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Mandracchia B, Zheng C, Rajendran S, Liu W, Forghani P, Xu C, Jia S. High-speed optical imaging with sCMOS pixel reassignment. Nat Commun 2024; 15:4598. [PMID: 38816394 PMCID: PMC11139943 DOI: 10.1038/s41467-024-48987-7] [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: 08/11/2023] [Accepted: 05/13/2024] [Indexed: 06/01/2024] Open
Abstract
Fluorescence microscopy has undergone rapid advancements, offering unprecedented visualization of biological events and shedding light on the intricate mechanisms governing living organisms. However, the exploration of rapid biological dynamics still poses a significant challenge due to the limitations of current digital camera architectures and the inherent compromise between imaging speed and other capabilities. Here, we introduce sHAPR, a high-speed acquisition technique that leverages the operating principles of sCMOS cameras to capture fast cellular and subcellular processes. sHAPR harnesses custom fiber optics to convert microscopy images into one-dimensional recordings, enabling acquisition at the maximum camera readout rate, typically between 25 and 250 kHz. We have demonstrated the utility of sHAPR with a variety of phantom and dynamic systems, including high-throughput flow cytometry, cardiomyocyte contraction, and neuronal calcium waves, using a standard epi-fluorescence microscope. sHAPR is highly adaptable and can be integrated into existing microscopy systems without requiring extensive platform modifications. This method pushes the boundaries of current fluorescence imaging capabilities, opening up new avenues for investigating high-speed biological phenomena.
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Affiliation(s)
- Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- E.T.S.I. Telecomunicación, Universidad de Valladolid, Valladolid, Spain
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Suraj Rajendran
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Parvin Forghani
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
| | - Chunhui Xu
- Department of Pediatrics, School of Medicine, Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
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2
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Dimitriadis S, Dova L, Kotsianidis I, Hatzimichael E, Kapsali E, Markopoulos GS. Imaging Flow Cytometry: Development, Present Applications, and Future Challenges. Methods Protoc 2024; 7:28. [PMID: 38668136 PMCID: PMC11054958 DOI: 10.3390/mps7020028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/13/2024] [Accepted: 03/21/2024] [Indexed: 04/29/2024] Open
Abstract
Imaging flow cytometry (ImFC) represents a significant technological advancement in the field of cytometry, effectively merging the high-throughput capabilities of flow analysis with the detailed imaging characteristics of microscopy. In our comprehensive review, we adopt a historical perspective to chart the development of ImFC, highlighting its origins and current state of the art and forecasting potential future advancements. The genesis of ImFC stemmed from merging the hydraulic system of a flow cytometer with advanced camera technology. This synergistic coupling facilitates the morphological analysis of cell populations at a high-throughput scale, effectively evolving the landscape of cytometry. Nevertheless, ImFC's implementation has encountered hurdles, particularly in developing software capable of managing its sophisticated data acquisition and analysis needs. The scale and complexity of the data generated by ImFC necessitate the creation of novel analytical tools that can effectively manage and interpret these data, thus allowing us to unlock the full potential of ImFC. Notably, artificial intelligence (AI) algorithms have begun to be applied to ImFC, offering promise for enhancing its analytical capabilities. The adaptability and learning capacity of AI may prove to be essential in knowledge mining from the high-dimensional data produced by ImFC, potentially enabling more accurate analyses. Looking forward, we project that ImFC may become an indispensable tool, not only in research laboratories, but also in clinical settings. Given the unique combination of high-throughput cytometry and detailed imaging offered by ImFC, we foresee a critical role for this technology in the next generation of scientific research and diagnostics. As such, we encourage both current and future scientists to consider the integration of ImFC as an addition to their research toolkit and clinical diagnostic routine.
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Affiliation(s)
- Savvas Dimitriadis
- Hematology Laboratory, Unit of Molecular Biology and Translational Flow Cytometry, University Hospital of Ioannina, 45100 Ioannina, Greece; (S.D.); (L.D.)
| | - Lefkothea Dova
- Hematology Laboratory, Unit of Molecular Biology and Translational Flow Cytometry, University Hospital of Ioannina, 45100 Ioannina, Greece; (S.D.); (L.D.)
| | - Ioannis Kotsianidis
- Department of Hematology, University Hospital of Alexandroupolis, Democritus University of Thrace, 69100 Alexandroupolis, Greece;
| | - Eleftheria Hatzimichael
- Department of Hematology, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (E.H.); (E.K.)
| | - Eleni Kapsali
- Department of Hematology, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece; (E.H.); (E.K.)
| | - Georgios S. Markopoulos
- Hematology Laboratory, Unit of Molecular Biology and Translational Flow Cytometry, University Hospital of Ioannina, 45100 Ioannina, Greece; (S.D.); (L.D.)
- Department of Surgery, Faculty of Medicine, University of Ioannina, 45110 Ioannina, Greece
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3
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Hua X, Han K, Mandracchia B, Radmand A, Liu W, Kim H, Yuan Z, Ehrlich SM, Li K, Zheng C, Son J, Silva Trenkle AD, Kwong GA, Zhu C, Dahlman JE, Jia S. Light-field flow cytometry for high-resolution, volumetric and multiparametric 3D single-cell analysis. Nat Commun 2024; 15:1975. [PMID: 38438356 PMCID: PMC10912605 DOI: 10.1038/s41467-024-46250-7] [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: 04/19/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024] Open
Abstract
Imaging flow cytometry (IFC) combines flow cytometry and fluorescence microscopy to enable high-throughput, multiparametric single-cell analysis with rich spatial details. However, current IFC techniques remain limited in their ability to reveal subcellular information with a high 3D resolution, throughput, sensitivity, and instrumental simplicity. In this study, we introduce a light-field flow cytometer (LFC), an IFC system capable of high-content, single-shot, and multi-color acquisition of up to 5,750 cells per second with a near-diffraction-limited resolution of 400-600 nm in all three dimensions. The LFC system integrates optical, microfluidic, and computational strategies to facilitate the volumetric visualization of various 3D subcellular characteristics through convenient access to commonly used epi-fluorescence platforms. We demonstrate the effectiveness of LFC in assaying, analyzing, and enumerating intricate subcellular morphology, function, and heterogeneity using various phantoms and biological specimens. The advancement offered by the LFC system presents a promising methodological pathway for broad cell biological and translational discoveries, with the potential for widespread adoption in biomedical research.
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Affiliation(s)
- Xuanwen Hua
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Keyi Han
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Biagio Mandracchia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Afsane Radmand
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Chemical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Wenhao Liu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Hyejin Kim
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Zhou Yuan
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Samuel M Ehrlich
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- Georgia W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kaitao Li
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Corey Zheng
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Jeonghwan Son
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Aaron D Silva Trenkle
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Gabriel A Kwong
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cheng Zhu
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Shu Jia
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Parker H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, GA, USA.
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Tian D, Liu Y, Zhang Y, Liu Y, Xia Y, Xu B, Xu J, Yomo T. Implementation of Fluorescent-Protein-Based Quantification Analysis in L-Form Bacteria. Bioengineering (Basel) 2024; 11:81. [PMID: 38247958 PMCID: PMC10813599 DOI: 10.3390/bioengineering11010081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/09/2024] [Accepted: 01/12/2024] [Indexed: 01/23/2024] Open
Abstract
Cell-wall-less (L-form) bacteria exhibit morphological complexity and heterogeneity, complicating quantitative analysis of them under internal and external stimuli. Stable and efficient labeling is needed for the fluorescence-based quantitative cell analysis of L-forms during growth and proliferation. Here, we evaluated the expression of multiple fluorescent proteins (FPs) under different promoters in the Bacillus subtilis L-form strain LR2 using confocal microscopy and imaging flow cytometry. Among others, Pylb-derived NBP3510 showed a superior performance for inducing several FPs including EGFP and mKO2 in both the wild-type and L-form strains. Moreover, NBP3510 was also active in Escherichia coli and its L-form strain NC-7. Employing these established FP-labeled strains, we demonstrated distinct morphologies in the L-form bacteria in a quantitative manner. Given cell-wall-deficient bacteria are considered protocell and synthetic cell models, the generated cell lines in our work could be valuable for L-form-based research.
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Affiliation(s)
| | | | | | | | | | | | - Jian Xu
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
| | - Tetsuya Yomo
- Laboratory of Biology and Information Science, School of Life Sciences, East China Normal University, Shanghai 200062, China
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5
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Pozzi P, Candeo A, Paiè P, Bragheri F, Bassi A. Artificial intelligence in imaging flow cytometry. FRONTIERS IN BIOINFORMATICS 2023; 3:1229052. [PMID: 37877042 PMCID: PMC10593470 DOI: 10.3389/fbinf.2023.1229052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 09/11/2023] [Indexed: 10/26/2023] Open
Affiliation(s)
- Paolo Pozzi
- Department of Physics, Politecnico di Milano, Milano, Italy
| | - Alessia Candeo
- Department of Physics, Politecnico di Milano, Milano, Italy
| | - Petra Paiè
- Department of Physics, Politecnico di Milano, Milano, Italy
| | - Francesca Bragheri
- Institute for Photonics and Nanotechnologies, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Andrea Bassi
- Department of Physics, Politecnico di Milano, Milano, Italy
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6
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Wang H, Zhang Y, Dai L, Bo X, Liu X, Zhao X, Yu J, Kwok LY, Bao Q. Metabolomic Differences between Viable but Nonculturable and Recovered Lacticaseibacillus paracasei Zhang. Foods 2023; 12:3472. [PMID: 37761181 PMCID: PMC10527867 DOI: 10.3390/foods12183472] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
The fermentation process can be affected when the starter culture enters the viable but nonculturable (VBNC) state. Therefore, it is of interest to investigate how VBNC cells change physiologically. Lacticaseibacillus (L.) paracasei Zhang is both a probiotic and a starter strain. This study aimed to investigate the metabolomic differences between VBNC and recovered L. paracasei Zhang cells. First, L. paracasei Zhang was induced to enter the VBNC state by keeping the cells in a liquid de Man-Rogosa-Sharpe (MRS) medium at 4 °C for 220 days. Flow cytometry was used to sort the induced VBNC cells, and three different types of culture media (MRS medium, skim milk with 1% yeast extract, and skim milk) were used for cell resuscitation. Cell growth responses in the three types of recovery media suggested that the liquid MRS medium was the most effective in reversing the VBNC state in L. paracasei Zhang. Metabolomics analysis revealed 25 differential metabolites from five main metabolite classes (amino acid, carbohydrate, lipid, vitamin, and purine and pyrimidine). The levels of L-cysteine, L-alanine, L-lysine, and L-arginine notably increased in the revived cells, while cellulose, alginose, and guanine significantly decreased. This study confirmed that VBNC cells had an altered physiology.
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Affiliation(s)
- Huiying Wang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Yuhong Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lixia Dai
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiaoyu Bo
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xiangyun Liu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Xin Zhao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Lai-Yu Kwok
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Qiuhua Bao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Inner Mongolia Agricultural University, Hohhot 010018, China; (H.W.); (Y.Z.); (L.D.); (X.B.); (X.L.); (X.Z.); (J.Y.); (L.-Y.K.)
- Key Laboratory of Dairy Products Processing, Ministry of Agriculture and Rural Affairs, Inner Mongolia Agricultural University, Hohhot 010018, China
- Inner Mongolia Key Laboratory of Dairy Biotechnology and Engineering, Inner Mongolia Agricultural University, Hohhot 010018, China
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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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8
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Oldham RC, Held MA. Methods for detection and identification of beer-spoilage microbes. Front Microbiol 2023; 14:1217704. [PMID: 37637116 PMCID: PMC10448528 DOI: 10.3389/fmicb.2023.1217704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
It is critical that breweries of all sizes routinely monitor the microbiome of their process to limit financial losses due to microbial contamination. Contamination by beer-spoiling microbes (BSMs) at any point during the brewing process may lead to significant losses for breweries if gone undetected and allowed to spread. Testing and detection of BSMs must be routine and rapid, and because even small breweries need the capability of BSM detection and identification, the method also needs to be affordable. Lactic acid bacteria (LAB) are responsible for most spoilage incidents, many of which have been shown to enter the viable but nonculturable (VBNC) state under conditions present in beer such as cold or oxidative stress. These bacteria are invisible to traditional methods of detection using selective media. This article describes several methods of BSM detection and identification that may be useful in the majority of craft breweries. While there are several genomic methods that meet some or many qualifications of being useful in craft breweries, real-time quantitative polymerase chain reaction (qPCR) currently best meets the desired method characteristics and holds the most utility in this industry, specifically SYBR Green qPCR. qPCR is a targeted method of detection and identification of microbes that is affordable, rapid, specific, sensitive, quantitative, and reliable, and when paired with valid DNA extraction techniques can be used to detect BSMs, including those in the VBNC state.
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Affiliation(s)
- Ryanne C. Oldham
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
- Quality Assurance and Quality Control Laboratory, Jackie O’s Brewery, Athens, OH, United States
| | - Michael A. Held
- Department of Chemistry and Biochemistry, Ohio University, Athens, OH, United States
- Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
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9
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Goubet AG. Could the tumor-associated microbiota be the new multi-faceted player in the tumor microenvironment? Front Oncol 2023; 13:1185163. [PMID: 37287916 PMCID: PMC10242102 DOI: 10.3389/fonc.2023.1185163] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 05/02/2023] [Indexed: 06/09/2023] Open
Abstract
Microorganisms have been identified in tumor specimens for over a century. It is only in recent years that tumor-associated microbiota has become a rapidly expanding field. Assessment techniques encompass methods at the frontiers of molecular biology, microbiology, and histology, requiring a transdisciplinary process to carefully decipher this new component of the tumor microenvironment. Due to the low biomass, the study of tumor-associated microbiota poses technical, analytical, biological, and clinical challenges and must be approached as a whole. To date, several studies have begun to shed light on the composition, functions, and clinical relevance of the tumor-associated microbiota. This new piece of the tumor microenvironment puzzle could potentially change the way we think about and treat patients with cancer.
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Affiliation(s)
- Anne-Gaëlle Goubet
- Department of Pathology and Immunology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
- AGORA Cancer Research Center, Lausanne, Switzerland
- Swiss Cancer Center Léman, Lausanne, Switzerland
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10
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Tian D, Wang C, Liu Y, Zhang Y, Caliari A, Lu H, Xia Y, Xu B, Xu J, Yomo T. Cell Sorting-Directed Selection of Bacterial Cells in Bigger Sizes Analyzed by Imaging Flow Cytometry during Experimental Evolution. Int J Mol Sci 2023; 24:ijms24043243. [PMID: 36834655 PMCID: PMC9966196 DOI: 10.3390/ijms24043243] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/20/2023] [Accepted: 01/26/2023] [Indexed: 02/10/2023] Open
Abstract
Cell morphology is an essential and phenotypic trait that can be easily tracked during adaptation and evolution to environmental changes. Thanks to the rapid development of quantitative analytical techniques for large populations of cells based on their optical properties, morphology can be easily determined and tracked during experimental evolution. Furthermore, the directed evolution of new culturable morphological phenotypes can find use in synthetic biology to refine fermentation processes. It remains unknown whether and how fast we can obtain a stable mutant with distinct morphologies using fluorescence-activated cell sorting (FACS)-directed experimental evolution. Taking advantage of FACS and imaging flow cytometry (IFC), we direct the experimental evolution of the E. coli population undergoing continuous passage of sorted cells with specific optical properties. After ten rounds of sorting and culturing, a lineage with large cells resulting from incomplete closure of the division ring was obtained. Genome sequencing highlighted a stop-gain mutation in amiC, leading to a dysfunctional AmiC division protein. The combination of FACS-based selection with IFC analysis to track the evolution of the bacteria population in real-time holds promise to rapidly select and culture new morphologies and association tendencies with many potential applications.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Jian Xu
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
| | - Tetsuya Yomo
- Correspondence: (J.X.); (T.Y.); Tel.: +86-(21)-62233727 (J.X. & T.Y.)
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11
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Wagley S. The Viable but Non-Culturable (VBNC) State in Vibrio Species: Why Studying the VBNC State Now Is More Exciting than Ever. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1404:253-268. [PMID: 36792880 DOI: 10.1007/978-3-031-22997-8_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
During periods that are not conducive for growth or when facing stressful conditions, Vibrios enter a dormant state called the Viable But Non-Culturable (VBNC) state. In this chapter, I will analyse the role of the VBNC state in Vibrio species survival and pathogenesis and the molecular mechanisms regulating this complex phenomenon. I will emphasise some of the novel findings that make studying the VBNC state now more exciting than ever and its significance in the epidemiology of these pathogens and critical role in food safety.
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Affiliation(s)
- Sariqa Wagley
- Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, Devon, UK.
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Sergaki C, Anwar S, Fritzsche M, Mate R, Francis RJ, MacLellan-Gibson K, Logan A, Amos GCA. Developing whole cell standards for the microbiome field. MICROBIOME 2022; 10:123. [PMID: 35945640 PMCID: PMC9361656 DOI: 10.1186/s40168-022-01313-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 06/24/2022] [Indexed: 05/08/2023]
Abstract
BACKGROUND Effective standardisation of the microbiome field is essential to facilitate global translational research and increase the reproducibility of microbiome studies. In this study, we describe the development and validation of a whole cell reference reagent specific to the gut microbiome by the UK National Institute for Biological Standards and Control. We also provide and test a two-step reporting framework to allow microbiome researchers to quickly and accurately validate choices of DNA extraction, sequencing, and bioinformatic pipelines. RESULTS Using 20 strains that are commonly found in the gut, we developed a whole cell reference reagent (WC-Gut RR) for the evaluation of the DNA extraction protocols commonly used in microbiome pipelines. DNA was first analysed using the physicochemical measures of yield, integrity, and purity, which demonstrated kits widely differed in the quality of the DNA they produced. Importantly, the combination of the WC-Gut RR and the three physicochemical measures allowed us to differentiate clearly between kit performance. We next assessed the ability of WC-Gut RR to evaluate kit performance in the reconstitution of accurate taxonomic profiles. We applied a four-measure framework consisting of Sensitivity, false-positive relative abundance (FPRA), Diversity, and Similarity as previously described for DNA reagents. Using the WC-Gut RR and these four measures, we could reliably identify the DNA extraction kits' biases when using with both 16S rRNA sequencing and shotgun sequencing. Moreover, when combining this with complementary DNA standards, we could estimate the relative bias contributions of DNA extraction kits vs bioinformatic analysis. Finally, we assessed WC-Gut RR alongside other commercially available reagents. The analysis here clearly demonstrates that reagents of lower complexity, not composed of anaerobic and hard-to-lyse strains from the gut, can artificially inflate the performance of microbiome DNA extraction kits and bioinformatic pipelines. CONCLUSIONS We produced a complex whole cell reagent that is specific for the gut microbiome and can be used to evaluate and benchmark DNA extractions in microbiome studies. Used alongside a DNA standard, the NIBSC DNA-Gut-Mix RR helps estimating where biases occur in microbiome pipelines. In the future, we aim to establish minimum thresholds for data quality through an interlaboratory collaborative study. Video Abstract.
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Affiliation(s)
- Chrysi Sergaki
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK.
| | - Saba Anwar
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Martin Fritzsche
- Division of Analytical and Biological Sciences, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Ryan Mate
- Division of Analytical and Biological Sciences, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Robert J Francis
- Division of Analytical and Biological Sciences, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Kirsty MacLellan-Gibson
- Division of Analytical and Biological Sciences, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Alastair Logan
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
| | - Gregory C A Amos
- Division of Bacteriology, National Institute for Biological Standards and Control, Potters Bar, Hertfordshire, EN6 3QG, UK
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Imaging Flow Cytometry to Study Biofilm-Associated Microbial Aggregates. Molecules 2021; 26:molecules26237096. [PMID: 34885675 PMCID: PMC8659131 DOI: 10.3390/molecules26237096] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/19/2021] [Accepted: 11/21/2021] [Indexed: 12/01/2022] Open
Abstract
The aim of the research was to design an advanced analytical tool for the precise characterization of microbial aggregates from biofilms formed on food-processing surfaces. The approach combined imaging flow cytometry with a machine learning-based interpretation protocol. Biofilm samples were collected from three diagnostic points of the food-processing lines at two independent time points. The samples were investigated for the complexity of microbial aggregates and cellular metabolic activity. Thus, aggregates and singlets of biofilm-associated microbes were simultaneously examined for the percentages of active, mid-active, and nonactive (dead) cells to evaluate the physiology of the microbial cells forming the biofilm structures. The tested diagnostic points demonstrated significant differences in the complexity of microbial aggregates. The significant percentages of the bacterial aggregates were associated with the dominance of active microbial cells, e.g., 75.3% revealed for a mushroom crate. This confirmed the protective role of cellular aggregates for the survival of active microbial cells. Moreover, the approach enabled discriminating small and large aggregates of microbial cells. The developed tool provided more detailed characteristics of bacterial aggregates within a biofilm structure combined with high-throughput screening potential. The designed methodology showed the prospect of facilitating the detection of invasive biofilm forms in the food industry environment.
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Hare PJ, LaGree TJ, Byrd BA, DeMarco AM, Mok WWK. Single-Cell Technologies to Study Phenotypic Heterogeneity and Bacterial Persisters. Microorganisms 2021; 9:2277. [PMID: 34835403 PMCID: PMC8620850 DOI: 10.3390/microorganisms9112277] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 10/20/2021] [Accepted: 10/27/2021] [Indexed: 11/16/2022] Open
Abstract
Antibiotic persistence is a phenomenon in which rare cells of a clonal bacterial population can survive antibiotic doses that kill their kin, even though the entire population is genetically susceptible. With antibiotic treatment failure on the rise, there is growing interest in understanding the molecular mechanisms underlying bacterial phenotypic heterogeneity and antibiotic persistence. However, elucidating these rare cell states can be technically challenging. The advent of single-cell techniques has enabled us to observe and quantitatively investigate individual cells in complex, phenotypically heterogeneous populations. In this review, we will discuss current technologies for studying persister phenotypes, including fluorescent tags and biosensors used to elucidate cellular processes; advances in flow cytometry, mass spectrometry, Raman spectroscopy, and microfluidics that contribute high-throughput and high-content information; and next-generation sequencing for powerful insights into genetic and transcriptomic programs. We will further discuss existing knowledge gaps, cutting-edge technologies that can address them, and how advances in single-cell microbiology can potentially improve infectious disease treatment outcomes.
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Affiliation(s)
- Patricia J. Hare
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Dental Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Travis J. LaGree
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Brandon A. Byrd
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
- School of Medicine, University of Connecticut, Farmington, CT 06032, USA
| | - Angela M. DeMarco
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
| | - Wendy W. K. Mok
- Department of Molecular Biology & Biophysics, UConn Health, Farmington, CT 06032, USA; (P.J.H.); (T.J.L.); (B.A.B.); (A.M.D.)
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