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Hasan MS, Sundberg C, Gilotte E, Ge X, Kostov Y, Rao G. Bioburden detection on surface and water samples in a rapid, ultra-sensitive and high-throughput manner. Biotechnol Prog 2024:e3457. [PMID: 38494865 DOI: 10.1002/btpr.3457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 03/02/2024] [Accepted: 03/05/2024] [Indexed: 03/19/2024]
Abstract
Bioburden detection is crucial for food, water, and biopharmaceutical applications as it can directly impact public health. The objective of this study is to develop and validate an assay and protocol for detecting bioburden on solid surfaces, as well as in water, with high sensitivity and accuracy in a rapid manner. Henceforth, a resazurin-based assay optimized for detecting bioburden has been integrated with a previously developed portable multichannel fluorometer. The microbes were isolated from solid surfaces in different laboratory settings by swabbing technique, and stream water was collected for contamination analysis. Based on the results, the assay and protocol can successfully detect bioburden as low as 20 CFU/cm2 and 10 CFU/mL present in both surface and water samples, respectively.
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Affiliation(s)
- Md Sadique Hasan
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland, USA
- Department of Computer Science and Electrical Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Chad Sundberg
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland, USA
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Elias Gilotte
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland, USA
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Xudong Ge
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland, USA
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Yordan Kostov
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland, USA
| | - Govind Rao
- Center for Advanced Sensor Technology, University of Maryland Baltimore County, Baltimore, Maryland, USA
- Department of Chemical, Biochemical and Environmental Engineering, University of Maryland Baltimore County, Baltimore, Maryland, USA
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Boyte ME, Benkowski A, Pane M, Shehata HR. Probiotic and postbiotic analytical methods: a perspective of available enumeration techniques. Front Microbiol 2023; 14:1304621. [PMID: 38192285 PMCID: PMC10773886 DOI: 10.3389/fmicb.2023.1304621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/20/2023] [Indexed: 01/10/2024] Open
Abstract
Probiotics are the largest non-herbal/traditional dietary supplements category worldwide. To be effective, a probiotic strain must be delivered viable at an adequate dose proven to deliver a health benefit. The objective of this article is to provide an overview of the various technologies available for probiotic enumeration, including a general description of each technology, their advantages and limitations, and their potential for the future of the probiotics industry. The current "gold standard" for analytical quantification of probiotics in the probiotic industry is the Plate Count method (PC). PC measures the bacterial cell's ability to proliferate into detectable colonies, thus PC relies on cultivability as a measure of viability. Although viability has widely been measured by cultivability, there has been agreement that the definition of viability is not limited to cultivability. For example, bacterial cells may exist in a state known as viable but not culturable (VBNC) where the cells lose cultivability but can maintain some of the characteristics of viable cells as well as probiotic properties. This led to questioning the association between viability and cultivability and the accuracy of PC in enumerating all the viable cells in probiotic products. PC has always been an estimate of the number of viable cells and not a true cell count. Additionally, newer probiotic categories such as Next Generation Probiotics (NGPs) are difficult to culture in routine laboratories as NGPs are often strict anaerobes with extreme sensitivity to atmospheric oxygen. Thus, accurate quantification using culture-based techniques will be complicated. Another emerging category of biotics is postbiotics, which are inanimate microorganisms, also often referred to as tyndallized or heat-killed bacteria. Obviously, culture dependent methods are not suitable for these products, and alternative methods are needed for their quantification. Different methodologies provide a more complete picture of a heterogeneous bacterial population versus PC focusing exclusively on the eventual multiplication of the cells. Alternative culture-independent techniques including real-time PCR, digital PCR and flow cytometry are discussed. These methods can measure viability beyond cultivability (i.e., by measuring cellular enzymatic activity, membrane integrity or membrane potential), and depending on how they are designed they can achieve strain-specific enumeration.
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Affiliation(s)
- Marie-Eve Boyte
- NutraPharma Consulting Services Inc., Sainte-Anne-des-Plaines, QC, Canada
| | | | - Marco Pane
- Probiotical Research s.r.l., Novara, Italy
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Allkja J, Goeres DM, Azevedo AS, Azevedo NF. Interactions of microorganisms within a urinary catheter polymicrobial biofilm model. Biotechnol Bioeng 2023; 120:239-249. [PMID: 36123299 DOI: 10.1002/bit.28241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 09/07/2022] [Accepted: 09/11/2022] [Indexed: 11/11/2022]
Abstract
Biofilms are often polymicrobial in nature, which can impact their behavior and overall structure, often resulting in an increase in biomass and enhanced antimicrobial resistance. Using plate counts and locked nucleic acid/2'-O-methyl-RNA fluorescence in situ hybridization (LNA/2'OMe-FISH), we studied the interactions of four species commonly associated with catheter-associated urinary tract infections (CAUTI): Enterococcus faecalis, Escherichia coli, Candida albicans, and Proteus mirabilis. Eleven combinations of biofilms were grown on silicone coupons placed in 24-well plates for 24 h, 37°C, in artificial urine medium (AUM). Results showed that P. mirabilis was the dominant species and was able to inhibit both E. coli and C. albicans growth. In the absence of P. mirabilis, an antagonistic relationship between E. coli and C. albicans was observed, with the former being dominant. E. faecalis growth was not affected in any combination, showing a more mutualistic relationship with the other species. Imaging results correlated with the plate count data and provided visual verification of species undetected using the viable plate count. Moreover, the three bacterial species showed overall good repeatability SD (Sr ) values (0.1-0.54) in all combinations tested, whereas C. albicans had higher repeatability Sr values (0.36-1.18). The study showed the complexity of early-stage interactions in polymicrobial biofilms. These interactions could serve as a starting point when considering targets for preventing or treating CAUTI biofilms containing these species.
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Affiliation(s)
- Jontana Allkja
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal.,Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
| | - Darla M Goeres
- Center for Biofilm Engineering, Montana State University, Bozeman, Montana, USA
| | - Andreia S Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal.,Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (i3S), Universidade do Porto, Porto, Portugal.,Instituto de Patologia e Imunologia Molecular (IPATIMUP), Universidade do Porto, Porto, Portugal
| | - Nuno F Azevedo
- Laboratory for Process Engineering, Environment, Biotechnology and Energy (LEPABE), Faculty of Engineering, University of Porto, Porto, Portugal.,Associate Laboratory in Chemical Engineering (ALiCE), Faculty of Engineering, University of Porto, Porto, Portugal
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Hansen SJZ, Tang P, Kiefer A, Galles K, Wong C, Morovic W. Droplet Digital PCR Is an Improved Alternative Method for High-Quality Enumeration of Viable Probiotic Strains. Front Microbiol 2020; 10:3025. [PMID: 32038522 PMCID: PMC6987037 DOI: 10.3389/fmicb.2019.03025] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/17/2019] [Indexed: 12/15/2022] Open
Abstract
Traditional microbiological enumeration methods have long been employed as the standard evaluation procedure for probiotic microorganisms. These methods are labor intensive, have long-time to results and inherently have a high degree of variability – up to 35%. As clinical probiotic and microbiome science continues to grow and develop, it is increasingly important that researchers thoroughly define and deliver the targeted probiotic dose. Furthermore, to establish high quality commercial products, the same dosage level must be administered to consumers. An ISO method for the use of flow cytometry has been established which does speed up the time to results and reduce variability, but the method has not yet gained widespread adoption across the probiotic industry. This is possibly due to expertise needed to implement and maintain a new testing platform in an established quality system. In this study we compare enumeration using plate counts and flow cytometry to the use of droplet digital PCR (ddPCR), which in addition to giving faster time to results than plate count and less variability than both plate count and flow cytometry, has additional benefits such as strain-specific counts. Use of ddPCR gives the ability to design primers to target deletions and single base pair differences which will allow for strain profiling in microbiome analyses. We demonstrate that ddPCR probiotic enumeration results are positively correlated to both plate count and flow cytometry results and should be considered a viable, next generation enumeration method for the evaluation of probiotics.
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Affiliation(s)
| | - Peipei Tang
- DuPont Nutrition & Biosciences, Madison, WI, United States
| | - Anthony Kiefer
- DuPont Nutrition & Biosciences, Madison, WI, United States
| | - Kevin Galles
- DuPont Nutrition & Biosciences, Madison, WI, United States
| | - Connie Wong
- DuPont Nutrition & Biosciences, Madison, WI, United States
| | - Wesley Morovic
- DuPont Nutrition & Biosciences, Madison, WI, United States
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Grossi M, Parolin C, Vitali B, Riccò B. Computer Vision Approach for the Determination of Microbial Concentration and Growth Kinetics Using a Low Cost Sensor System. Sensors (Basel) 2019; 19:s19245367. [PMID: 31817434 PMCID: PMC6960508 DOI: 10.3390/s19245367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 11/30/2019] [Accepted: 12/02/2019] [Indexed: 11/26/2022]
Abstract
The measurement of microbial contamination is of primary importance in different fields, from environmental monitoring to food safety and clinical analysis. Today, almost all microbiology laboratories make microbial concentration measurements using the standard Plate Count Technique (PCT), a manual method that must be performed by trained personnel. Since manual PCT analysis can result in eye fatigue and errors, in particular when hundreds of samples are processed every day, automatic colony counters have been built and are commercially available. While quick and reliable, these instruments are generally expensive, thus, portable colony counters based on smartphones have been developed and are of low cost but also not accurate as the commercial benchtop instruments. In this paper, a novel computer vision sensor system is presented that can measure the microbial concentration of a sample under test and also estimate the microbial growth kinetics by monitoring the colonies grown on a Petri dish at regular time intervals. The proposed method has been in-house validated by performing PCT analysis in parallel under the same conditions and using these results as a reference. All the measurements have been carried out in a laboratory using benchtop instruments, however, such a system can also be realized as an embedded sensor system to be deployed for microbial analysis outside a laboratory environment.
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Affiliation(s)
- Marco Grossi
- Department of Electrical Energy and Information Engineering “Guglielmo Marconi” (DEI), University of Bologna, 40136 Bologna, Italy;
- Correspondence: ; Tel.: +39-051-2093038
| | - Carola Parolin
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40127 Bologna, Italy; (C.P.); (B.V.)
| | - Beatrice Vitali
- Department of Pharmacy and Biotechnology (FaBiT), University of Bologna, 40127 Bologna, Italy; (C.P.); (B.V.)
| | - Bruno Riccò
- Department of Electrical Energy and Information Engineering “Guglielmo Marconi” (DEI), University of Bologna, 40136 Bologna, Italy;
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Hansen SJZ, Morovic W, DeMeules M, Stahl B, Sindelar CW. Absolute Enumeration of Probiotic Strains Lactobacillus acidophilus NCFM ® and Bifidobacterium animalis subsp. lactis Bl-04 ® via Chip-Based Digital PCR. Front Microbiol 2018; 9:704. [PMID: 29696008 PMCID: PMC5904286 DOI: 10.3389/fmicb.2018.00704] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2017] [Accepted: 03/27/2018] [Indexed: 12/16/2022] Open
Abstract
The current standard for enumeration of probiotics to obtain colony forming units by plate counts has several drawbacks: long time to results, high variability and the inability to discern between bacterial strains. Accurate probiotic cell counts are important to confirm the delivery of a clinically documented dose for its associated health benefits. A method is described using chip-based digital PCR (cdPCR) to enumerate Bifidobacterium animalis subsp. lactis Bl-04 and Lactobacillus acidophilus NCFM both as single strains and in combination. Primers and probes were designed to differentiate the target strains against other strains of the same species using known single copy, genetic differences. The assay was optimized to include propidium monoazide pre-treatment to prevent amplification of DNA associated with dead probiotic cells as well as liberation of DNA from cells with intact membranes using bead beating. The resulting assay was able to successfully enumerate each strain whether alone or in multiplex. The cdPCR method had a 4 and 5% relative standard deviation (RSD) for Bl-04 and NCFM, respectively, making it more precise than plate counts with an industry accepted RSD of 15%. cdPCR has the potential to replace traditional plate counts because of its precision, strain specificity and the ability to obtain results in a matter of hours.
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Affiliation(s)
- Sarah J Z Hansen
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
| | - Wesley Morovic
- Genomics and Microbiome Sciences, DuPont Nutrition & Health, Madison, WI, United States
| | - Martha DeMeules
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
| | - Buffy Stahl
- Genomics and Microbiome Sciences, DuPont Nutrition & Health, Madison, WI, United States
| | - Connie W Sindelar
- Probiotic Development, DuPont Nutrition & Health, Madison, WI, United States
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Lin WR, Wang PH, Chen WC, Lai CM, Winder RS. Responses of Soil Fungal Populations and Communities to the Thinning of Cryptomeria Japonica Forests. Microbes Environ 2016; 31:19-26. [PMID: 26903369 PMCID: PMC4791111 DOI: 10.1264/jsme2.me15127] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/19/2015] [Indexed: 11/12/2022] Open
Abstract
Forest management activities, such as tree thinning, alter forest ecology, including key components of forest ecosystems, including fungal communities. In the present study, we investigate the effects of forest thinning intensity on the populations and structures of fungal soil communities in the Cryptomeria japonica forests of central Taiwan as well as the dynamics of soil fungi communities in these forests after a thinning disturbance. Although the populations of soil fungi significantly increased in the first 6 months after thinning, these increases had subsided by 9 months. This pulse was attributed to a transient increase in the populations of rapid colonizers. A multiple regression analysis positively correlated fungal populations with organic matter content and cellulase activity. Thinning initially provided large amounts of fresh leaves and roots as nutrient-rich substrates for soil fungi. Denaturing gradient gel electrophoresis (DGGE) profiles indicated that soil fungal communities significantly differed among plots with 0% (control), 25%, and 50% tree thinning in the first 21 months post-thinning, with no significant differences being observed after 21 months. The fungal communities of these forest soils also changed with the seasons, and an interactive relationship was detected between seasons and treatments. Seasonal variations in fungal communities were the most pronounced after 50% tree thinning. The results of the present study demonstrate that the soil fungi of Taiwanese C. japonica forests are very sensitive to thinning disturbances, but recover stability after a relatively short period of time.
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Affiliation(s)
- Wan-Rou Lin
- Department of Life Sciences, Tunghai UniversityNo. 1727, Sec. 4, Taiwan Boulevard, Taichung 40704Taiwan
| | - Pi-Han Wang
- Department of Life Sciences, Tunghai UniversityNo. 1727, Sec. 4, Taiwan Boulevard, Taichung 40704Taiwan
| | - Wen-Cheng Chen
- Department of Life Sciences, Tunghai UniversityNo. 1727, Sec. 4, Taiwan Boulevard, Taichung 40704Taiwan
| | - Chao-Ming Lai
- Department of Agricultural Chemistry, National Taiwan UniversityNo. 1, Sec. 4, Roosevelt Road, Taipei, Taiwan 10617
| | - Richard Scott Winder
- Natural Resources Canada, Canadian Forest Service, Pacific Forestry Centre506 West Burnside Road, Victoria, British Columbia V8Z 1M5Canada
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Bajwa A, Tan ST, Mehta R, Bahreyni B. Rapid detection of viable microorganisms based on a plate count technique using arrayed microelectrodes. Sensors (Basel) 2013; 13:8188-98. [PMID: 23803788 PMCID: PMC3758590 DOI: 10.3390/s130708188] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/22/2013] [Accepted: 06/06/2013] [Indexed: 12/19/2022]
Abstract
Development of a miniaturized biosensor system that can be used for rapid detection and counting of microorganisms in food or water samples is described. The developed microsystem employs a highly sensitive impedimetric array of biosensors to monitor the growth of bacterial colonies that are dispersed across an agar growth medium. To use the system, a sample containing the bacteria is cultured above the agar layer. Using a multiplexing network, the electrical properties of the medium at different locations are continuously measured, recorded, and compared against a baseline signal. Variations of signals from different biosensors are used to reveal the presence of bacteria in the sample, as well as the locations of bacterial colonies across the biochip. This technique forms the basis for a label-free bacterial detection for rapid analysis of food samples, reducing the detection time by at least a factor of four compared to the current required incubation times of 24 to 72 hours for plate count techniques. The developed microsystem has the potential for miniaturization to a stage where it could be deployed for rapid analysis of food samples at commercial scale at laboratories, food processing facilities, and retailers.
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Affiliation(s)
- Avneet Bajwa
- Alberta Health Services, Calgary, AB T2N 2T9, Canada; E-Mail:
| | - Shaoqing Tim Tan
- School of Mechatronic Systems Engineering, Simon Fraser University, Surrey, BC V3T 0A3, Canada; E-Mail:
| | - Ram Mehta
- PBR Laboratories Inc., Edmonton, AB T6E 0P5, Canada; E-Mail:
| | - Behraad Bahreyni
- School of Mechatronic Systems Engineering, Simon Fraser University, Surrey, BC V3T 0A3, Canada; E-Mail:
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