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Lahmamsi H, Ananou S, Lahlali R, Tahiri A. Lactic acid bacteria as an eco-friendly approach in plant production: Current state and prospects. Folia Microbiol (Praha) 2024; 69:465-489. [PMID: 38393576 DOI: 10.1007/s12223-024-01146-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 01/31/2024] [Indexed: 02/25/2024]
Abstract
Since the late nineteenth century, the agricultural sector has experienced a tremendous increase in chemical use in response to the growing population. Consequently, the intensive and indiscriminate use of these substances caused serious damage on several levels, including threatening human health, disrupting soil microbiota, affecting wildlife ecosystems, and causing groundwater pollution. As a solution, the application of microbial-based products presents an interesting and ecological restoration tool. The use of Plant Growth-Promoting Microbes (PGPM) affected positive production, by increasing its efficiency, reducing production costs, environmental pollution, and chemical use. Among these microbial communities, lactic acid bacteria (LAB) are considered an interesting candidate to be formulated and applied as effective microbes. Indeed, these bacteria are approved by the European Food Safety Authority (EFSA) and Food and Drug Administration (FDA) as Qualified Presumption of Safety statute and Generally Recognized as Safe for various applications. To do so, this review comes as a road map for future research, which addresses the different steps included in LAB formulation as biocontrol, bioremediation, or plant growth promoting agents from the isolation process to their field application passing by the different identification methods and their various uses. The plant application methods as well as challenges limiting their use in agriculture are also discussed.
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Affiliation(s)
- Haitam Lahmamsi
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco
| | - Samir Ananou
- Laboratoire de Biotechnologie Microbienne et Molécules Bioactives, Faculté des Sciences et Techniques, Université Sidi Mohamed Ben Abdellah, Route Immouzer BP 2202, Fez, Morocco
| | - Rachid Lahlali
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
| | - Abdessalem Tahiri
- Unité de Phytopathologie, Département de Protection des Plantes, Ecole Nationale d'Agriculture, Km10, Rt Haj Kaddour, BP S/40, 50001, Meknes, Morocco.
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Stachelska MA, Ekielski A, Karpiński P, Żelaziński T, Kruszewski B. New Genetic Determinants for qPCR Identification and the Enumeration of Selected Lactic Acid Bacteria in Raw-Milk Cheese. Molecules 2024; 29:1533. [PMID: 38611811 PMCID: PMC11013805 DOI: 10.3390/molecules29071533] [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: 02/09/2024] [Revised: 03/21/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
Lactic acid bacteria (LAB) play an important role in the ripening of cheeses and contribute to the development of the desired profile of aroma and flavor compounds. Therefore, it is very important to monitor the dynamics of bacterial proliferation in order to obtain an accurate and reliable number of their cells at each stage of cheese ripening. This work aimed to identify and conduct a quantitative assessment of the selected species of autochthonous lactic acid bacteria from raw cow's milk cheese by the development of primers and probe pairs based on the uniqueness of the genetic determinants with which the target microorganisms can be identified. For that purpose, we applied real-time quantitative PCR (qPCR) protocols to quantify Lactobacillus delbrueckii subsp. bulgaricus, Streptococcus thermophilus, and Lactococcus lactis subsp. cremoris cells in cheese directly after production and over three-month and six-month ripening periods. While L. lactis subsp. cremoris shows good acidification ability and the ability to produce antimicrobial compounds, L. delbrueckii subsp. bulgaricus has good proteolytic ability and produces exo-polysaccharides, and S. thermophilus takes part in the formation of the diacetyl flavor compound by metabolizing citrate to develop aroma, they all play an important role in the cheese ripening. The proposed qPCR protocols are very sensitive and reliable methods for a precise enumeration of L. delbrueckii subsp. bulgaricus, S. thermophilus, and L. lactis subsp. cremoris in cheese samples.
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Affiliation(s)
- Milena Alicja Stachelska
- Faculty of Computer Science and Technology, University of Lomza, Akademicka 14, 18-400 Lomza, Poland;
| | - Adam Ekielski
- Department of Production Engineering, Institute of Mechanical Engineering, Warsaw University of Life Sciences-SGGW, Nowoursynowska 164, 02-787 Warsaw, Poland; (A.E.); (T.Ż.)
| | - Piotr Karpiński
- Faculty of Computer Science and Technology, University of Lomza, Akademicka 14, 18-400 Lomza, Poland;
| | - Tomasz Żelaziński
- Department of Production Engineering, Institute of Mechanical Engineering, Warsaw University of Life Sciences-SGGW, Nowoursynowska 164, 02-787 Warsaw, Poland; (A.E.); (T.Ż.)
| | - Bartosz Kruszewski
- Department of Food Technology and Assessment, Institute of Food Sciences, Warsaw University of Life Sciences-SGGW, Nowoursynowska 159 C, 02-776 Warsaw, Poland
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White K, Eraclio G, McDonnell B, Bottacini F, Lugli GA, Ventura M, Volontè F, Dal Bello F, Mahony J, van Sinderen D. A multifaceted investigation of lactococcal strain diversity in undefined mesophilic starter cultures. Appl Environ Microbiol 2024; 90:e0215223. [PMID: 38334291 PMCID: PMC10952461 DOI: 10.1128/aem.02152-23] [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: 11/29/2023] [Accepted: 12/20/2023] [Indexed: 02/10/2024] Open
Abstract
The dairy fermentation industry relies on the activity of lactic acid bacteria in robust starter cultures to accomplish milk acidification. Maintenance of the composition of these starter cultures, whether defined or undefined, is essential to ensure consistent and high-quality fermentation end products. To date, limited information exists regarding the microbial composition of undefined starter culture systems. Here, we describe a culture-based analysis combined with a metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, we describe a qPCR-based genotype detection assay, which is capable of discerning nine distinct lactococcal genotypes to characterize these undefined starter cultures, and which can be applied to monitor compositional changes in an undefined starter culture during a fermentation. IMPORTANCE This study reports on the development of a combined culture-based analysis and metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, a novel qPCR-based genotype detection assay, capable of discerning nine distinct lactococcal genotypes (based on lactococcal cell wall polysaccharide biosynthesis gene clusters), was used to monitor compositional changes in an undefined starter culture following phage attack. These analytical approaches facilitate a multifaceted assessment of starter culture compositional stability during milk fermentation, which has become an important QC aspect due to the increasing demand for consistent and high-quality dairy products.
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Affiliation(s)
- Kelsey White
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | | | - Brian McDonnell
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Francesca Bottacini
- APC Microbiome Ireland, University College Cork, Cork, Ireland
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | - Gabriele Andrea Lugli
- Department of Chemistry, Life Sciences, and Environmental Sustainability, Laboratory of Probiogenomics,University of Parma, Parma, Italy
| | - Marco Ventura
- Department of Chemistry, Life Sciences, and Environmental Sustainability, Laboratory of Probiogenomics,University of Parma, Parma, Italy
| | | | | | - Jennifer Mahony
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Douwe van Sinderen
- School of Microbiology, University College Cork, Cork, Ireland
- APC Microbiome Ireland, University College Cork, Cork, Ireland
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Marcos-Fernández R, Sánchez B, Ruiz L, Margolles A. Convergence of flow cytometry and bacteriology. Current and future applications: a focus on food and clinical microbiology. Crit Rev Microbiol 2023; 49:556-577. [PMID: 35749433 DOI: 10.1080/1040841x.2022.2086035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 05/12/2022] [Accepted: 05/31/2022] [Indexed: 11/03/2022]
Abstract
Since its development in the 1960s, flow cytometry (FCM) was quickly revealed a powerful tool to analyse cell populations in medical studies, yet, for many years, was almost exclusively used to analyse eukaryotic cells. Instrument and methodological limitations to distinguish genuine bacterial signals from the background, among other limitations, have hampered FCM applications in bacteriology. In recent years, thanks to the continuous development of FCM instruments and methods with a higher discriminatory capacity to detect low-size particles, FCM has emerged as an appealing technique to advance the study of microbes, with important applications in research, clinical and industrial settings. The capacity to rapidly enumerate and classify individual bacterial cells based on viability facilitates the monitoring of bacterial presence in foodstuffs or clinical samples, reducing the time needed to detect contamination or infectious processes. Besides, FCM has stood out as a valuable tool to advance the study of complex microbial communities, or microbiomes, that are very relevant in the context of human health, as well as to understand the interaction of bacterial and host cells. This review highlights current developments in, and future applications of, FCM in bacteriology, with a focus on those related to food and clinical microbiology.
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Affiliation(s)
- Raquel Marcos-Fernández
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Borja Sánchez
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Lorena Ruiz
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
| | - Abelardo Margolles
- Department of Microbiology and Biochemistry of Dairy Products, Dairy Research Institute of Asturias, Spanish National Research Council (IPLA-CSIC), Asturias, Spain
- Functionality and Ecology of Beneficial Microbes (MicroHealth) Group, Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), Asturias, Spain
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5
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Jha S, Anand S. Development and Control of Biofilms: Novel Strategies Using Natural Antimicrobials. MEMBRANES 2023; 13:579. [PMID: 37367783 DOI: 10.3390/membranes13060579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/30/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023]
Abstract
Separation membranes have a wide application in the food industry, for instance, in the clarification/fractionation of milk, the concentration/separation of selected components, and wastewater treatment. They provide a large area for bacteria to attach and colonize. When a product comes into contact with a membrane, it initiates bacterial attachment/colonization and eventually forms biofilms. Several cleaning and sanitation protocols are currently utilized in the industry; however, the heavy fouling of the membrane over a prolonged duration affects the overall cleaning efficiency. In view of this, alternative approaches are being developed. Therefore, the objective of this review is to describe the novel strategies for controlling membrane biofilms such as enzyme-based cleaner, naturally produced antimicrobials of microbial origin, and preventing biofilm development using quorum interruption. Additionally, it aims to report the constitutive microflora of the membrane and the development of the predominance of resistant strains over prolonged usage. The emergence of predominance could be associated with several factors, of which, the release of antimicrobial peptides by selective strains is a prominent factor. Therefore, naturally produced antimicrobials of microbial origin could thus provide a promising approach to control biofilms. Such an intervention strategy could be implemented by developing a bio-sanitizer exhibiting antimicrobial activity against resistant biofilms.
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Affiliation(s)
- Sheetal Jha
- Dairy and Food Science Department, South Dakota State University, Brookings, SD 57007, USA
| | - Sanjeev Anand
- Dairy and Food Science Department, South Dakota State University, Brookings, SD 57007, USA
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6
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Wang J, Kong K, Guo C, Yin G, Meng S, Lan L, Luo L, Song Y. Cultureless enumeration of live bacteria in urinary tract infection by single-cell Raman spectroscopy. Front Microbiol 2023; 14:1144607. [PMID: 37032883 PMCID: PMC10076591 DOI: 10.3389/fmicb.2023.1144607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Accepted: 03/06/2023] [Indexed: 04/11/2023] Open
Abstract
Urinary tract infections (UTIs) are the most common outpatient infections. Obtaining the concentration of live pathogens in the sample is crucial for the treatment. Still, the enumeration depends on urine culture and plate counting, which requires days of turn-around time (TAT). Single-cell Raman spectra combined with deuterium isotope probing (Raman-DIP) has been proven to identify the metabolic-active bacteria with high accuracy but is not able to reveal the number of live pathogens due to bacteria replication during the Raman-DIP process. In this study, we established a new approach of using sodium acetate to inhibit the replication of the pathogen and applying Raman-DIP to identify the active single cells. By combining microscopic image stitching and recognition, we could further improve the efficiency of the new method. Validation of the new method on nine artificial urine samples indicated that the exact number of live pathogens obtained with Raman-DIP is consistent with plate-counting while shortening the TAT from 18 h to within 3 h, and the potential of applying Raman-DIP for pathogen enumeration in clinics is promising.
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Affiliation(s)
- Jingkai Wang
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Kang Kong
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Chen Guo
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China
| | - Guangyao Yin
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Siyu Meng
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
| | - Lu Lan
- VibroniX, Inc., Suzhou, China
| | - Liqiang Luo
- Department of Chemistry, College of Sciences, Shanghai University, Shanghai, China
| | - Yizhi Song
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou, China
- Division of Life Sciences and Medicine, School of Biomedical Engineering (Suzhou), University of Science and Technology of China, Suzhou, China
- Chongqing Guoke Medical Technology Development Co., Ltd., Chongqing, China
- *Correspondence: Yizhi Song,
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7
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Comparative qualitative and quantitative analysis of lactic acid bacteria by molecular methods in different Greek cheeses. J DAIRY RES 2022; 89:449-452. [PMID: 36484133 DOI: 10.1017/s0022029922000760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In the present research communication, we report on identification and quantification of four main lactic acid bacteria (LAB) genera (Lactococcus, Lactobacillus, Streptococcus and Leuconostoc), most common in Greek cheeses, by a novel culture-independent method. More specifically, new primers were designed to be used in both multiplex PCR for simultaneous identification and in real-time PCR for quantification of the LAB. The method was validated by applying it in parallel to culture-dependent method in a variety of cheeses from different Greek geographical locations, of different animal milk origins and of different production methods. While the standard plate culture method showed absence of Leuconostoc sp. in all cheeses, the culture-independent methods detected all four LAB genera studied. Furthermore, the relative presence of the four genera detected by the culture-independent method showed a pattern present in almost all cheese samples tested, indicating Lactococcus genus as the dominant one.
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8
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Pereira AC, Tenreiro A, Cunha MV. When FLOW-FISH met FACS: Combining multiparametric, dynamic approaches for microbial single-cell research in the total environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150682. [PMID: 34600998 DOI: 10.1016/j.scitotenv.2021.150682] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/22/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
In environmental microbiology, the ability to assess, in a high-throughput way, single-cells within microbial communities is key to understand their heterogeneity. Fluorescence in situ hybridization (FISH) uses fluorescently labeled oligonucleotide probes to detect, identify, and quantify single cells of specific taxonomic groups. The combination of Flow Cytometry (FLOW) with FISH (FLOW-FISH) enables high-throughput quantification of complex whole cell populations, which when associated with fluorescence-activated cell sorting (FACS) enables sorting of target microorganisms. These sorted cells may be investigated in many ways, for instance opening new avenues for cytomics at a single-cell scale. In this review, an overview of FISH and FLOW methodologies is provided, addressing conventional methods, signal amplification approaches, common fluorophores for cell physiology parameters evaluation, and model variation techniques as well. The coupling of FLOW-FISH-FACS is explored in the context of different downstream applications of sorted cells. Current and emerging applications in environmental microbiology to outline the interactions and processes of complex microbial communities within soil, water, animal microbiota, polymicrobial biofilms, and food samples, are described.
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Affiliation(s)
- André C Pereira
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Ana Tenreiro
- Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências da Universidade de Lisboa, Lisboa, Portugal.
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9
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Zand E, Froehling A, Schoenher C, Zunabovic-Pichler M, Schlueter O, Jaeger H. Potential of Flow Cytometric Approaches for Rapid Microbial Detection and Characterization in the Food Industry-A Review. Foods 2021; 10:3112. [PMID: 34945663 PMCID: PMC8701031 DOI: 10.3390/foods10123112] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/14/2021] [Accepted: 11/16/2021] [Indexed: 12/11/2022] Open
Abstract
As microbial contamination is persistent within the food and bioindustries and foodborne infections are still a significant cause of death, the detection, monitoring, and characterization of pathogens and spoilage microorganisms are of great importance. However, the current methods do not meet all relevant criteria. They either show (i) inadequate sensitivity, rapidity, and effectiveness; (ii) a high workload and time requirement; or (iii) difficulties in differentiating between viable and non-viable cells. Flow cytometry (FCM) represents an approach to overcome such limitations. Thus, this comprehensive literature review focuses on the potential of FCM and fluorescence in situ hybridization (FISH) for food and bioindustry applications. First, the principles of FCM and FISH and basic staining methods are discussed, and critical areas for microbial contamination, including abiotic and biotic surfaces, water, and air, are characterized. State-of-the-art non-specific FCM and specific FISH approaches are described, and their limitations are highlighted. One such limitation is the use of toxic and mutagenic fluorochromes and probes. Alternative staining and hybridization approaches are presented, along with other strategies to overcome the current challenges. Further research needs are outlined in order to make FCM and FISH even more suitable monitoring and detection tools for food quality and safety and environmental and clinical approaches.
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Affiliation(s)
- Elena Zand
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
| | - Antje Froehling
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Christoph Schoenher
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Marija Zunabovic-Pichler
- Institute of Sanitary Engineering and Water Pollution Control, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (C.S.); (M.Z.-P.)
| | - Oliver Schlueter
- Leibniz Institute for Agricultural Engineering and Bioeconomy, Quality and Safety of Food and Feed, 14469 Potsdam, Germany; (A.F.); (O.S.)
| | - Henry Jaeger
- Department of Food Science and Technology, Institute of Food Technology, University of Natural Resources and Life Sciences Vienna (BOKU), 1190 Vienna, Austria;
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10
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Azevedo AS, Rocha R, Dias N. Flow-FISH Using Nucleic Acid Mimic Probes for the Detection of Bacteria. Methods Mol Biol 2021; 2246:263-277. [PMID: 33576995 DOI: 10.1007/978-1-0716-1115-9_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Flow-Fluorescence in situ hybridization (Flow-FISH) enables multiparametric high-throughput detection of target nucleic acid sequences at the single cell-level, allowing an accurate quantification of different cell populations by using a combination of flow cytometry and fluorescent in situ hybridization (FISH). In this chapter, a flow-FISH protocol is described with labeled nucleic acid mimics (NAMs) (e.g. LNA/2'OMe and PNA) acting as the reporter molecules. This protocol allows for the specific detection of bacterial cells. Hence, this protocol can be carried out with minor adjustments, in order to simultaneously detect different species of bacteria in different types of clinical, food, or environmental samples.
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Affiliation(s)
- Andreia S Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal. .,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal. .,IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, University of Porto, Porto, Portugal. .,CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal.
| | - Rui Rocha
- CISAS - Centre for Research and Development in Agrifood Systems and Sustainability, Escola Superior de Tecnologia e Gestão, Instituto Politécnico de Viana do Castelo, Viana do Castelo, Portugal
| | - Nicolina Dias
- CEB - Centre of Biological Engineering, University of Minho, Braga, Portugal
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11
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Thompson HF, Summers S, Yuecel R, Gutierrez T. Hydrocarbon-Degrading Bacteria Found Tightly Associated with the 50-70 μm Cell-Size Population of Eukaryotic Phytoplankton in Surface Waters of a Northeast Atlantic Region. Microorganisms 2020; 8:microorganisms8121955. [PMID: 33317100 PMCID: PMC7763645 DOI: 10.3390/microorganisms8121955] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 11/30/2020] [Accepted: 12/03/2020] [Indexed: 11/17/2022] Open
Abstract
The surface of marine eukaryotic phytoplankton can harbour communities of hydrocarbon-degrading bacteria; however, this algal–bacterial association has, hitherto, been only examined with non-axenic laboratory cultures of micro-algae. In this study, we isolated an operationally-defined community of phytoplankton, of cell size 50–70 μm, from a natural community in sea surface waters of a subarctic region in the northeast Atlantic. Using MiSeq 16S rRNA sequencing, we identified several recognized (Alcanivorax, Marinobacter, Oleispira, Porticoccus, Thalassospira) and putative hydrocarbon degraders (Colwelliaceae, Vibrionaceae) tightly associated with the phytoplankton population. We combined fluorescence in situ hybridisation with flow-cytometry (FISH-Flow) to examine the association of Marinobacter with this natural eukaryotic phytoplankton population. About 1.5% of the phytoplankton population contained tightly associated Marinobacter. The remaining Marinobacter population were loosely associated with either eukaryotic phytoplankton cells or non-chlorophyll particulate material. This work is the first to show the presence of obligate, generalist and putative hydrocarbonoclastic bacteria associated with natural populations of eukaryotic phytoplankton directly from sea surface water samples. It also highlights the suitability of FISH-Flow for future studies to examine the spatial and temporal structure and dynamics of these and other algal–bacterial associations in natural seawater samples.
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Affiliation(s)
- Haydn Frank Thompson
- Institute of Mechanical, Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (H.F.T.); (S.S.)
| | - Stephen Summers
- Institute of Mechanical, Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (H.F.T.); (S.S.)
- The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551, Singapore
| | - Raif Yuecel
- Iain Fraser Cytometry Centre, Institute of Medical Sciences IMS, University of Aberdeen, Aberdeen AB25 2ZD, UK;
- Exeter Centre for Cytomics (EXCC), College of Life and Environmental Sciences, University of Exeter, Exeter, EX4 4QD, UK
| | - Tony Gutierrez
- Institute of Mechanical, Process and Energy Engineering (IMPEE), School of Engineering and Physical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; (H.F.T.); (S.S.)
- Correspondence:
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12
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Sharma A, Lee S, Park YS. Molecular typing tools for identifying and characterizing lactic acid bacteria: a review. Food Sci Biotechnol 2020; 29:1301-1318. [PMID: 32995049 PMCID: PMC7492335 DOI: 10.1007/s10068-020-00802-x] [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: 05/01/2020] [Revised: 07/21/2020] [Accepted: 07/24/2020] [Indexed: 02/08/2023] Open
Abstract
Identification and classification of beneficial microbes is of the highest significance in food science and related industries. Conventional phenotypic approaches pose many challenges, and they may misidentify a target, limiting their use. Genotyping tools show comparatively better prospects, and they are widely used for distinguishing microorganisms. The techniques already employed in genotyping of lactic acid bacteria (LAB) are slightly different from one another, and each tool has its own advantages and disadvantages. This review paper compiles the comprehensive details of several fingerprinting tools that have been used for identifying and characterizing LAB at the species, sub-species, and strain levels. Notably, most of these approaches are based on restriction digestion, amplification using polymerase chain reaction, and sequencing. Nowadays, DNA sequencing technologies have made considerable progress in terms of cost, throughput, and methodology. A research journey to develop improved versions of generally applicable and economically viable tools for fingerprinting analysis is ongoing globally.
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Affiliation(s)
- Anshul Sharma
- Department of Food and Nutrition, Gachon University, Seongnam, 13120 Republic of Korea.,Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Bajhol, Solan, Himachal Pradesh 173229 India
| | - Sulhee Lee
- Research Group of Healthcare, Korea Food Research Institute, Wanju, 55365 Republic of Korea
| | - Young-Seo Park
- Department of Food Science and Biotechnology, Gachon University, Seongnam, 13120 Republic of Korea
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Branco P, Candeias A, Caldeira AT, González-Pérez M. A simple procedure for detecting Dekkera bruxellensis in wine environment by RNA-FISH using a novel probe. Int J Food Microbiol 2020; 314:108415. [PMID: 31707175 DOI: 10.1016/j.ijfoodmicro.2019.108415] [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] [Received: 05/17/2019] [Revised: 09/30/2019] [Accepted: 10/28/2019] [Indexed: 11/30/2022]
Abstract
Dekkera bruxellensis, considered the major microbial contaminant in wine production, produces 4-ethylphenol, a cause of unpleasant odors. Thus, identification of this yeast before wine spoilage is crucial. Although challenging, it could be achieved using a simple technique: RNA-FISH. To reach it is necessary to design probes that allow specific detection/identification of D. bruxellensis among the wine microorganisms and in the wine environment and, if possible, using low formamide concentrations. Therefore, this study was focused on: a) designing a DNA-FISH probe to identify D. bruxellensis that matches these requirements and b) determining the applicability of the RNA-FISH procedure after the end of the alcoholic fermentation and in wine. A novel DNA-FISH D. bruxellensis probe with good performance and specificity was designed. The application of this probe using an in-suspension RNA-FISH protocol (applying only 5% of formamide) allowed the early detection/identification of D. bruxellensis at low cell densities (5 × 102 cell/mL). This was possible by flow cytometry independently of the growth stage of the target cells, both at the end of the alcoholic fermentation and in wine even in the presence of high S. cerevisiae cell densities. Thus, this study aims to contribute to facilitate the identification of D. bruxellensis before wine spoilage occurs, preventing economic losses to the wine industry.
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Affiliation(s)
- Patrícia Branco
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal
| | - António Candeias
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; Chemistry Department, School of Sciences and Technology, Évora University, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - Ana Teresa Caldeira
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal; Chemistry Department, School of Sciences and Technology, Évora University, Rua Romão Ramalho 59, 7000-671 Évora, Portugal
| | - Marina González-Pérez
- HERCULES Laboratory, Évora University, Largo Marquês de Marialva 8, 7000-809 Évora, Portugal.
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Branco P, Candeias A, Caldeira AT, González‐Pérez M. An important step forward for the future development of an easy and fast procedure for identifying the most dangerous wine spoilage yeast, Dekkera bruxellensis, in wine environment. Microb Biotechnol 2019; 12:1237-1248. [PMID: 31197952 PMCID: PMC6801150 DOI: 10.1111/1751-7915.13422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 04/04/2019] [Accepted: 04/18/2019] [Indexed: 12/21/2022] Open
Abstract
Dekkera bruxellensis is the main reason for spoilage in the wine industry. It renders the products unacceptable leading to large economic losses. Fluorescence In Situ Hybridization (FISH) technique has the potential for allowing its specific detection. Nevertheless, some experimental difficulties can be encountered when FISH technique is applied in the wine environment (e.g. matrix and cells' autofluorescence, fluorophore inadequate selection and probes' low specificity to the target organisms). An easy and fast in-suspension RNA-FISH procedure was applied for the first time for identifying D. bruxellensis in wine. A previously designed RNA-FISH probe to detect D. bruxellensis (26S D. brux.5.1) was used, and the matrix and cells' fluorescence interferences, the influence of three fluorophores in FISH performance and the probe specificity were evaluated. The results revealed that to apply RNA-FISH technique in the wine environment, a red-emitting fluorophore should be used. Good probe performance and specificity were achieved with 25% of formamide. The resulting RNA-FISH protocol was applied in wine samples artificially inoculated with D. bruxellensis. This spoilage microorganism was detected in wine at cell densities lower than those associated with phenolic off-flavours. Thus, the RNA-FISH procedure described in this work represents an advancement to facilitate early detection of the most dangerous wine spoilage yeast and, consequently, to reduce the economic losses caused by this yeast to the wine industry.
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Affiliation(s)
- Patrícia Branco
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
| | - António Candeias
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
- Chemistry DepartmentSchool of Sciences and TechnologyÉvora UniversityRua Romão Ramalho 597000‐671ÉvoraPortugal
| | - Ana Teresa Caldeira
- HERCULES LaboratoryÉvora UniversityLargo Marquês de Marialva 87000‐809ÉvoraPortugal
- Chemistry DepartmentSchool of Sciences and TechnologyÉvora UniversityRua Romão Ramalho 597000‐671ÉvoraPortugal
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15
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Wilkinson MG. Flow cytometry as a potential method of measuring bacterial viability in probiotic products: A review. Trends Food Sci Technol 2018. [DOI: 10.1016/j.tifs.2018.05.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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16
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Quantitative assessment of Lactococcus lactis subsp. cremoris present in artisanal raw cow’s milk cheese. ACTA VET BRNO 2018. [DOI: 10.2754/avb201887020189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Lactococcus lactis subsp. cremoris belongs to lactic acid bacteria that play a crucial role in cheese production and it is known to be beneficial to human health. The aim of the study was to establish a rapid and accurate quantitative real-time polymerase chain reaction (qPCR) method to detect and enumerate L. lactis subsp. cremoris in artisanal raw cow’s milk cheese. Artisanal raw cow’s milk cheese samples were used to check for presence and number of L. lactis subsp. cremoris strains. The method applies a set of target-specific PCR (polymerase chain reaction) primers and a fluorogenic probe, and amplifies a part of the LACR_RS01280 gene that encodes the aminoacetone oxidase family flavin adenine dinucleotide (FAD) binding enzyme. All 5 L. lactis subsp. cremoris strains examined were found to be qPCR positive. There was no signal recorded for 8 strains which belong to closely related species. The limit of detection amounted to ten copies per reaction and the assay indicated a linear dynamic range of seven logs. This method may be applied in detection and enumeration of L. lactis subsp. cremoris in cheese during its ripening. Moreover, it may be applied to examine the distribution of L. lactis subsp. cremoris during the cheese production and ripening.
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Mudroňová D. Flow cytometry as an auxiliary tool for the selection of probiotic bacteria. Benef Microbes 2015; 6:727-34. [DOI: 10.3920/bm2014.0145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Selection of appropriate bacterial strains is crucial for development of new probiotic preparations. The fundamental prerequisite for potential efficacy of a probiotic preparation for oral application is the selection of appropriate bacterial strains with good gastrointestinal colonisation abilities, antimicrobial activity, and tolerance of conditions in the gastrointestinal tract, resistance to different antimicrobial agents, survival during processing and storage. The strain should be genetically stable, it should have good growth properties, to maintain its high viability at processing and when in storage. Mostly, the properties of promising strains are tested in the first phase in vitro, and only the best ones undergo subsequent in vivo testing. in vitro tests are often performed by classical microbiological cultivation methods which are material and time consuming, and they are not able to distinguish between ‘viable but nonculturable’ and dead bacteria. Flow cytometry is usually used for counting, phenotyping or functional characterisation of immune cells. Nowadays, flow cytometry is increasingly used in microbiology for counting bacteria, determining their viability and metabolic activity, detecting specific strains or testing their adherence abilities. The utilisation of flow cytometry in combination with an appropriate fluorescent labelling represents an effective and rapid method for the selection of probiotic bacteria.
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Affiliation(s)
- D. Mudroňová
- Department of Microbiology and Immunology, University of Veterinary Medicine and Pharmacy, Komenského 73, 04181 Košice, Slovakia
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Manaresi E, Bua G, Bonvicini F, Gallinella G. A flow-FISH assay for the quantitative analysis of parvovirus B19 infected cells. J Virol Methods 2015; 223:50-4. [DOI: 10.1016/j.jviromet.2015.07.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Revised: 06/26/2015] [Accepted: 07/24/2015] [Indexed: 01/27/2023]
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The use of flow cytometry to accurately ascertain total and viable counts of Lactobacillus rhamnosus in chocolate. Food Microbiol 2015; 46:176-183. [DOI: 10.1016/j.fm.2014.07.002] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 06/05/2014] [Accepted: 07/02/2014] [Indexed: 11/18/2022]
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20
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Liu W, Zheng Y, Kwok LY, Sun Z, Zhang J, Guo Z, Hou Q, Menhe B, Zhang H. High-throughput sequencing for the detection of the bacterial and fungal diversity in Mongolian naturally fermented cow's milk in Russia. BMC Microbiol 2015; 15:45. [PMID: 25887414 PMCID: PMC4345014 DOI: 10.1186/s12866-015-0385-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 02/12/2015] [Indexed: 11/10/2022] Open
Abstract
Background Traditional fermented dairy products are major components of the typical Mongolian diet since ancient times. However, almost all the previous studies on the microbial composition of traditional Mongolian fermented dairy products analyzed food samples from the Chinese Mongolian region and Mongolia but not the Russian Mongolian region. In this study, the bacterial and fungal community diversity of nineteen naturally fermented cow’s milk (NFCM) samples from local Mongolian families residing in Kalmykia and Chita of Russia was investigated with pyrosequencing. Results Firmicutes and Ascomycota were the predominant phyla respectively for bacteria and fungi. The abundance of the bacterial phylum Acidobacteria was considerably different between the samples from the two regions. At genus level, Lactobacillus and Pichia were the predominating bacterial and fungal genera, respectively, while six bacterial genera significantly differed between the Kalmykia (enrichment of Aeromonas, Bacillus, Clostridium, Streptococcus, Vogesella) and Chita (enrichment of Lactococcus) samples. The results of principal coordinate analysis (PCoA) based on the bacterial or fungal composition of the Kalmykia and Chita samples revealed a different microbiota structure between the samples collected in these two locations. The redundancy analysis (RDA) identified 60 bacterial and 21 fungal OTUs as the key variables responsible for such microbiota structural difference. Conclusions Our results suggest that structural differences existed in the microbiota of NFCM between Kalmykia and Chita. The difference in geographic environment may be an important factor influencing the microbial diversity of NFCM made by the Mongolians in Russia. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0385-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenjun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
| | - Yi Zheng
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Zhihong Sun
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
| | - Jiachao Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Zhuang Guo
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Qiangchuan Hou
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Bilige Menhe
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China.
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot, 010018, P. R. China. .,Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, P. R. China.
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Børsting MW, Stallknecht MK, Vogensen FK, Ardö Y. Influence of proteolytic Lactococcus lactis subsp. cremoris on ripening of reduced-fat Cheddar cheese made with camel chymosin. Int Dairy J 2015. [DOI: 10.1016/j.idairyj.2014.09.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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22
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Bagheripoor-Fallah N, Mortazavian A, Hosseini H, Khoshgozaran-Abras S, Rad AH. Comparison of Molecular Techniques with other Methods for Identification and Enumeration of Probiotics in Fermented Milk Products. Crit Rev Food Sci Nutr 2014; 55:396-413. [DOI: 10.1080/10408398.2012.656771] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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23
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Nagarajan K, Loh KC. Molecular biology-based methods for quantification of bacteria in mixed culture: perspectives and limitations. Appl Microbiol Biotechnol 2014; 98:6907-19. [DOI: 10.1007/s00253-014-5870-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 05/30/2014] [Accepted: 05/31/2014] [Indexed: 02/07/2023]
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Influence of autochthonous lactic acid bacteria and enzymatic yeast extracts on the microbiological, biochemical and sensorial properties of Lben generic products. J DAIRY RES 2014; 81:193-201. [DOI: 10.1017/s0022029914000119] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
In this study we identified Lactococcus lactis subsp. lactis, Lc. lactis subsp. lactis biovar diacetylactis, Kluyveromices lactis and Saccharomyces cerevisiae as the dominant microorganisms of traditional Moroccan acid-alcoholic fermented milk named Lben. The low pH (3·8±0·3), lactose (16·8±3·4 mg/l) and lactic acid (8·16±0·6 mg/l) content indicated that a strong fermentation occurred in the traditional product which was also characterised by the substantial presence of ethanol and typical volatile carbonyl compounds (i.e., acetoin, diacetyl and acetaldehyde). Microbiological analyses of experimental Lben manufactured with selected strains (isolated from the traditional product) of Lc. lactis subsp. lactis and Lc. lactis subsp. lactis biovar. diacetylactis alone (batch A) and in combination with enzymatic extract of a K. lactis strain (batch B) indicated a good effectiveness of the starters employed (∼1010 CFU/g of lactococci after 8 h of incubation) and a significant effect of the yeast enzyme extract on lactococci viability. Despite slight changes in the physicochemical characteristics of the two Lben during the 15 d storage period, volatile compounds (i.e. ethanol, acetaldehyde, diacetyl and acetoin) were consistently higher in batch B. Moreover, sensorial analysis performed after 15 d of storage, highlighted higher odour and flavour intensity, vegetable odour and viscosity in batch B while batch A displayed higher astringency.
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Johansen P, Vindeløv J, Arneborg N, Brockmann E. Development of quantitative PCR and metagenomics-based approaches for strain quantification of a defined mixed-strain starter culture. Syst Appl Microbiol 2014; 37:186-93. [PMID: 24582508 DOI: 10.1016/j.syapm.2013.12.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Revised: 12/04/2013] [Accepted: 12/23/2013] [Indexed: 11/30/2022]
Abstract
Although the strain composition of mixed cultures may hugely affect production of various fermented foods, such as e.g. cheese, tools for investigating it have so far been limited. In this study, two new approaches for quantification of seven Lactococcus lactis subsp. cremoris strains (S1-S7) in a defined mixed-strain starter culture were developed and verified. By mapping NGS reads from 47 sequenced L. lactis strains to de novo assembly contigs of the seven strains, two strain-specific sequence regions (SEQ1 and SEQ2) were identified for each strain for qPCR primer design (A1 and A2). The qPCR assays amplified their strain-specific sequence region target efficiently. Additionally, high reproducibility was obtained in a validation sample containing equal amounts of the seven strains, and assay-to-assay coefficients of variance (CVs) for six (i.e. S1, S2, S4-S7) of the seven strains correlated to the inter-plate CVs. Hence, at least for six strains, the qPCR assay design approach was successful. The metagenomics-based approach quantified the seven strains based on average coverage of SEQ1 and SEQ2 by mapping sequencing reads from the validation sample to the strain-specific sequence regions. Average coverages of the SEQ1 and SEQ2 in the metagenomics data showed CVs of ≤17.3% for six strains (i.e. S1-S4, S6, S7). Thus, the metagenomics-based quantification approach was considered successful for six strains, regardless of the strain-specific sequence region used. When comparing qPCR- and metagenomics-based quantifications of the validation sample, the identified strain-specific sequence regions were considered suitable and applicable for quantification at a strain level of defined mixed-strain starter cultures.
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Affiliation(s)
- Pernille Johansen
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark
| | | | - Nils Arneborg
- Department of Food Science, Faculty of Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark.
| | - Elke Brockmann
- Chr. Hansen A/S, Bøge Allé 10-12, 2970 Hørsholm, Denmark
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Sohier D, Pavan S, Riou A, Combrisson J, Postollec F. Evolution of microbiological analytical methods for dairy industry needs. Front Microbiol 2014; 5:16. [PMID: 24570675 PMCID: PMC3916730 DOI: 10.3389/fmicb.2014.00016] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 01/10/2014] [Indexed: 11/13/2022] Open
Abstract
Traditionally, culture-based methods have been used to enumerate microbial populations in dairy products. Recent developments in molecular methods now enable faster and more sensitive analyses than classical microbiology procedures. These molecular tools allow a detailed characterization of cell physiological states and bacterial fitness and thus, offer new perspectives to integration of microbial physiology monitoring to improve industrial processes. This review summarizes the methods described to enumerate and characterize physiological states of technological microbiota in dairy products, and discusses the current deficiencies in relation to the industry’s needs. Recent studies show that Polymerase chain reaction-based methods can successfully be applied to quantify fermenting microbes and probiotics in dairy products. Flow cytometry and omics technologies also show interesting analytical potentialities. However, they still suffer from a lack of validation and standardization for quality control analyses, as reflected by the absence of performance studies and official international standards.
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Affiliation(s)
- Danièle Sohier
- Food Safety and Quality Unit, ADRIA Développement, Agri-Food Technical Institute, Quimper, France
| | - Sonia Pavan
- Food Safety and Quality Unit, ADRIA Développement, Agri-Food Technical Institute, Quimper, France
| | - Armelle Riou
- Food Safety and Quality Unit, ADRIA Développement, Agri-Food Technical Institute, Quimper, France
| | - Jérôme Combrisson
- Bretagne Biotechnologie Alimentaire dairy association member, Analytical Sciences, Danone Research, Palaiseau, France
| | - Florence Postollec
- Food Safety and Quality Unit, ADRIA Développement, Agri-Food Technical Institute, Quimper, France
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27
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Nettmann E, Fröhling A, Heeg K, Klocke M, Schlüter O, Mumme J. Development of a flow-fluorescence in situ hybridization protocol for the analysis of microbial communities in anaerobic fermentation liquor. BMC Microbiol 2013; 13:278. [PMID: 24304697 PMCID: PMC4235175 DOI: 10.1186/1471-2180-13-278] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2013] [Accepted: 11/21/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The production of bio-methane from renewable raw material is of high interest because of the increasing scarcity of fossil fuels. The process of biomethanation is based on the inter- and intraspecific metabolic activity of a highly diverse and dynamic microbial community. The community structure of the microbial biocenosis varies between different biogas reactors and the knowledge about these microbial communities is still fragmentary. However, up to now no approaches are available allowing a fast and reliable access to the microbial community structure. Hence, the aim of this study was to originate a Flow-FISH protocol, namely a combination of flow cytometry and fluorescence in situ hybridization, for the analysis of the metabolically active microorganisms in biogas reactor samples. With respect to the heterogenic texture of biogas reactor samples and to collect all cells including those of cell aggregates and biofilms the development of a preceding purification procedure was indispensable. RESULTS Six different purification procedures with in total 29 modifications were tested. The optimized purification procedure combines the use of the detergent sodium hexametaphosphate with ultrasonic treatment and a final filtration step. By this treatment, the detachment of microbial cells from particles as well as the disbandment of cell aggregates was obtained at minimized cell loss. A Flow-FISH protocol was developed avoiding dehydration and minimizing centrifugation steps. In the exemplary application of this protocol on pure cultures as well as biogas reactor samples high hybridization rates were achieved for commonly established domain specific oligonucleotide probes enabling the specific detection of metabolically active bacteria and archaea. Cross hybridization and autofluorescence effects could be excluded by the use of a nonsense probe and negative controls, respectively. CONCLUSIONS The approach described in this study enables for the first time the analysis of the metabolically active fraction of the microbial communities within biogas reactors by Flow-FISH.
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Affiliation(s)
- Edith Nettmann
- APECS junior research group, Leibniz Institute for Agricultural Engineering, Max-Eyth-Allee 100, 14469 Potsdam, Germany.
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Achilleos C, Berthier F. Quantitative PCR for the specific quantification of Lactococcus lactis and Lactobacillus paracasei and its interest for Lactococcus lactis in cheese samples. Food Microbiol 2013; 36:286-95. [PMID: 24010609 DOI: 10.1016/j.fm.2013.06.024] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Revised: 05/01/2013] [Accepted: 06/29/2013] [Indexed: 02/04/2023]
Abstract
The first objective of this work was to develop real-time quantitative PCR (qPCR) assays to quantify two species of mesophilic lactic acid bacteria technologically active in food fermentation, including cheese making: Lactococcus lactis and Lactobacillus paracasei. The second objective was to compare qPCR and plate counts of these two species in cheese samples. Newly designed primers efficiently amplified a region of the tuf gene from the target species. Sixty-three DNA samples from twenty different bacterial species, phylogenetically related or commonly found in raw milk and dairy products, were selected as positive and negative controls. Target DNA was successfully amplified showing a single peak on the amplicon melting curve; non-target DNA was not amplified. Quantification was linear over 5 log units (R(2) > 0.990), down to 22 gene copies/μL per well for Lc. lactis and 73 gene copies/μL per well for Lb. paracasei. qPCR efficiency ranged from 82.9% to 93.7% for Lc. lactis and from 81.1% to 99.5% for Lb. paracasei. At two stages of growth, Lc. lactis was quantified in 12 soft cheeses and Lb. paracasei in 24 hard cooked cheeses. qPCR proved to be useful for quantifying Lc. lactis, but not Lb. paracasei.
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Affiliation(s)
- Christine Achilleos
- INRA, UR342 Technologie et Analyses Laitières, BP 20089, F-39800 Poligny, France.
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29
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Bioinformatics and molecular biology for the quantification of closely related bacteria. Appl Microbiol Biotechnol 2013; 97:6489-502. [DOI: 10.1007/s00253-013-4943-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Revised: 04/18/2013] [Accepted: 04/19/2013] [Indexed: 10/26/2022]
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Laksmi Suryaatmadja Jenie* BS, Yusup Saputra M, - W. SENSORY EVALUATION AND SURVIVAL OF PROBIOTICS IN MODIFIED BANANA FLOUR YOGHURT DURING STORAGE. JURNAL TEKNOLOGI DAN INDUSTRI PANGAN 2013. [DOI: 10.6066/jtip.2013.24.1.40] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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31
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Salma M, Rousseaux S, Sequeira-Le Grand A, Alexandre H. Cytofluorometric detection of wine lactic acid bacteria: application of malolactic fermentation to the monitoring. ACTA ACUST UNITED AC 2013; 40:63-73. [DOI: 10.1007/s10295-012-1200-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2012] [Accepted: 09/15/2012] [Indexed: 11/29/2022]
Abstract
Abstract
In this study we report for the first time a rapid, efficient and cost-effective method for the enumeration of lactic acid bacteria (LAB) in wine. Indeed, up to now, detection of LAB in wine, especially red wine, was not possible. Wines contain debris that cannot be separated from bacteria using flow cytometry (FCM). Furthermore, the dyes tested in previous reports did not allow an efficient staining of bacteria. Using FCM and a combination of BOX/PI dyes, we were able to count bacteria in wines. The study was performed in wine inoculated with Oenococcus oeni (106 CFU ml−1) stained with either FDA or BOX/PI and analyzed by FCM during the malolactic fermentation (MLF). The analysis show a strong correlation between the numbers of BOX/PI-stained cells determined by FCM and the cell numbers determined by plate counts (red wine: R2 ≥ 0.97, white wine R2 ≥ 0.965). On the other hand, we found that the enumeration of O. oeni labeled with FDA was only possible in white wine (R2 ≥ 0.97). Viable yeast and LAB populations can be rapidly discriminated and quantified in simultaneous malolactic-alcoholic wine fermentations using BOX/PI and scatter parameters in a one single measurement. This rapid procedure is therefore a suitable method for monitoring O. oeni populations during winemaking, offers a detection limit of <104 CFU ml−1 and can be considered a useful method for investigating the dynamics of microbial growth in wine and applied for microbiological quality control in wineries.
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Affiliation(s)
- Mohammad Salma
- grid.5613.1 0000000122989313 UMR 02102 PAM Université de Bourgogne-AgroSup Dijon Laboratoire VALMIS Institut Universitaire de la Vigne et du Vin Jules Guyot Université de Bourgogne 21078 Dijon Cedex France
| | - Sandrine Rousseaux
- grid.5613.1 0000000122989313 UMR 02102 PAM Université de Bourgogne-AgroSup Dijon Laboratoire VALMIS Institut Universitaire de la Vigne et du Vin Jules Guyot Université de Bourgogne 21078 Dijon Cedex France
| | - Anabelle Sequeira-Le Grand
- grid.5613.1 0000000122989313 Plateforme de Cytométrie, Structure Fédérative de Recherche Santé STIC, Fac. Médecine Université de Bourgogne 7, Bd Jeanne D’Arc 21000 Dijon France
| | - Hervé Alexandre
- grid.5613.1 0000000122989313 UMR 02102 PAM Université de Bourgogne-AgroSup Dijon Laboratoire VALMIS Institut Universitaire de la Vigne et du Vin Jules Guyot Université de Bourgogne 21078 Dijon Cedex France
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Biodiversity in Oscypek, a traditional Polish cheese, determined by culture-dependent and -independent approaches. Appl Environ Microbiol 2012; 78:1890-8. [PMID: 22247135 DOI: 10.1128/aem.06081-11] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Oscypek is a traditional Polish scalded-smoked cheese, with a protected-designation-of-origin (PDO) status, manufactured from raw sheep's milk without starter cultures in the Tatra Mountains region of Poland. This study was undertaken in order to gain insight into the microbiota that develops and evolves during the manufacture and ripening stages of Oscypek. To this end, we made use of both culturing and the culture-independent methods of PCR followed by denaturing gradient gel electrophoresis (PCR-DGGE) and pyrosequencing of 16S rRNA gene amplicons. The culture-dependent technique and PCR-DGGE fingerprinting detected the predominant microorganisms in traditional Oscypek, whereas the next-generation sequencing technique (454 pyrosequencing) revealed greater bacterial diversity. Besides members of the most abundant bacterial genera in dairy products, e.g., Lactococcus, Lactobacillus, Leuconostoc, Streptococcus, and Enterococcus, identified by all three methods, other, subdominant bacteria belonging to the families Bifidobacteriaceae and Moraxellaceae (mostly Enhydrobacter), as well as various minor bacteria, were identified by pyrosequencing. The presence of bifidobacterial sequences in a cheese system is reported for the first time. In addition to bacteria, a great diversity of yeast species was demonstrated in Oscypek by the PCR-DGGE method. Culturing methods enabled the determination of a number of viable microorganisms from different microbial groups and their isolation for potential future applications in specific cheese starter cultures.
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Robertson KL, Vora GJ. Locked nucleic acid flow cytometry-fluorescence in situ hybridization (LNA flow-FISH): a method for bacterial small RNA detection. J Vis Exp 2012:e3655. [PMID: 22258228 PMCID: PMC3369778 DOI: 10.3791/3655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a powerful technique that is used to detect and localize specific nucleic acid sequences in the cellular environment. In order to increase throughput, FISH can be combined with flow cytometry (flow-FISH) to enable the detection of targeted nucleic acid sequences in thousands of individual cells. As a result, flow-FISH offers a distinct advantage over lysate/ensemble-based nucleic acid detection methods because each cell is treated as an independent observation, thereby permitting stronger statistical and variance analyses. These attributes have prompted the use of FISH and flow-FISH methods in a number of different applications and the utility of these methods has been successfully demonstrated in telomere length determination1,2, cellular identification and gene expression3,4, monitoring viral multiplication in infected cells5, and bacterial community analysis and enumeration6. Traditionally, the specificity of FISH and flow-FISH methods has been imparted by DNA oligonucleotide probes. Recently however, the replacement of DNA oligonucleotide probes with nucleic acid analogs as FISH and flow-FISH probes has increased both the sensitivity and specificity of each technique due to the higher melting temperatures (Tm) of these analogs for natural nucleic acids7,8. Locked nucleic acid (LNA) probes are a type of nucleic acid analog that contain LNA nucleotides spiked throughout a DNA or RNA sequence9,10. When coupled with flow-FISH, LNA probes have previously been shown to outperform conventional DNA probes7,11 and have been successfully used to detect eukaryotic mRNA12 and viral RNA in mammalian cells5. Here we expand this capability and describe a LNA flow-FISH method which permits the specific detection of RNA in bacterial cells (Figure 1). Specifically, we are interested in the detection of small non-coding regulatory RNA (sRNA) which have garnered considerable interest in the past few years as they have been found to serve as key regulatory elements in many critical cellular processes13. However, there are limited tools to study sRNAs and the challenges of detecting sRNA in bacterial cells is due in part to the relatively small size (typically 50-300 nucleotides in length) and low abundance of sRNA molecules as well as the general difficulty in working with smaller biological cells with varying cellular membranes. In this method, we describe fixation and permeabilzation conditions that preserve the structure of bacterial cells and permit the penetration of LNA probes as well as signal amplification steps which enable the specific detection of low abundance sRNA (Figure 2).
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Affiliation(s)
- Kelly L Robertson
- Center for Bio/Molecular Science and Engineering, Naval Research Laboratory, USA
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Locked nucleic acid and flow cytometry-fluorescence in situ hybridization for the detection of bacterial small noncoding RNAs. Appl Environ Microbiol 2011; 78:14-20. [PMID: 22057868 DOI: 10.1128/aem.06399-11] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We describe the development and testing of a high-throughput method that enables the detection of small noncoding RNAs (ncRNAs) from single bacterial cells using locked nucleic acid probes (LNA) and flow cytometry-fluorescence in situ hybridization (flow-FISH). The LNA flow-FISH method and quantitative reverse transcription-PCR (qRT-PCR) were used to monitor the expression of three ncRNAs (6S, CsrB, and TPP-2) in Vibrio campbellii ATCC BAA-1116 cultures during lag phase, mid-log phase, and stationary phase. Both LNA flow-FISH and qRT-PCR revealed that CsrB and TPP-2 were highly expressed during lag phase but markedly reduced in mid-log phase and stationary phase, whereas 6S demonstrated no to little expression during lag phase but increased thereafter. Importantly, while LNA flow-FISH and qRT-PCR demonstrated similar overall expression trends, only LNA flow-FISH, which enabled the detection of ncRNAs in individual cells as opposed to the lysate-based ensemble measurements generated by qRT-PCR, was able to capture the cell-to-cell heterogeneity in ncRNA expression. As such, this study demonstrates a new method that simultaneously enables the in situ detection of ncRNAs and the determination of gene expression heterogeneity within an isogenic bacterial population.
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Zhou M, McAllister T, Guan L. Molecular identification of rumen methanogens: Technologies, advances and prospects. Anim Feed Sci Technol 2011. [DOI: 10.1016/j.anifeedsci.2011.04.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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Vinderola G, Binetti A, Burns P, Reinheimer J. Cell viability and functionality of probiotic bacteria in dairy products. Front Microbiol 2011; 2:70. [PMID: 21833320 PMCID: PMC3153040 DOI: 10.3389/fmicb.2011.00070] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Accepted: 03/26/2011] [Indexed: 12/13/2022] Open
Abstract
Probiotic bacteria, according to the definition adopted by the World Health Organization in 2002, are live microorganisms, which when administered in adequate amounts confer a health benefit to the host. Recent studies show that the same probiotic strain produced and/or preserved under different storage conditions, may present different responses regarding their susceptibility to the adverse conditions of the gastrointestinal tract, its capacity to adhere to the intestinal epithelium, or its immunomodulating capacity, the functionality being affected without changes in cell viability. This could imply that the control of cell viability is not always enough to guarantee the functionality (probiotic capacity) of a strain. Therefore, a new challenge arises for food technologists and microbiologists when it comes to designing and monitoring probiotic food: to be able to monitor the functionality of a probiotic microorganism throughout all the stages the strain goes through from the moment it is produced and included in the food vehicle, until the moment of consumption. Conventional methodological tools or others still to be developed must be used. The application of cell membrane functionality markers, the use of tests of resistance to intestinal barriers, the study of surface properties and the application of in vivo models come together as complementary tools to assess the actual capacity of a probiotic organism in a specific food, to exert functional effects regardless of the number of viable cells present at the moment of consumption.
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Affiliation(s)
- Gabriel Vinderola
- Instituto de Lactología Industrial, Facultad de Ingeniería Química, Universidad Nacional del Litoral Santa Fe, Argentina
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Agustiandari H, Peeters E, de Wit JG, Charlier D, Driessen AJM. LmrR-mediated gene regulation of multidrug resistance in Lactococcus lactis. MICROBIOLOGY-SGM 2011; 157:1519-1530. [PMID: 21330438 DOI: 10.1099/mic.0.048025-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Multidrug resistance (MDR) in Lactococcus lactis is due to the expression of the membrane ATP-binding cassette (ABC) transporter LmrCD. In the absence of drugs, the transcriptional regulator LmrR prevents expression of the lmrCD operon by binding to its operator site. Through an autoregulatory mechanism LmrR also suppresses its own expression. Although the lmrR and lmrCD genes have their own promoters, primer extension analysis showed the presence of a long transcript spanning the entire lmrR-lmrCD cluster, in addition to various shorter transcripts harbouring the lmrCD genes only. 'In-gel' Cu-phenanthroline footprinting analysis indicated an extensive interaction between LmrR and the lmrR promoter/operator region. Atomic force microscopy imaging of the binding of LmrR to the control region of lmrR DNA showed severe deformations indicative of DNA wrapping and looping, while LmrR binding to a fragment containing the lmrCD control region induced DNA bending. The results further suggest a drug-dependent regulation mechanism in which the lmrCD genes are co-transcribed with lmrR as a polycistronic messenger. This leads to an LmrR-mediated regulation of lmrCD expression that is exerted from two different locations and by distinct regulatory mechanisms.
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Affiliation(s)
- Herfita Agustiandari
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and The Kluyver Centre for the Genomics of Industrial Fermentation, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Eveline Peeters
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Janny G de Wit
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and The Kluyver Centre for the Genomics of Industrial Fermentation, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Daniel Charlier
- Erfelijkheidsleer en Microbiologie, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Arnold J M Driessen
- Department of Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute and The Kluyver Centre for the Genomics of Industrial Fermentation, University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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Donofrio RS, Bestervelt LL, Saha R, Bagley ST. Quantitative real-time PCR and fluorescence in situ hybridization approaches for enumerating Brevundimonas diminuta in drinking water. J Ind Microbiol Biotechnol 2010; 37:909-18. [DOI: 10.1007/s10295-010-0738-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2010] [Accepted: 04/28/2010] [Indexed: 11/30/2022]
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Matijašić BB, Obermajer T, Rogelj I. Quantification of Lactobacillus gasseri, Enterococcus faecium and Bifidobacterium infantis in a probiotic OTC drug by real-time PCR. Food Control 2010. [DOI: 10.1016/j.foodcont.2009.07.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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Tracy BP, Gaida SM, Papoutsakis ET. Flow cytometry for bacteria: enabling metabolic engineering, synthetic biology and the elucidation of complex phenotypes. Curr Opin Biotechnol 2010; 21:85-99. [DOI: 10.1016/j.copbio.2010.02.006] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2009] [Revised: 01/29/2010] [Accepted: 02/02/2010] [Indexed: 02/01/2023]
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Cronin U, Wilkinson M. The potential of flow cytometry in the study of Bacillus cereus. J Appl Microbiol 2010; 108:1-16. [DOI: 10.1111/j.1365-2672.2009.04370.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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Poulain S, Lacomme S, Battaglia-Hsu SF, du Manoir S, Brochin L, Vignaud JM, Martinet N. Signalling with retinoids in the human lung: validation of new tools for the expression study of retinoid receptors. BMC Cancer 2009; 9:423. [PMID: 19961602 PMCID: PMC2797528 DOI: 10.1186/1471-2407-9-423] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2009] [Accepted: 12/04/2009] [Indexed: 01/09/2023] Open
Abstract
Background Retinoid Receptors are involved in development and cell homeostasis. Alterations of their expressions have been observed in lung cancer. However, retinoid chemoprevention trials in populations at risk to develop such tumors have failed. Therefore, the pertinence of new clinical trials using second generation retinoid requires prior better understanding of retinoid signalling. This is our aim when validating extensively research tools, focused on Retinoic Acid Receptor beta, whose major role in lung cancer is documented. Methods Biocomputing was used to assess the genomic organization of RAR beta. Its putative RAR-beta1' promoter features were investigated experimentally. Specific measures realized, with qRT-PCR Syber Green assays and a triplex of Taqman probes, were extensively validated to establish Retinoid Receptors mRNAs reference values for in vivo normal human bronchial cells, lung tumors and cell lines. Finally, a pan-RAR-beta antibody was generated and extensively validated by western-blot and immunoprecipitation. Results No promoter-like activity was found for RAR-beta1'. RAR-beta2 mRNAs increase signs the normal differentiation of the human bronchial epithelium while a decrease is observed in most lung cancer cell lines. Accordingly, it is also, along with RXR beta, down-regulated in lung tumors. When using nuclear extracts of BEAS-2B and normal lung cells, only the RAR-beta2 long protein isoform was recognized by our antibody. Conclusion Rigorous samples processing and extensive biocomputing, were the key factors for this study. mRNA reference values and validated tools can now be used to advance researches on retinoid signalling in the lung.
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Affiliation(s)
- Stéphane Poulain
- Faculté de Médecine, Laboratoire de Pathologie Cellulaire et Moléculaire en Nutrition, INSERM U724, Centre de Ressources Biologiques, CHU de Nancy, 54505 Vandoeuvre-Lès-Nancy, France.
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Reimann S, Grattepanche F, Rezzonico E, Lacroix C. Development of a real-time RT-PCR method for enumeration of viable Bifidobacterium longum cells in different morphologies. Food Microbiol 2009; 27:236-42. [PMID: 20141941 DOI: 10.1016/j.fm.2009.10.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2009] [Revised: 10/08/2009] [Accepted: 10/14/2009] [Indexed: 11/27/2022]
Abstract
Viability of probiotic bacteria is traditionally assessed by plate counting which has several limitations, including underestimation of cells in aggregates or chains morphology. We describe a quantitative PCR (qPCR)-based method for an accurate enumeration of viable cells of Bifidobacterium longum NCC2705 exhibiting different morphologies by measuring the mRNA levels of cysB and purB, two constitutively expressed housekeeping genes. Three primer-sets targeting short fragments of 57-bp of cysS and purB and one 400-bp fragment of purB were used. Cell quantification of serially diluted samples showed a good correlation coefficient of R(2) 0.984 +/- 0.003 between plate counts and qRT-PCR for all tested primer sets. Loss of viable cells exposed to a lethal heat stress (56 degrees C, 10, 20 and 30 min) was estimated by qRT-PCR and plate counts. No significant difference was observed using qRT-PCR targeting the 400-bp fragment of purB compared to plate counts indicating that this fragment is a suitable marker of cell viability. In contrast, the use of the 57-bp fragments led to a significant overestimation of viable cell counts (18 +/- 3 and 7 +/- 2 fold for cysB and purB, respectively). Decay of the mRNA fragments was studied by treatment of growing cells with rifampicin prior qRT-PCR. The 400-bp fragment of purB was faster degraded than the 57-bp fragments of cysB and purB. The 400-bp fragment of purB was further used to enumerate viable cells in aggregate state. Cell counts were more than 2 log(10) higher using the qRT-PCR method compared to plate counts. Growing interest in probiotic characteristics of aggregating bacteria cells make this technique a valuable tool to accurately quantify viable probiotic bacteria exhibiting heterogeneous morphology.
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Affiliation(s)
- Sebastian Reimann
- Laboratory of Food Biotechnology, Institute of Food Science and Nutrition, Swiss Federal Institute of Technology, Schmelzbergstrasse. 7 8092 Zurich, Switzerland
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Detection and quantification of Enterococcus gilvus in cheese by real-time PCR. Syst Appl Microbiol 2009; 32:514-21. [DOI: 10.1016/j.syapm.2009.07.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Indexed: 11/20/2022]
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Tang X, Flint S, Brooks J, Bennett R. Factors affecting the attachment of micro-organisms isolated from ultrafiltration and reverse osmosis membranes in dairy processing plants. J Appl Microbiol 2009; 107:443-51. [DOI: 10.1111/j.1365-2672.2009.04214.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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46
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Flow cytometry applications in the food industry. J Ind Microbiol Biotechnol 2009; 36:999-1011. [DOI: 10.1007/s10295-009-0608-x] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 06/02/2009] [Indexed: 11/25/2022]
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FISH glossary: an overview of the fluorescence in situ hybridization technique. Biotechniques 2008; 45:385-6, 388, 390 passim. [PMID: 18855767 DOI: 10.2144/000112811] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The introduction of FISH (fluorescence in situ hybridization) marked the beginning of a new era for the study of chromosome structure and function. As a combined molecular and cytological approach, the major advantage of this visually appealing technique resides in its unique ability to provide an intermediate degree of resolution between DNA analysis and chromosomal investigations while retaining information at the single-cell level. Used to support large-scale mapping and sequencing efforts related to the human genome project, FISH accuracy and versatility were subsequently capitalized on in biological and medical research, providing a wealth of diverse applications and FISH-based diagnostic assays. The diversification of the original FISH protocol into the impressive number of procedures available these days has been promoted throughout the years by a number of interconnected factors: the improvement in sensitivity, specificity and resolution, together with the advances in the fields of fluorescence microscopy and digital imaging, and the growing availability of genomic and bioinformatic resources. By assembling in a glossary format many of the "acronymed" FISH applications published so far, this review intends to celebrate the ability of FISH to re-invent itself and thus remain at the forefront of biomedical research.
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Roessler A, Friedrich U, Vogelsang H, Bauer A, Kaatz M, Hipler UC, Schmidt I, Jahreis G. The immune system in healthy adults and patients with atopic dermatitis seems to be affected differently by a probiotic intervention. Clin Exp Allergy 2007; 38:93-102. [PMID: 18028460 DOI: 10.1111/j.1365-2222.2007.02876.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
BACKGROUND Probiotic bacteria are proposed to alleviate atopic dermatitis (AD) in infants. There are few indications about the effect of probiotics on AD in adults. OBJECTIVE The purpose of this study was to elucidate the influence of a probiotic drink containing a combination of the probiotics Lactobacillus paracasei Lpc-37, Lactobacillus acidophilus 74-2 and Bifidobacterium animalis subsp. lactis DGCC 420 (B. lactis 420) in healthy volunteers and in patients with AD on clinical and immunological parameters and their detection in feces. METHODS A double-blind, placebo-controlled, randomized cross-over study was conducted in 15 healthy adults and 15 patients with AD. The probiotic product or placebo was given over 8 weeks. A 2-week washout period was interconnected before the intervention was crossed. At the end of each period, blood and stool samples were collected. In patients, the severity of AD was evaluated using the Scoring of Atopic Dermatitis (SCORAD). RESULTS L. paracasei and B. lactis were recovered in high numbers in feces after supplementation, whereas L. acidophilus marginally increased. In patients, the SCORAD tended to decrease by 15.5% (P=0.081). Major lymphocyte subsets were not affected by the probiotic intervention. However, CD57(+) increased significantly (P=0.034) in healthy subjects after probiotic intake and was not changed in patients, whereas CD4(+)CD54(+) decreased significantly (P=0.031) in patients with AD and remained uninfluenced in healthy subjects. The expression of CD4(+)CD25(+) T cells was similar in healthy subjects and AD patients. The phagocytic activity of monocytes and granulocytes was significantly increased in healthy subjects after probiotic intervention (P=0.014). CONCLUSION L. paracasei Lpc-37 and B. lactis 420 are able to colonize the intestine transiently. This study reveals that the probiotics differently modulate peripheral immune parameters in healthy subjects and patients with AD.
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Affiliation(s)
- A Roessler
- Department of Nutritional Physiology, Institute of Nutrition, Friedrich Schiller University, Jena, Germany
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Olsen KN, Brockmann E, Molin S. Quantification ofLeuconostocpopulations in mixed dairy starter cultures using fluorescencein situhybridization. J Appl Microbiol 2007; 103:855-63. [PMID: 17897187 DOI: 10.1111/j.1365-2672.2007.03298.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AIMS Development of a rapid method to identify and quantify Leuconostoc populations in mesophilic starter cultures. METHODS AND RESULTS 16S rRNA-targeted oligonucleotide probes were used in a whole cell in situ hybridization assay for the identification of the genus Leuconostoc and an undescribed Leuconostoc ribospecies. The probes were fluorescently labelled and used to quantify the Leuconostoc populations in five different mixed starter cultures. CONCLUSIONS There was a good correlation between the results obtained using fluorescence in situ hybridization (FISH) with that of standard plate counting methods. SIGNIFICANCE AND IMPACT OF THE STUDY To develop a FISH method capable of identifying and quantifying the Leuconostoc population in starter cultures within 1 day.
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Affiliation(s)
- K N Olsen
- Chr. Hansen A/S, Bøge Allé 10-12, Hørsholm, Denmark.
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50
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Fanjul-Bolado P, González-García MB, Costa-García A. Quantitative analysis of enzymatic assays using indoxyl-based substrates. Anal Bioanal Chem 2006; 386:1849-54. [PMID: 17036214 DOI: 10.1007/s00216-006-0808-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2006] [Revised: 08/18/2006] [Accepted: 08/28/2006] [Indexed: 11/28/2022]
Abstract
Hydrolysis of indoxyl-based substrates by hydrolytic enzymes is a commonly used semiquantitative detection system that generates a water-insoluble indigo dye which is difficult to quantify. This work describes the quantitative analysis and enzyme kinetics for alkaline phosphatase (AP) and 5-bromo-4-chloro-3-indoxyl phosphate (BCIP) in solution obtained by applying known solubilization methodology from the textiles industry to the enzymatic product. This proposal is based on the reduction of the tetrahalo-indigo blue dye in a basic medium with the aim of generating its aqueous-soluble parent compound termed indigo white, which gives a rich yellow color in solution and is fluorescent. A quantitative ELISA (where a soluble end product is required) is accomplished for first time using BCIP as substrate.
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Affiliation(s)
- Pablo Fanjul-Bolado
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006, Oviedo, Asturias, Spain
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