L*), more redness (a∗), similar yellowness (b*), stronger chroma (C*), and weaker hue angle (h*) during 6 days of storage. Therefore, these findings indicate that ATCE has antimicrobial activities against S. aureus and possesses latent energy to become a natural preservative to maintain the quality of lean cooked pork.
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Aiyer KS, Rai R, Vijayakumar BS. Assessing Activity of Antimicrobial Agents and Screening Antibiotic-Resistant Bacteria Through DREAM Assay. Appl Biochem Biotechnol 2019; 188:1158-1167. [DOI: 10.1007/s12010-019-02981-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 02/20/2019] [Indexed: 11/25/2022]
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Acid-happy: Survival and recovery of enteropathogenic Escherichia coli (EPEC) in simulated gastric fluid. Microb Pathog 2019; 128:396-404. [PMID: 30660737 DOI: 10.1016/j.micpath.2019.01.022] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 12/14/2018] [Accepted: 01/16/2019] [Indexed: 02/06/2023]
Abstract
BACKGROUND Gastric fluid pH serves an important function as an ecological filter to kill unwanted microbial taxa that would otherwise colonise the intestines, thereby shaping the diversity and composition of microbial communities found in the gut. The typical American-based diet causes the gastric pH to increase to pH 4 to 5, and it takes ∼2 h to return to pH 1.5 (normal). This window of increased gastric pH may allow potential pathogens to negotiate the hostile environment of the stomach. Another factor to consider is that in developing countries many people experience hypochlorhydria related to malnutrition and various gastric diseases. Enteropathogenic E. coli (EPEC) is a leading cause of infantile diarrhoea and has a high incidence in the developing world. The aim of this study was to assess the survival and recovery of non-acid adapted EPEC exposed to simulated gastric fluid (SGF) over a period of 180 min. RESULTS EPEC were grown in nutrient-rich medium and acid challenged in SGF at pH 1.5, 2.5, 3.5 and 4.5. Culturability was evaluated using a standard plate count method, and metabolic viability was assessed via cellular energy (adenosine triphosphate [ATP] assay) and respiratory activity (3-bis(2-methyloxy-4-nitro-5-sulfophenyl)-5-[(phenylamino)carbonyl]-2H-tetrazolium hydroxide [XTT] assay), and recovery and proliferation by means of optical density in liquid cultures. Sampling was performed at 0, 30, 60, 120, and 180 min post-SGF exposure. The results of this study showed that EPEC is remarkably acid resistant and was able to survive a simulated gastric environment for up to 3 h (180 min) at various pH (1.5, 2.5, 3.5, and 4.5). EPEC was culturable at all pH (1.5, 2.5, 3.5 and 4.5) at the higher inoculum size of 5.4-7.1 × 106 CFU/ml, and at all pH except pH 1.5 at the lower inoculums of 5.4-7.1 × 103 CFU/ml or 5.4-7.1 × 101 CFU/ml. The organism remained metabolically viable at pH 1.5, 2.5, 3.5, and 4.5 and was able to recover and proliferate once placed in a neutral, nutrient-rich environment. CONCLUSION In this study, EPEC demonstrated remarkable acid resistance and recovery at low pH without prior acid adaptation, which could prove to be problematic even in healthy people. In individuals with decreased gastric acidity, there is a higher probability of pathogen colonization and a resulting change in the gut microbiome. The results highlight the potential increase of food- and waterborne diseases in persons with compromised gastric function, or who are malnourished or immunocompromised. The data herein may possibly help in calculating more precisely the risk associated with consuming bacterial contaminated food and water in these individuals.
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Otte JM, Blackwell N, Soos V, Rughöft S, Maisch M, Kappler A, Kleindienst S, Schmidt C. Sterilization impacts on marine sediment---Are we able to inactivate microorganisms in environmental samples? FEMS Microbiol Ecol 2018; 94:5104375. [DOI: 10.1093/femsec/fiy189] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Accepted: 09/18/2018] [Indexed: 12/20/2022] Open
Affiliation(s)
- Julia M Otte
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Nia Blackwell
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Viktoria Soos
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Saskia Rughöft
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Markus Maisch
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Andreas Kappler
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
- Geomicrobiology, Center for Geomicrobiology, Aarhus University, Ny Munkegade 116, 8000 Aarhus, Denmark
| | - Sara Kleindienst
- Microbial Ecology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
| | - Caroline Schmidt
- Geomicrobiology, Center for Applied Geosciences, University of Tübingen, Hölderlinstrasse 12, 72074 Tübingen, Germany
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Vondrakova L, Turonova H, Scholtz V, Pazlarova J, Demnerova K. Impact of various killing methods on EMA/PMA-qPCR efficacy. Food Control 2018. [DOI: 10.1016/j.foodcont.2017.09.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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21
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McClary JS, Boehm AB. Transcriptional Response of Staphylococcus aureus to Sunlight in Oxic and Anoxic Conditions. Front Microbiol 2018; 9:249. [PMID: 29599752 PMCID: PMC5863498 DOI: 10.3389/fmicb.2018.00249] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/31/2018] [Indexed: 12/20/2022] Open
Abstract
The transcriptional response of Staphylococcus aureus strain Newman to sunlight exposure was investigated under both oxic and anoxic conditions using RNA sequencing to gain insight into potential mechanisms of inactivation. S. aureus is a pathogenic bacterium detected at recreational beaches which can cause gastrointestinal illness and skin infections, and is of increasing public health concern. To investigate the S. aureus photostress response in oligotrophic seawater, S. aureus cultures were suspended in seawater and exposed to full spectrum simulated sunlight. Experiments were performed under oxic or anoxic conditions to gain insight into the effects of oxygen-mediated and non-oxygen-mediated inactivation mechanisms. Transcript abundance was measured after 6 h of sunlight exposure using RNA sequencing and was compared to transcript abundance in paired dark control experiments. Culturable S. aureus decayed following biphasic inactivation kinetics with initial decay rate constants of 0.1 and 0.03 m2 kJ−1 in oxic and anoxic conditions, respectively. RNA sequencing revealed that 71 genes had different transcript abundance in the oxic sunlit experiments compared to dark controls, and 18 genes had different transcript abundance in the anoxic sunlit experiments compared to dark controls. The majority of genes showed reduced transcript abundance in the sunlit experiments under both conditions. Three genes (ebpS, NWMN_0867, and NWMN_1608) were found to have the same transcriptional response to sunlight between both oxic and anoxic conditions. In the oxic condition, transcripts associated with porphyrin metabolism, nitrate metabolism, and membrane transport functions were increased in abundance during sunlight exposure. Results suggest that S. aureus responds differently to oxygen-dependent and oxygen-independent photostress, and that endogenous photosensitizers play an important role during oxygen-dependent indirect photoinactivation.
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Affiliation(s)
- Jill S McClary
- Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Alexandria B Boehm
- Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
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22
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Gweon E, Choi C, Kim J, Kim B, Kang H, Park T, Ban S, Bae M, Park S, Jeong J. Development of a New Approach to Determine the Potency of Bacille Calmette-Guérin Vaccines Using Flow Cytometry. Osong Public Health Res Perspect 2017; 8:389-396. [PMID: 29354397 PMCID: PMC5749480 DOI: 10.24171/j.phrp.2017.8.6.06] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 10/20/2017] [Accepted: 11/26/2017] [Indexed: 11/25/2022] Open
Abstract
Objectives To circumvent the limitations of the current golden standard method, colony-forming unit (CFU) assay, for viability of Bacille Calmette–Guérin (BCG) vaccines, we developed a new method to rapidly and accurately determine the potency of BCG vaccines. Methods Based on flow cytometry (FACS) and fluorescein diacetate (FDA) as the most appropriate fluorescent staining reagent, 17 lots of BCG vaccines for percutaneous administration and 5 lots of BCG vaccines for intradermal administration were analyzed in this study. The percentage of viable cells measured by flow cytometry along with the total number of organisms in BCG vaccines, as determined on a cell counter, was used to quantify the number of viable cells. Results Pearson correlation coefficients of FACS and CFU assays for percutaneous and intradermal BCG vaccines were 0.6962 and 0.7428, respectively, indicating a high correlation. The coefficient of variation value of the FACS assay was less than 7%, which was 11 times lower than that of the CFU assay. Conclusion This study contributes to the evaluation of new potency test method for FACS-based determination of viable cells in BCG vaccines. Accordingly, quality control of BCG vaccines can be significantly improved.
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Affiliation(s)
- Eunjeong Gweon
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Chanwoong Choi
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Jaeok Kim
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Byungkuk Kim
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Hyunkyung Kang
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Taejun Park
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Sangja Ban
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Minseok Bae
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Sangjin Park
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
| | - Jayoung Jeong
- Biologics Research Division, National Institute of Food and Drug Safety Evaluation, Cheongju, Korea
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Selective and concurrent detection of viable Salmonella spp., E. coli, Staphylococcus aureus, E. coli O157:H7, and Shigella spp., in low moisture food products by PMA-mPCR assay with internal amplification control. Lebensm Wiss Technol 2017. [DOI: 10.1016/j.lwt.2017.08.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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Van Nevel S, Koetzsch S, Proctor CR, Besmer MD, Prest EI, Vrouwenvelder JS, Knezev A, Boon N, Hammes F. Flow cytometric bacterial cell counts challenge conventional heterotrophic plate counts for routine microbiological drinking water monitoring. WATER RESEARCH 2017; 113:191-206. [PMID: 28214393 DOI: 10.1016/j.watres.2017.01.065] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 01/30/2017] [Accepted: 01/31/2017] [Indexed: 06/06/2023]
Abstract
Drinking water utilities and researchers continue to rely on the century-old heterotrophic plate counts (HPC) method for routine assessment of general microbiological water quality. Bacterial cell counting with flow cytometry (FCM) is one of a number of alternative methods that challenge this status quo and provide an opportunity for improved water quality monitoring. After more than a decade of application in drinking water research, FCM methodology is optimised and established for routine application, supported by a considerable amount of data from multiple full-scale studies. Bacterial cell concentrations obtained by FCM enable quantification of the entire bacterial community instead of the minute fraction of cultivable bacteria detected with HPC (typically < 1% of all bacteria). FCM measurements are reproducible with relative standard deviations below 3% and can be available within 15 min of samples arriving in the laboratory. High throughput sample processing and complete automation are feasible and FCM analysis is arguably less expensive than HPC when measuring more than 15 water samples per day, depending on the laboratory and selected staining procedure(s). Moreover, many studies have shown FCM total (TCC) and intact (ICC) cell concentrations to be reliable and robust process variables, responsive to changes in the bacterial abundance and relevant for characterising and monitoring drinking water treatment and distribution systems. The purpose of this critical review is to initiate a constructive discussion on whether FCM could replace HPC in routine water quality monitoring. We argue that FCM provides a faster, more descriptive and more representative quantification of bacterial abundance in drinking water.
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Affiliation(s)
- S Van Nevel
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - S Koetzsch
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - C R Proctor
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland; Department of Environmental Systems Science, Institute of Biogeochemistry and Pollutant Dynamics, ETH Zürich, Zürich, Switzerland
| | - M D Besmer
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland
| | - E I Prest
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - J S Vrouwenvelder
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands; Wetsus, Centre of Excellence for Sustainable Water Technology, Oostergoweg 9, 8911 MA, Leeuwarden, The Netherlands; King Abdullah University of Science and Technology (KAUST), Water Desalination and Reuse Center (WDRC), Division of Biological and Environmental Science and Engineering (BESE), Thuwal, 23955-6900, Saudi Arabia
| | - A Knezev
- Het Waterlaboratorium, J.W. Lucasweg 2, 2031 BE, Haarlem, The Netherlands
| | - N Boon
- Center for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, B-9000, Gent, Belgium
| | - F Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, Überlandstrasse 133, CH-8600, Dübendorf, Switzerland.
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Rubbens P, Props R, Boon N, Waegeman W. Flow Cytometric Single-Cell Identification of Populations in Synthetic Bacterial Communities. PLoS One 2017; 12:e0169754. [PMID: 28122063 PMCID: PMC5266259 DOI: 10.1371/journal.pone.0169754] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Accepted: 12/21/2016] [Indexed: 01/14/2023] Open
Abstract
Bacterial cells can be characterized in terms of their cell properties using flow cytometry. Flow cytometry is able to deliver multiparametric measurements of up to 50,000 cells per second. However, there has not yet been a thorough survey concerning the identification of the population to which bacterial single cells belong based on flow cytometry data. This paper not only aims to assess the quality of flow cytometry data when measuring bacterial populations, but also suggests an alternative approach for analyzing synthetic microbial communities. We created so-called in silico communities, which allow us to explore the possibilities of bacterial flow cytometry data using supervised machine learning techniques. We can identify single cells with an accuracy >90% for more than half of the communities consisting out of two bacterial populations. In order to assess to what extent an in silico community is representative for its synthetic counterpart, we created so-called abundance gradients, a combination of synthetic (i.e., in vitro) communities containing two bacterial populations in varying abundances. By showing that we are able to retrieve an abundance gradient using a combination of in silico communities and supervised machine learning techniques, we argue that in silico communities form a viable representation for synthetic bacterial communities, opening up new opportunities for the analysis of synthetic communities and bacterial flow cytometry data in general.
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Affiliation(s)
- Peter Rubbens
- KERMIT, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
- * E-mail:
| | - Ruben Props
- Center for Microbial Technology and Ecology (CMET), Ghent University, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Technology and Ecology (CMET), Ghent University, Ghent, Belgium
| | - Willem Waegeman
- KERMIT, Department of Mathematical Modelling, Statistics and Bioinformatics, Ghent University, Ghent, Belgium
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Qiu TA, Nguyen THT, Hudson-Smith NV, Clement PL, Forester DC, Frew H, Hang MN, Murphy CJ, Hamers RJ, Feng ZV, Haynes CL. Growth-Based Bacterial Viability Assay for Interference-Free and High-Throughput Toxicity Screening of Nanomaterials. Anal Chem 2017; 89:2057-2064. [PMID: 28208291 DOI: 10.1021/acs.analchem.6b04652] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Current high-throughput approaches evaluating toxicity of chemical agents toward bacteria typically rely on optical assays, such as luminescence and absorbance, to probe the viability of the bacteria. However, when applied to toxicity induced by nanomaterials, scattering and absorbance from the nanomaterials act as interferences that complicate quantitative analysis. Herein, we describe a bacterial viability assay that is free of optical interference from nanomaterials and can be performed in a high-throughput format on 96-well plates. In this assay, bacteria were exposed to various materials and then diluted by a large factor into fresh growth medium. The large dilution ensured minimal optical interference from the nanomaterial when reading optical density, and the residue left from the exposure mixture after dilution was confirmed not to impact the bacterial growth profile. The fractions of viable cells after exposure were allowed to grow in fresh medium to generate measurable growth curves. Bacterial viability was then quantitatively correlated to the delay of bacterial growth compared to a reference regarded as 100% viable cells; data analysis was inspired by that in quantitative polymerase chain reactions, where the delay in the amplification curve is correlated to the starting amount of the template nucleic acid. Fast and robust data analysis was achieved by developing computer algorithms carried out using R. This method was tested on four bacterial strains, including both Gram-negative and Gram-positive bacteria, showing great potential for application to all culturable bacterial strains. With the increasing diversity of engineered nanomaterials being considered for large-scale use, this high-throughput screening method will facilitate rapid screening of nanomaterial toxicity and thus inform the risk assessment of nanoparticles in a timely fashion.
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Affiliation(s)
- Tian A Qiu
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Thu Ha Thi Nguyen
- Chemistry Department, Augsburg College , Minneapolis, Minnesota 55454, United States
| | - Natalie V Hudson-Smith
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Peter L Clement
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Dona-Carla Forester
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Hilena Frew
- Chemistry Department, Augsburg College , Minneapolis, Minnesota 55454, United States
| | - Mimi N Hang
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Catherine J Murphy
- Department of Chemistry, University of Illinois at Urbana-Champaign , 600 South Mathews Avenue, Urbana, Illinois 61801, United States
| | - Robert J Hamers
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Z Vivian Feng
- Chemistry Department, Augsburg College , Minneapolis, Minnesota 55454, United States
| | - Christy L Haynes
- Department of Chemistry, University of Minnesota , 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
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Buysschaert B, Byloos B, Leys N, Van Houdt R, Boon N. Reevaluating multicolor flow cytometry to assess microbial viability. Appl Microbiol Biotechnol 2016; 100:9037-9051. [PMID: 27687990 DOI: 10.1007/s00253-016-7837-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/29/2016] [Accepted: 09/01/2016] [Indexed: 01/14/2023]
Abstract
Flow cytometry is a rapid and quantitative method to determine bacterial viability. Although different stains can be used to establish viability, staining protocols are inconsistent and lack a general optimization approach. Very few "true" multicolor protocols, where dyes are combined in one sample, have been developed for microbiological applications. In this mini-review, the discrepancy between protocols for cell-permeant nucleic acid and functional stains are discussed as well as their use as viability dyes. Furthermore, optimization of staining protocols for a specific setup are described. Original data using the red-excitable SYTO dyes SYTO 59 to 64 and SYTO 17, combined with functional stains, for double and triple staining applications is also included. As each dye and dye combination behaves differently within a certain combination of medium matrix, microorganism, and instrument, protocols need to be tuned to obtain reproducible results. Therefore, single, double, and triple stains are reviewed, including the different parameters that influence staining such as stain kinetics, optimal stain concentration, and the effect of the chelator EDTA as membrane permeabilizer. In the last section, we highlight the need to investigate the stability of multicolor assays to ensure correct results as multiwell autoloaders are now commonly used.
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Affiliation(s)
- Benjamin Buysschaert
- Centre for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Bo Byloos
- Centre for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.,Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400, Mol, Belgium
| | - Natalie Leys
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400, Mol, Belgium
| | - Rob Van Houdt
- Unit of Microbiology, Belgian Nuclear Research Centre (SCK-CEN), Boeretang 200, 2400, Mol, Belgium
| | - Nico Boon
- Centre for Microbial Ecology and Technology (CMET), Ghent University, Coupure Links 653, 9000, Ghent, Belgium.
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Bonatti TR, Franco RMB. Real scale environmental monitoring of zoonotic protozoa and helminth eggs in biosolid samples in Brazil. J Parasit Dis 2016; 40:633-42. [PMID: 27605758 PMCID: PMC4996162 DOI: 10.1007/s12639-014-0549-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 08/25/2014] [Indexed: 11/26/2022] Open
Abstract
Biosolid is the product of the activated sludge treatment system and its final disposition is subject of ongoing discussion as this residue can therefore harbor a great number and variety of pathogens. This study was aimed to (1) monitor the presence of Giardia and Cryptosporidium in biosolid samples from a treatment plant in Campinas, SP, Brazil, (2) observe Giardia cyst wall morphological integrity in treated samples using scanning electron microscopy (SEM) and (3) verify the presence and viability of helminth eggs. Cysts were present in 33.3 % of the samples, whereas oocysts were detected in 8.3 %. Viable Ascaris sp. Toxocara sp. and similar to Trichuris sp. eggs were found through the use of Mexican Official Norm. Results demonstrate the difficulties inherent in working with biosolid as factors such as temperature, ionic strength and pH influenced the recovery of cysts and oocysts. Pores and ruptures were not observed in cyst wall visualized by SEM following 45 days of exposure to sunlight, only minimal morphological changes. These observations emphasize both the importance of adequate treatment of sewage sludge and the need to develop appropriate techniques for the detection of Giardia and Cryptosporidium in this type of sample. This is the first time that a study was done in a real scale for biosolid samples in determining the presence of pathogenic protozoa as Giardia and Cryptosporidium in Brazil, and also observed minimal cyst wall damage after sunlight treatment.
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Affiliation(s)
- Taís Rondello Bonatti
- Animal Biology Department, Biology Institute, State University of Campinas, PO Box 6109, Campinas, SP CEP: 13083-970 Brazil
| | - Regina Maura Bueno Franco
- Animal Biology Department, Biology Institute, State University of Campinas, PO Box 6109, Campinas, SP CEP: 13083-970 Brazil
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Prest EI, Hammes F, van Loosdrecht MCM, Vrouwenvelder JS. Biological Stability of Drinking Water: Controlling Factors, Methods, and Challenges. Front Microbiol 2016; 7:45. [PMID: 26870010 PMCID: PMC4740787 DOI: 10.3389/fmicb.2016.00045] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/11/2016] [Indexed: 12/27/2022] Open
Abstract
Biological stability of drinking water refers to the concept of providing consumers with drinking water of same microbial quality at the tap as produced at the water treatment facility. However, uncontrolled growth of bacteria can occur during distribution in water mains and premise plumbing, and can lead to hygienic (e.g., development of opportunistic pathogens), aesthetic (e.g., deterioration of taste, odor, color) or operational (e.g., fouling or biocorrosion of pipes) problems. Drinking water contains diverse microorganisms competing for limited available nutrients for growth. Bacterial growth and interactions are regulated by factors, such as (i) type and concentration of available organic and inorganic nutrients, (ii) type and concentration of residual disinfectant, (iii) presence of predators, such as protozoa and invertebrates, (iv) environmental conditions, such as water temperature, and (v) spatial location of microorganisms (bulk water, sediment, or biofilm). Water treatment and distribution conditions in water mains and premise plumbing affect each of these factors and shape bacterial community characteristics (abundance, composition, viability) in distribution systems. Improved understanding of bacterial interactions in distribution systems and of environmental conditions impact is needed for better control of bacterial communities during drinking water production and distribution. This article reviews (i) existing knowledge on biological stability controlling factors and (ii) how these factors are affected by drinking water production and distribution conditions. In addition, (iii) the concept of biological stability is discussed in light of experience with well-established and new analytical methods, enabling high throughput analysis and in-depth characterization of bacterial communities in drinking water. We discussed, how knowledge gained from novel techniques will improve design and monitoring of water treatment and distribution systems in order to maintain good drinking water microbial quality up to consumer's tap. A new definition and methodological approach for biological stability is proposed.
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Affiliation(s)
- Emmanuelle I Prest
- Environmental Biotechnology Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology Delft, Netherlands
| | - Frederik Hammes
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute of Aquatic Science and Technology Dübendorf, Switzerland
| | - Mark C M van Loosdrecht
- Environmental Biotechnology Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology Delft, Netherlands
| | - Johannes S Vrouwenvelder
- Environmental Biotechnology Group, Department of Biotechnology, Faculty of Applied Sciences, Delft University of TechnologyDelft, Netherlands; Division of Biological and Environmental Science and Engineering, Water Desalination and Reuse Center, King Abdullah University of Science and TechnologyThuwal, Saudi Arabia; Wetsus - European Centre of Excellence for Sustainable Water TechnologyLeeuwarden, Netherlands
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Krämer CEM, Singh A, Helfrich S, Grünberger A, Wiechert W, Nöh K, Kohlheyer D. Non-Invasive Microbial Metabolic Activity Sensing at Single Cell Level by Perfusion of Calcein Acetoxymethyl Ester. PLoS One 2015; 10:e0141768. [PMID: 26513257 PMCID: PMC4625966 DOI: 10.1371/journal.pone.0141768] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/13/2015] [Indexed: 12/25/2022] Open
Abstract
Phase contrast microscopy cannot give sufficient information on bacterial metabolic activity, or if a cell is dead, it has the fate to die or it is in a viable but non-growing state. Thus, a reliable sensing of the metabolic activity helps to distinguish different categories of viability. We present a non-invasive instantaneous sensing method using a fluorogenic substrate for online monitoring of esterase activity and calcein efflux changes in growing wild type bacteria. The fluorescent conversion product of calcein acetoxymethyl ester (CAM) and its efflux indicates the metabolic activity of cells grown under different conditions at real-time. The dynamic conversion of CAM and the active efflux of fluorescent calcein were analyzed by combining microfluidic single cell cultivation technology and fluorescence time lapse microscopy. Thus, an instantaneous and non-invasive sensing method for apparent esterase activity was created without the requirement of genetic modification or harmful procedures. The metabolic activity sensing method consisting of esterase activity and calcein secretion was demonstrated in two applications. Firstly, growing colonies of our model organism Corynebacterium glutamicum were confronted with intermittent nutrient starvation by interrupting the supply of iron and carbon, respectively. Secondly, bacteria were exposed for one hour to fatal concentrations of antibiotics. Bacteria could be distinguished in growing and non-growing cells with metabolic activity as well as non-growing and non-fluorescent cells with no detectable esterase activity. Microfluidic single cell cultivation combined with high temporal resolution time-lapse microscopy facilitated monitoring metabolic activity of stressed cells and analyzing their descendants in the subsequent recovery phase. Results clearly show that the combination of CAM with a sampling free microfluidic approach is a powerful tool to gain insights in the metabolic activity of growing and non-growing bacteria.
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Affiliation(s)
| | - Abhijeet Singh
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Stefan Helfrich
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | | | - Wolfgang Wiechert
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Katharina Nöh
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Dietrich Kohlheyer
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- * E-mail:
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Königs AM, Flemming HC, Wingender J. Nanosilver induces a non-culturable but metabolically active state in Pseudomonas aeruginosa. Front Microbiol 2015; 6:395. [PMID: 25999929 PMCID: PMC4419727 DOI: 10.3389/fmicb.2015.00395] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/16/2015] [Indexed: 12/27/2022] Open
Abstract
The antimicrobial properties of silver nanoparticles (AgNPs) have raised expectations for the protection of medical devices and consumer products against biofilms. The effect of silver on bacteria is commonly determined by culture-dependent methods. It is as yet unknown if silver-exposed bacteria can enter a metabolically active but non-culturable state. In this study, the efficacy of chemically synthesized AgNPs and silver as silver nitrate (AgNO3) against planktonic cells and biofilms of Pseudomonas aeruginosa AdS was investigated in microtiter plate assays, using cultural as well as culture-independent methods. In liquid medium, AgNPs and AgNO3 inhibited both planktonic growth and biofilm formation. The efficacy of AgNPs and AgNO3 against established, 24 h-old biofilms and planktonic stationary-phase cells was compared by exposure to silver in deionized water. Loss of culturability of planktonic cells was always higher than that of the attached biofilms. However, resuspended biofilm cells became more susceptible to AgNPs and AgNO3 than attached biofilms. Thus, the physical state of bacteria within biofilms rendered them more tolerant to silver compared with the planktonic state. Silver-exposed cells that had become unculturable still displayed signs of viability: they contained rRNA, determined by fluorescent in situ hybridization, as an indicator for potential protein synthesis, maintained their membrane integrity as monitored by differential live/dead staining, and displayed significant levels of adenosine triphosphate. It was concluded that AgNPs and AgNO3 in concentrations at which culturability was inhibited, both planktonic and biofilm cells of P. aeruginosa were still intact and metabolically active, reminiscent of the viable but non-culturable state known to be induced in pathogenic bacteria in response to stress conditions. This observation is important for a realistic assessment of the antimicrobial properties of AgNPs.
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Affiliation(s)
- Alexa M. Königs
- Department of Aquatic Microbiology – Biofilm Centre, University Duisburg-Essen, EssenGermany
| | | | - Jost Wingender
- Department of Aquatic Microbiology – Biofilm Centre, University Duisburg-Essen, EssenGermany
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Bloomfield S, Exner M, Flemming HC, Goroncy-Bermes P, Hartemann P, Heeg P, Ilschner C, Krämer I, Merkens W, Oltmanns P, Rotter M, Rutala WA, Sonntag HG, Trautmann M. Lesser-known or hidden reservoirs of infection and implications for adequate prevention strategies: Where to look and what to look for. GMS HYGIENE AND INFECTION CONTROL 2015; 10:Doc04. [PMID: 25699227 PMCID: PMC4332272 DOI: 10.3205/dgkh000247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In developing hygiene strategies, in recent years, the major focus has been on the hands as the key route of infection transmission. However, there is a multitude of lesser-known and underestimated reservoirs for microorganisms which are the triggering sources and vehicles for outbreaks or sporadic cases of infection. Among those are water reservoirs such as sink drains, fixtures, decorative water fountains and waste-water treatment plants, frequently touched textile surfaces such as private curtains in hospitals and laundry, but also transvaginal ultrasound probes, parenteral drug products, and disinfectant wipe dispensers. The review of outbreak reports also reveals Gram-negative and multiple-drug resistant microorganisms to have become an increasingly frequent and severe threat in medical settings. In some instances, the causative organisms are particularly difficult to identify because they are concealed in biofilms or in a state referred to as viable but nonculturable, which eludes conventional culture media-based detection methods. There is an enormous preventative potential in these insights, which has not been fully tapped. New and emerging pathogens, novel pathogen detection methods, and hidden reservoirs of infection should hence be given special consideration when designing the layout of buildings and medical devices, but also when defining the core competencies for medical staff, establishing programmes for patient empowerment and education of the general public, and when implementing protocols for the prevention and control of infections in medical, community and domestic settings.
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Affiliation(s)
- Sally Bloomfield
- London School of Hygiene and Tropical Medicine, International Scientific Forum on Home Hygiene, London, UK
| | - Martin Exner
- Institute of Hygiene and Public Health, Bonn University, Bonn, Germany
| | | | | | - Philippe Hartemann
- Departement Environment et Santé Publique S.E.R.E.S., Faculté de Médicine, Nancy, France
| | - Peter Heeg
- Institute of Medical Microbiology and Hygiene, Tübingen, Germany
| | - Carola Ilschner
- Institute of Hygiene and Public Health, Bonn University, Bonn, Germany
| | - Irene Krämer
- Pharmacy Department of Mainz University, Mainz, Germany
| | | | | | | | | | | | - Matthias Trautmann
- Department of Hospital Hygiene at Stuttgart Hospital, Stuttgart, Germany
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Utility of propidium monoazide viability assay as a biomarker for a tuberculosis disease. Tuberculosis (Edinb) 2014; 95:179-85. [PMID: 25534168 DOI: 10.1016/j.tube.2014.11.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Accepted: 11/22/2014] [Indexed: 11/21/2022]
Abstract
Reliable laboratory diagnosis of tuberculosis (TB), including laboratory biomarkers of cure, remains a challenge. In our study we evaluated the performance of a Propidium Monoazide (PMA) assay for the detection of viable TB bacilli in sputum specimens during anti-TB chemotherapy and its potential use as a TB biomarker. The study was conducted at three centres on 1937 sputum specimens from 310 adult bacteriologically confirmed pulmonary TB patients obtained before commencing anti-TB treatment and at regular intervals afterwards. Performance of the PMA assay was assessed using various readout assays with bacteriology culture results and time to positivity on liquid media used as reference standards. Treatment of sputum with N-acetyl-cysteine was found to be fully compatible with the PMA assay. Good sensitivity and specificity (97.5% and 70.7-80.0%) for detection of live TB bacilli was achieved using the Xpert(®) MTB/RIF test as a readout assay. Tentative Ct and ΔCt thresholds for the Xpert(®) MTB/RIF system were proposed. Good correlation (r = 0.61) between Ct values and time to positivity of TB cultures on liquid media was demonstrated. The PMA method has potential in monitoring bacterial load in sputum specimens and so may have a role as a biomarker of cure in TB treatment.
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Arnoldini M, Heck T, Blanco-Fernández A, Hammes F. Monitoring of dynamic microbiological processes using real-time flow cytometry. PLoS One 2013; 8:e80117. [PMID: 24244624 PMCID: PMC3828236 DOI: 10.1371/journal.pone.0080117] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 09/29/2013] [Indexed: 11/18/2022] Open
Abstract
We describe a straightforward approach to continuously monitor a variety of highly dynamic microbiological processes in millisecond resolution with flow cytometry, using standard bench-top instrumentation. Four main experimental examples are provided, namely: (1) green fluorescent protein expression by antibiotic-stressed Escherichia coli, (2) fluorescent labeling of heat-induced membrane damage in an autochthonous freshwater bacterial community, (3) the initial growth response of late stationary E. coli cells inoculated into fresh growth media, and (4) oxidative disinfection of a mixed culture of auto-fluorescent microorganisms. These examples demonstrate the broad applicability of the method to diverse biological experiments, showing that it allows the collection of detailed, time-resolved information on complex processes.
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Affiliation(s)
- Markus Arnoldini
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute for Aquatic Science and Technology, Dübendorf, Switzerland
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Tobias Heck
- Laboratory for Biomaterials, Empa -Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
| | - Alfonso Blanco-Fernández
- Flow Cytometry Core Facilities, UCD-Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Dublin, Ireland
| | - Frederik Hammes
- Department of Environmental Microbiology, Eawag - Swiss Federal Institute for Aquatic Science and Technology, Dübendorf, Switzerland
- * E-mail:
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Brognaux A, Han S, Sørensen SJ, Lebeau F, Thonart P, Delvigne F. A low-cost, multiplexable, automated flow cytometry procedure for the characterization of microbial stress dynamics in bioreactors. Microb Cell Fact 2013; 12:100. [PMID: 24176169 PMCID: PMC4228430 DOI: 10.1186/1475-2859-12-100] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2013] [Accepted: 10/30/2013] [Indexed: 12/20/2022] Open
Abstract
Background Microbial cell population heterogeneity is now recognized as a major source of issues in the development and optimization of bioprocesses. Even if single cell technologies are available for the study of microbial population heterogeneity, only a few of these methods are available in order to study the dynamics of segregation directly in bioreactors. In this context, specific interfaces have been developed in order to connect a flow cytometer directly to a bioreactor for automated analyses. In this work, we propose a simplified version of such an interface and demonstrate its usefulness for multiplexed experiments. Results A low-cost automated flow cytometer has been used in order to monitor the synthesis of a destabilized Green Fluorescent Protein (GFP) under the regulation of the fis promoter and propidium iodide (PI) uptake. The results obtained showed that the dynamics of GFP synthesis are complex and can be attributed to a complex set of biological parameters, i.e. on the one hand the release of protein into the extracellular medium and its uptake modifying the activity of the fis promoter, and on the other hand the stability of the GFP molecule itself, which can be attributed to the protease content and energy status of the cells. In this respect, multiplexed experiments have shown a correlation between heat shock and ATP content and the stability of the reporter molecule. Conclusion This work demonstrates that a simplified version of on-line FC can be used at the process level or in a multiplexed version to investigate the dynamics of complex physiological mechanisms. In this respect, the determination of new on-line parameters derived from automated FC is of primary importance in order to fully integrate the power of FC in dedicated feedback control loops.
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Affiliation(s)
| | | | | | | | | | - Frank Delvigne
- Unité de Bio-industries/CWBI, Gembloux Agro-Bio Tech, Université de Liège, Passage des Déportés 2, Gembloux 5030, Belgium.
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Baldock D, Nebe-von-Caron G, Bongaerts R, Nocker A. Effect of acidic pH on flow cytometric detection of bacteria stained with SYBR Green I and their distinction from background. Methods Appl Fluoresc 2013; 1:045001. [PMID: 29148447 DOI: 10.1088/2050-6120/1/4/045001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Unspecific background caused by biotic or abiotic particles, cellular debris, or autofluorescence is a well-known interfering parameter when applying flow cytometry to the detection of microorganisms in combination with fluorescent dyes. We present here an attempt to suppress the background signal intensity and thus to improve the detection of microorganisms using the nucleic acid stain SYBR® Green I. It has been observed that the fluorescent signals from SYBR Green I are greatly reduced at acidic pH. When lowering the pH of pre-stained samples directly prior to flow cytometric analysis, we hypothesized that the signals from particles and cells with membrane damage might therefore be reduced. Signals from intact cells, temporarily maintaining a neutral cytosolic pH, should not be affected. We show here that this principle holds true for lowering background interference, whereas the signals of membrane-compromised dead cells are only affected weakly. Signals from intact live cells at low pH were mostly comparable to signals without acidification. Although this study was solely performed with SYBR® Green I, the principle of low pH flow cytometry (low pH-FCM) might hold promise when analyzing complex matrices with an abundance of non-cellular matter, especially when expanded to non-DNA binding dyes with a stronger pH dependence of fluorescence than SYBR Green I and a higher pKa value.
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Affiliation(s)
- Daniel Baldock
- Cranfield Water Science Institute, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
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Van Nevel S, Koetzsch S, Weilenmann HU, Boon N, Hammes F. Routine bacterial analysis with automated flow cytometry. J Microbiol Methods 2013; 94:73-76. [PMID: 23684992 DOI: 10.1016/j.mimet.2013.05.007] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/30/2022]
Abstract
The impact of multi-well plate automation on bacterial flow cytometric analyses was investigated. Cell concentrations in up to 96 samples can be measured accurately, as long as a reproducible staining protocol and a total measurement time of below 80 min is used. Fluorescence distribution in the samples may, however, display some variability.
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Affiliation(s)
- Sam Van Nevel
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Stefan Koetzsch
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Hans-Ulrich Weilenmann
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland
| | - Nico Boon
- Laboratory of Microbial Ecology and Technology (LabMET), Ghent University, Coupure Links 653, B-9000 Gent, Belgium
| | - Frederik Hammes
- Eawag, Swiss Federal Institute of Aquatic Science and Technology, CH-8600 Dübendorf, Switzerland.
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38
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Vanhauteghem D, Janssens GPJ, Lauwaerts A, Sys S, Boyen F, Cox E, Meyer E. Exposure to the proton scavenger glycine under alkaline conditions induces Escherichia coli viability loss. PLoS One 2013; 8:e60328. [PMID: 23544135 PMCID: PMC3609748 DOI: 10.1371/journal.pone.0060328] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 02/25/2013] [Indexed: 11/29/2022] Open
Abstract
Our previous work described a clear loss of Escherichia coli (E. coli) membrane integrity after incubation with glycine or its N-methylated derivatives N-methylglycine (sarcosine) and N,N-dimethylglycine (DMG), but not N,N,N-trimethylglycine (betaine), under alkaline stress conditions. The current study offers a thorough viability analysis, based on a combination of real-time physiological techniques, of E. coli exposed to glycine and its N-methylated derivatives at alkaline pH. Flow cytometry was applied to assess various physiological parameters such as membrane permeability, esterase activity, respiratory activity and membrane potential. ATP and inorganic phosphate concentrations were also determined. Membrane damage was confirmed through the measurement of nucleic acid leakage. Results further showed no loss of esterase or respiratory activity, while an instant and significant decrease in the ATP concentration occurred upon exposure to either glycine, sarcosine or DMG, but not betaine. There was a clear membrane hyperpolarization as well as a significant increase in cellular inorganic phosphate concentration. Based on these results, we suggest that the inability to sustain an adequate level of ATP combined with a decrease in membrane functionality leads to the loss of bacterial viability when exposed to the proton scavengers glycine, sarcosine and DMG at alkaline pH.
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Affiliation(s)
- Donna Vanhauteghem
- Department of Nutrition, Genetics and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium.
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Abstract
A great number of the bacteria and archaea on Earth are found in subsurface environments in a physiological state that is poorly represented or explained by laboratory cultures. Microbial cells in these very stable and oligotrophic settings catabolize 10⁴- to 10⁶-fold more slowly than model organisms in nutrient-rich cultures, turn over biomass on timescales of centuries to millennia rather than hours to days, and subsist with energy fluxes that are 1,000-fold lower than the typical culture-based estimates of maintenance requirements. To reconcile this disparate state of being with our knowledge of microbial physiology will require a revised understanding of microbial energy requirements, including identifying the factors that comprise true basal maintenance and the adaptations that might serve to minimize these factors.
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Pan Y, Kaatz L. Use of Image‐Based Flow Cytometry in Bacterial Viability Analysis Using Fluorescent Probes. ACTA ACUST UNITED AC 2012. [DOI: 10.1002/9780471729259.mc02c05s27] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Youwen Pan
- Technology Resources/Sterility Assurance, Baxter Healthcare Corporation Round Lake Illinois
| | - Laura Kaatz
- Technology Resources/Sterility Assurance, Baxter Healthcare Corporation Round Lake Illinois
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Rüger M, Bensch G, Tüngler R, Reichl U. A flow cytometric method for viability assessment of Staphylococcus aureus and Burkholderia cepacia in mixed culture. Cytometry A 2012; 81:1055-66. [PMID: 23081865 DOI: 10.1002/cyto.a.22219] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Revised: 09/07/2012] [Accepted: 09/20/2012] [Indexed: 11/06/2022]
Abstract
Mixed bacterial communities are commonly encountered in microbial infections of humans. Knowledge on the composition of species and viability of each species in these communities allows for a detailed description of the complexity of interspecies dynamics and contributes to the assessment of the severity of infections. Several assays exist for quantification of specific species in mixed communities, including analysis of quantitative terminal restriction fragment length polymorphisms. While this method allows for species-specific cell enumeration, it cannot provide viability data. In this study, flow cytometry was applied to assess the viability of Staphylococcus aureus and Burkholderia cepacia in mixed culture by membrane integrity analysis using SYBR® Green I and propidium iodide staining. Both bacteria are relevant to pulmonary infections of cystic fibrosis patients. Fluorescence staining was optimized separately for each species in pure culture due to differences between species in cell wall structure and metabolic capabilities. To determine viability of species in mixed culture, a protocol was established as a compromise between optimum conditions determined before for pure cultures. This protocol allowed the detection of viable and dead cells of both species, exhibiting an intact and a permeabilized membrane, respectively. To discriminate between S. aureus and B. cepacia, the protocol was combined with Gram-specific fluorescent staining using wheat germ agglutinin. The established three-color staining method was successfully tested for viability determination of S. aureus and B. cepacia in mixed culture cultivations. In addition, growth of both species was monitored by quantitative terminal restriction fragment length polymorphisms. The obtained data revealed alterations in viability during cultivations for different growth phases and suggest interspecies effects in mixed culture. Overall, this method allows for rapid simultaneous Gram-differentiation and viability assessment of bacterial mixed cultures and is therefore suitable for the analysis of dynamics of mixed communities of medical, environmental, and biotechnological relevance.
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Affiliation(s)
- Marc Rüger
- Chair of Bioprocess Engineering, Otto von Guericke University, Magdeburg, Germany.
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