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Fernández-Fernández R, Olivenza DR, Sánchez-Romero MA. Identifying Bacterial Lineages in Salmonella by Flow Cytometry. EcoSal Plus 2022; 10:eESP00182021. [PMID: 35148202 PMCID: PMC10729938 DOI: 10.1128/ecosalplus.esp-0018-2021] [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: 04/30/2021] [Accepted: 12/21/2021] [Indexed: 12/16/2022]
Abstract
Advances in technologies that permit high-resolution analysis of events in single cells have revealed that phenotypic heterogeneity is a widespread phenomenon in bacteria. Flow cytometry has the potential to describe the distribution of cellular properties within a population of bacterial cells and has yielded invaluable information about the ability of isogenic cells to diversify into phenotypic subpopulations. This review will discuss several single-cell approaches that have recently been applied to define phenotypic heterogeneity in populations of Salmonella enterica.
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Affiliation(s)
| | - David R. Olivenza
- Departamento de Genética, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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van de Velde CC, Joseph C, Biclot A, Huys GRB, Pinheiro VB, Bernaerts K, Raes J, Faust K. Fast quantification of gut bacterial species in cocultures using flow cytometry and supervised classification. ISME COMMUNICATIONS 2022; 2:40. [PMID: 37938658 PMCID: PMC9723706 DOI: 10.1038/s43705-022-00123-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 03/26/2022] [Accepted: 04/14/2022] [Indexed: 09/07/2023]
Abstract
A bottleneck for microbial community experiments with many samples and/or replicates is the fast quantification of individual taxon abundances, which is commonly achieved through sequencing marker genes such as the 16S rRNA gene. Here, we propose a new approach for high-throughput and high-quality enumeration of human gut bacteria in a defined community, combining flow cytometry and supervised classification to identify and quantify species mixed in silico and in defined communities in vitro. We identified species in a 5-species in silico community with an F1 score of 71%. In addition, we demonstrate in vitro that our method performs equally well or better than 16S rRNA gene sequencing in two-species cocultures and agrees with 16S rRNA gene sequencing data on the most abundant species in a four-species community. We found that shape and size differences alone are insufficient to distinguish species, and that it is thus necessary to exploit the multivariate nature of flow cytometry data. Finally, we observed that variability of flow cytometry data across replicates differs between gut bacterial species. In conclusion, the performance of supervised classification of gut species in flow cytometry data is species-dependent, but is for some combinations accurate enough to serve as a faster alternative to 16S rRNA gene sequencing.
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Affiliation(s)
- Charlotte C van de Velde
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
| | - Clémence Joseph
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
| | - Anaïs Biclot
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
- VIB-KU Leuven, Center for Microbiology, B-3000, Leuven, Belgium
| | - Geert R B Huys
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
- VIB-KU Leuven, Center for Microbiology, B-3000, Leuven, Belgium
| | - Vitor B Pinheiro
- KU Leuven, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, Medicinal Chemistry, B-3000, Leuven, Belgium
| | - Kristel Bernaerts
- KU Leuven, Department of Chemical Engineering, Chemical and Biochemical Reactor Engineering and Safety (CREaS), B-3001, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium
- VIB-KU Leuven, Center for Microbiology, B-3000, Leuven, Belgium
| | - Karoline Faust
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, Laboratory of Molecular Bacteriology, B-3000, Leuven, Belgium.
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Perera IA, Abinandan S, Subashchandrabose SR, Venkateswarlu K, Naidu R, Megharaj M. Advances in the technologies for studying consortia of bacteria and cyanobacteria/microalgae in wastewaters. Crit Rev Biotechnol 2019; 39:709-731. [PMID: 30971144 DOI: 10.1080/07388551.2019.1597828] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The excessive generation and discharge of wastewaters have been serious concerns worldwide in the recent past. From an environmental friendly perspective, bacteria, cyanobacteria and microalgae, and the consortia have been largely considered for biological treatment of wastewaters. For efficient use of bacteria‒cyanobacteria/microalgae consortia in wastewater treatment, detailed knowledge on their structure, behavior and interaction is essential. In this direction, specific analytical tools and techniques play a significant role in studying these consortia. This review presents a critical perspective on physical, biochemical and molecular techniques such as microscopy, flow cytometry with cell sorting, nanoSIMS and omics approaches used for systematic investigations of the structure and function, particularly nutrient removal potential of bacteria‒cyanobacteria/microalgae consortia. In particular, the use of specific molecular techniques of genomics, transcriptomics, proteomics metabolomics and genetic engineering to develop more stable consortia of bacteria and cyanobacteria/microalgae with their improved biotechnological capabilities in wastewater treatment has been highlighted.
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Affiliation(s)
- Isiri Adhiwarie Perera
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia
| | - Sudharsanam Abinandan
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia
| | - Suresh R Subashchandrabose
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia.,b Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE) , The University of Newcastle , Callaghan , New South Wales , Australia
| | - Kadiyala Venkateswarlu
- c Formerly Department of Microbiology , Sri Krishnadevaraya University , Anantapuramu , Andhra Pradesh , India
| | - Ravi Naidu
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia.,b Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE) , The University of Newcastle , Callaghan , New South Wales , Australia
| | - Mallavarapu Megharaj
- a Global Centre for Environmental Remediation (GCER), Faculty of Science , The University of Newcastle , Callaghan , New South Wales , Australia.,b Cooperative Research Centre for Contamination Assessment and Remediation of Environment (CRC CARE) , The University of Newcastle , Callaghan , New South Wales , Australia
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Han Y, Gu Y, Zhang AC, Lo YH. Review: imaging technologies for flow cytometry. LAB ON A CHIP 2016; 16:4639-4647. [PMID: 27830849 PMCID: PMC5311077 DOI: 10.1039/c6lc01063f] [Citation(s) in RCA: 139] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
High-throughput single cell imaging is a critical enabling and driving technology in molecular and cellular biology, biotechnology, medicine and related areas. Imaging flow cytometry combines the single-cell imaging capabilities of microscopy with the high-throughput capabilities of conventional flow cytometry. Recent advances in imaging flow cytometry are remarkably revolutionizing single-cell analysis. This article describes recent imaging flow cytometry technologies and their challenges.
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Affiliation(s)
- Yuanyuan Han
- Department of Electrical and Computer Engineering, University of California, San Diego, California 92093, USA.
| | - Yi Gu
- Department of Electrical and Computer Engineering, University of California, San Diego, California 92093, USA.
| | - Alex Ce Zhang
- Department of Electrical and Computer Engineering, University of California, San Diego, California 92093, USA.
| | - Yu-Hwa Lo
- Department of Electrical and Computer Engineering, University of California, San Diego, California 92093, USA.
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Abstract
This chapter describes advantages and limitations of imaging flow cytometry (IFC) based on Imagestream instrumentation using a hybrid approach of morphometric measurement and quantitation of multiparametric fluorescent intensities' distribution in cells and particles. Brief comparison is given of IFC with conventional flow cytometry and fluorescent microscopy. Some future directions of the IFC technology are described and discussed.
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Affiliation(s)
- Ivan A Vorobjev
- Department of Cell Biology and Histology, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia.
- A.N. Belozersky Institute of Physico-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, 119992, Russia.
| | - Natasha S Barteneva
- Cellular and Molecular Medicine Program, Boston Childrens Hospital, Boston, MA, 02115, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
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Zheng G, Ou X, Yang C. 0.5 gigapixel microscopy using a flatbed scanner. BIOMEDICAL OPTICS EXPRESS 2013; 5:1-8. [PMID: 24466471 PMCID: PMC3891323 DOI: 10.1364/boe.5.000001] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Revised: 11/10/2013] [Accepted: 11/24/2013] [Indexed: 05/26/2023]
Abstract
The capability to perform high-resolution, wide field-of-view (FOV) microscopy imaging is highly sought after in biomedical applications. In this paper, we report a wide FOV microscopy system that uses a closed-circuit-television (CCTV) lens for image relay and a flatbed scanner for data acquisition. We show that such an imaging system is capable of capturing a 10 mm × 7.5 mm FOV image with 0.78 µm resolution, resulting in more than 0.5 billion pixels across the entire image. The resolution and field curve of the proposed system were characterized by imaging a USAF resolution target and a hole-array target. To demonstrate its application, 0.5 gigapixel images of histology slides were acquired using this system.
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Affiliation(s)
- Guoan Zheng
- Electrical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Presently at Biomedical Engineering & Electrical Engineering, University of Connecticut, Storss, CT, 06269 USA
- These authors contributed equally to this work
| | - Xiaoze Ou
- Electrical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- These authors contributed equally to this work
| | - Changhuei Yang
- Electrical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
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Combination of small molecule microarray and confocal microscopy techniques for live cell staining fluorescent dye discovery. Molecules 2013; 18:9999-10013. [PMID: 23966084 PMCID: PMC6270374 DOI: 10.3390/molecules18089999] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2013] [Revised: 08/13/2013] [Accepted: 08/14/2013] [Indexed: 01/25/2023] Open
Abstract
Discovering new fluorochromes is significantly advanced by high-throughput screening (HTS) methods. In the present study a combination of small molecule microarray (SMM) prescreening and confocal laser scanning microscopy (CLSM) was developed in order to discover novel cell staining fluorescent dyes. Compounds with high native fluorescence were selected from a 14,585-member library and further tested on living cells under the microscope. Eleven compartment-specific, cell-permeable (or plasma membrane-targeted) fluorochromes were identified. Their cytotoxicity was tested and found that between 1–10 micromolar range, they were non-toxic even during long-term incubations.
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Krylova I, Kumar RR, Kofoed EM, Schaufele F. A versatile, bar-coded nuclear marker/reporter for live cell fluorescent and multiplexed high content imaging. PLoS One 2013; 8:e63286. [PMID: 23691010 PMCID: PMC3653935 DOI: 10.1371/journal.pone.0063286] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Accepted: 04/01/2013] [Indexed: 11/18/2022] Open
Abstract
The screening of large numbers of compounds or siRNAs is a mainstay of both academic and pharmaceutical research. Most screens test those interventions against a single biochemical or cellular output whereas recording multiple complementary outputs may be more biologically relevant. High throughput, multi-channel fluorescence microscopy permits multiple outputs to be quantified in specific cellular subcompartments. However, the number of distinct fluorescent outputs available remains limited. Here, we describe a cellular bar-code technology in which multiple cell-based assays are combined in one well after which each assay is distinguished by fluorescence microscopy. The technology uses the unique fluorescent properties of assay-specific markers comprised of distinct combinations of different 'red' fluorescent proteins sandwiched around a nuclear localization signal. The bar-code markers are excited by a common wavelength of light but distinguished ratiometrically by their differing relative fluorescence in two emission channels. Targeting the bar-code to cell nuclei enables individual cells expressing distinguishable markers to be readily separated by standard image analysis programs. We validated the method by showing that the unique responses of different cell-based assays to specific drugs are retained when three assays are co-plated and separated by the bar-code. Based upon those studies, we discuss a roadmap in which even more assays may be combined in a well. The ability to analyze multiple assays simultaneously will enable screens that better identify, characterize and distinguish hits according to multiple biologically or clinically relevant criteria. These capabilities also enable the re-creation of complex mixtures of cell types that is emerging as a central area of interest in many fields.
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Affiliation(s)
- Irina Krylova
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Rachit R. Kumar
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Eric M. Kofoed
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
| | - Fred Schaufele
- Center for Reproductive Sciences, University of California San Francisco, San Francisco, California, United States of America
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Satori CP, Kostal V, Arriaga EA. Review on recent advances in the analysis of isolated organelles. Anal Chim Acta 2012; 753:8-18. [PMID: 23107131 PMCID: PMC3484375 DOI: 10.1016/j.aca.2012.09.041] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 09/22/2012] [Accepted: 09/24/2012] [Indexed: 10/27/2022]
Abstract
The analysis of isolated organelles is one of the pillars of modern bioanalytical chemistry. This review describes recent developments on the isolation and characterization of isolated organelles both from living organisms and cell cultures. Salient reports on methods to release organelles focused on reproducibility and yield, membrane isolation, and integrated devices for organelle release. New developments on organelle fractionation after their isolation were on the topics of centrifugation, immunocapture, free flow electrophoresis, flow field-flow fractionation, fluorescence activated organelle sorting, laser capture microdissection, and dielectrophoresis. New concepts on characterization of isolated organelles included atomic force microscopy, optical tweezers combined with Raman spectroscopy, organelle sensors, flow cytometry, capillary electrophoresis, and microfluidic devices.
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Affiliation(s)
- Chad P Satori
- Department of Chemistry, University of Minnesota, Minneapolis, MN 55455, USA
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