101
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The many facets of Raman spectroscopy for biomedical analysis. Anal Bioanal Chem 2014; 407:699-717. [DOI: 10.1007/s00216-014-8311-9] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Revised: 10/20/2014] [Accepted: 10/31/2014] [Indexed: 12/13/2022]
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102
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Development of a rapid capture-cum-detection method for Escherichia coli O157 from apple juice comprising nano-immunomagnetic separation in tandem with surface enhanced Raman scattering. Int J Food Microbiol 2014; 189:89-97. [DOI: 10.1016/j.ijfoodmicro.2014.07.036] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Revised: 07/25/2014] [Accepted: 07/30/2014] [Indexed: 11/20/2022]
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103
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Ji Y, He Y, Cui Y, Wang T, Wang Y, Li Y, Huang WE, Xu J. Raman spectroscopy provides a rapid, non-invasive method for quantitation of starch in live, unicellular microalgae. Biotechnol J 2014; 9:1512-8. [DOI: 10.1002/biot.201400165] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/04/2014] [Accepted: 06/04/2014] [Indexed: 11/07/2022]
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104
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Chemical composition of Enterococcus faecalis in biofilm cells initiated from different physiologic states. Folia Microbiol (Praha) 2014; 59:447-53. [PMID: 24895050 DOI: 10.1007/s12223-014-0319-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 04/22/2014] [Indexed: 02/08/2023]
Abstract
Enterococcus faecalis is a ubiquitous bacterium of the gut that is observed in persistent periradicular infections. Its pathogenicity is associated with biofilm formation and the ability to survive under nutrient-poor (starvation) conditions. However, characteristics of chemical composition of biofilm cells developed by starved E. faecalis cells remain poorly understood. In this study, E. faecalis cells in exponential, stationary, and starvation phases were prepared and separately cultured to form biofilms. Confocal laser scanning microscopy was performed to verify biofilm formation. Raman microscopy was used to investigate the chemical composition of cells within the biofilms. Compared to cells in exponential or stationary phase, starved cells developed biofilms with fewer culturable cells (P < 0.05). Raman analysis revealed that cells produced in the biofilms from starved planktonic cells contained more protein and less nucleic acids than either the corresponding planktonic cells or the cells in biofilms from planktonic cells in exponential or stationary phases, suggesting that biofilm-grown cells from the starvation phase were characterized by increased synthesis of proteins and decreased nucleic acids. This study provides an insight into the chemical composition of biofilm cells developed by starved E. faecalis.
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105
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Applications and impacts of stable isotope probing for analysis of microbial interactions. Appl Microbiol Biotechnol 2014; 98:4817-28. [PMID: 24715147 DOI: 10.1007/s00253-014-5705-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2013] [Revised: 03/17/2014] [Accepted: 03/17/2014] [Indexed: 10/25/2022]
Abstract
Probing the interactions between microbes and their environment with stable isotopes became a powerful technique over the last years. While quadruple mass spectrometry or isotope ratio mass spectrometry (IRMS) require at least 300,000 bacterial cells, analysis at the single-cell level is possible with secondary ion mass spectrometry (SIMS) or Raman microspectrometry. While SIMS needs enrichments of more than 0.1 and Raman microscopy of more than 25 at.-%, IRMS can deal with 0.0001 at.-%. To find out who eats what, one has to discern between the different species in a community. Several methods have been introduced to discern between the different taxa in microbial communities, e.g., by using fatty acids as biomarkers, density centrifugation of DNA/RNA, or fluorescent in situ hybridization (FISH) with phylogenetic probes. While the biomarker approach can be coupled with the high sensitivity of the IRMS, the DNA approach gives in general a better phylogenetic resolution of the metabolic active microbes. A combination of both is the separation via coupling of FISH-probes to magnetic beads or fluorescent assisted cell sorting (FACS) of stained cells leading to fractions which can be analyzed by IRMS. Applying these techniques over a time course can reveal the metabolic kinetics and food webs. In this review, the different methods are presented with examples and their advantages and disadvantages are discussed. An outlook on the combination of the various techniques and their applications in microbial ecology is given.
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106
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Abstract
Raman spectroscopy is a rapid nondestructive technique providing spectroscopic and structural information on both organic and inorganic molecular compounds. Extensive applications for the method in the characterization of pigments have been found. Due to the high sensitivity of Raman spectroscopy for the detection of chlorophylls, carotenoids, scytonemin, and a range of other pigments found in the microbial world, it is an excellent technique to monitor the presence of such pigments, both in pure cultures and in environmental samples. Miniaturized portable handheld instruments are available; these instruments can be used to detect pigments in microbiological samples of different types and origins under field conditions.
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107
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Marcoux PR, Dupoy M, Cuer A, Kodja JL, Lefebvre A, Licari F, Louvet R, Narassiguin A, Mallard F. Optical forward-scattering for identification of bacteria within microcolonies. Appl Microbiol Biotechnol 2014; 98:2243-54. [PMID: 24413976 DOI: 10.1007/s00253-013-5495-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2013] [Revised: 12/20/2013] [Accepted: 12/22/2013] [Indexed: 11/28/2022]
Abstract
The development of methods for the rapid identification of pathogenic bacteria is a major step towards accelerated clinical diagnosis of infectious diseases and efficient food and water safety control. Methods for identification of bacterial colonies on gelified nutrient broth have the potential to bring an attractive solution, combining simple optical instrumentation, no need for sample preparation or labelling, in a non-destructive process. Here, we studied the possibility of discriminating different bacterial species at a very early stage of growth (6 h of incubation at 37 °C), on thin layers of agar media (1 mm of Tryptic Soy Agar), using light forward-scattering and learning algorithms (Bayes Network, Continuous Naive Bayes, Sequential Minimal Optimisation). A first database of more than 1,000 scatterograms acquired on 7 gram-negative strains yielded a recognition rate of nearly 80%, after only 6 h of incubation. We investigated also the prospect of identifying different strains from a same species through forward scattering. We discriminated, thus, four strains of Escherichia coli with a recognition rate reaching 82%. Finally, we show the discrimination of two species of coagulase-negative Staphylococci (S. haemolyticus and S. cohnii), on a commercial selective pre-poured medium used in clinical diagnosis (ChromID MRSA, bioMérieux), without opening lids during the scatterogram acquisition. This shows the potential of this method--non-invasive, preventing cross-contaminations and requiring minimal dish handling--to provide early clinically-relevant information in the context of fully automated microbiology labs.
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Affiliation(s)
- Pierre R Marcoux
- Department of Technology for Biology and Healthcare, CEA-LETI MINATEC, 17 avenue des Martyrs, 38054, Grenoble, France,
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108
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Abstract
Single-cell Raman spectroscopy is a noninvasive and label-free technology for biochemical analysis of bacterial cells. A single-cell Raman spectrum functions as a metabolic "fingerprint" of an individual cell, which enables differentiation of cell types, physiological states, nutrient condition, and variable phenotypes. Raman tweezers combines single-cell Raman spectroscopy with optical laser tweezers to allow the identification and isolation of single living cells according to their Raman spectra. After cell sorting subsequent culturing and genomic sequencing has the potential to reveal totally new groups of microbes. Stable isotope probing with Raman tweezers offers a culture-independent toolbox to study genetic functions and physiology of unculturable microorganisms in the ecosystem.
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Affiliation(s)
- Mengqiu Li
- Kroto Research Institute, Sheffield University, Sheffield, UK
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109
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Wang T, Ji Y, Wang Y, Jia J, Li J, Huang S, Han D, Hu Q, Huang WE, Xu J. Quantitative dynamics of triacylglycerol accumulation in microalgae populations at single-cell resolution revealed by Raman microspectroscopy. BIOTECHNOLOGY FOR BIOFUELS 2014; 7:58. [PMID: 24716544 PMCID: PMC4022372 DOI: 10.1186/1754-6834-7-58] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 03/27/2014] [Indexed: 05/18/2023]
Abstract
BACKGROUND Rapid, real-time and label-free measurement of the cellular contents of biofuel molecules such as triacylglycerol (TAG) in populations at single-cell resolution are important for bioprocess control and understanding of the population heterogeneity. Raman microspectroscopy can directly detect the changes of metabolite profile in a cell and thus can potentially serve these purposes. RESULTS Single-cell Raman spectra (SCRS) of the unicellular oleaginous microalgae Nannochloropsis oceanica from the cultures under nitrogen depletion (TAG-producing condition) and nitrogen repletion (non-TAG-producing condition) were sampled at eight time points during the first 96 hours upon the onset of nitrogen depletion. Single N. oceanica cells were captured by a 532-nm laser and the SCRS were acquired by the same laser within one second per cell. Using chemometric methods, the SCRS were able to discriminate cells between nitrogen-replete and nitrogen-depleted conditions at as early as 6 hours with >93.3% accuracy, and among the eight time points under nitrogen depletion with >90.4% accuracy. Quantitative prediction of TAG content in single cells was achieved and validated via SCRS and liquid chromatography-mass spectrometry (LC-MS) analysis at population level. SCRS revealed the dynamics of heterogeneity in TAG production among cells in each isogenic population. A significant negative correlation between TAG content and lipid unsaturation degree in individual microalgae cells was observed. CONCLUSIONS Our results show that SCRS can serve as a label-free and non-invasive proxy for quantitatively tracking and screening cellular TAG content in real-time at single-cell level. Phenotypic comparison of single cells via SCRS should also help investigating the mechanisms of functional heterogeneity within a cellular population.
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Affiliation(s)
- Tingting Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China
| | - Yuetong Ji
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China
| | - Yun Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China
| | - Jing Jia
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China
| | - Jing Li
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China
| | - Shi Huang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China
| | - Danxiang Han
- Laboratory for Algae Research and Biotechnology, College of Technology and Innovation, Arizona State University, 7417 E. Unity Avenue, Mesa, Arizona 85212, USA
| | - Qiang Hu
- Laboratory for Algae Research and Biotechnology, College of Technology and Innovation, Arizona State University, 7417 E. Unity Avenue, Mesa, Arizona 85212, USA
| | - Wei E Huang
- Kroto Research Institute, University of Sheffield, Broad Lane, Sheffield, South Yorkshire S3 7HQ, United Kingdom
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, 189 Songling Road, Qingdao, Shandong 266101, China
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110
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Sharma B, Narzary D, Jha DK. Culture Independent Diversity Analysis of Soil Microbial Community and their Significance. SUSTAINABLE DEVELOPMENT AND BIODIVERSITY 2014. [DOI: 10.1007/978-3-319-05936-5_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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111
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112
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Phenotypic profiling of antibiotic response signatures in Escherichia coli using Raman spectroscopy. Antimicrob Agents Chemother 2013; 58:1302-14. [PMID: 24295982 DOI: 10.1128/aac.02098-13] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Identifying the mechanism of action of new potential antibiotics is a necessary but time-consuming and costly process. Phenotypic profiling has been utilized effectively to facilitate the discovery of the mechanism of action and molecular targets of uncharacterized drugs. In this research, Raman spectroscopy was used to profile the phenotypic response of Escherichia coli to applied antibiotics. The use of Raman spectroscopy is advantageous because it is noninvasive, label free, and prone to automation, and its results can be obtained in real time. In this research, E. coli cultures were subjected to three times the MICs of 15 different antibiotics (representing five functional antibiotic classes) with known mechanisms of action for 30 min before being analyzed by Raman spectroscopy (using a 532-nm excitation wavelength). The resulting Raman spectra contained sufficient biochemical information to distinguish between profiles induced by individual antibiotics belonging to the same class. The collected spectral data were used to build a discriminant analysis model that identified the effects of unknown antibiotic compounds on the phenotype of E. coli cultures. Chemometric analysis showed the ability of Raman spectroscopy to predict the functional class of an unknown antibiotic and to identify individual antibiotics that elicit similar phenotypic responses. Results of this research demonstrate the power of Raman spectroscopy as a cellular phenotypic profiling methodology and its potential impact on antibiotic drug development research.
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113
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Uysal RS, Soykut EA, Boyaci IH, Topcu A. Monitoring multiple components in vinegar fermentation using Raman spectroscopy. Food Chem 2013; 141:4333-43. [DOI: 10.1016/j.foodchem.2013.06.122] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 06/04/2013] [Accepted: 06/26/2013] [Indexed: 11/26/2022]
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114
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Vos M, Wolf AB, Jennings SJ, Kowalchuk GA. Micro-scale determinants of bacterial diversity in soil. FEMS Microbiol Rev 2013; 37:936-54. [DOI: 10.1111/1574-6976.12023] [Citation(s) in RCA: 338] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 03/08/2013] [Accepted: 03/15/2013] [Indexed: 11/29/2022] Open
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115
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Wang Y, Ji Y, Wharfe ES, Meadows RS, March P, Goodacre R, Xu J, Huang WE. Raman Activated Cell Ejection for Isolation of Single Cells. Anal Chem 2013; 85:10697-701. [DOI: 10.1021/ac403107p] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yun Wang
- Single-cell
Center, CAS Key Laboratory of Biofuels, and Shandong Key Laboratory
of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess
Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, P. R. China
| | - Yuetong Ji
- Single-cell
Center, CAS Key Laboratory of Biofuels, and Shandong Key Laboratory
of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess
Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, P. R. China
| | - Emma S. Wharfe
- Kroto
Research Institute, The University of Sheffield, Broad Lane, Sheffield, South Yorkshire, S3 7HQ, United Kingdom
| | - Roger S. Meadows
- Faculty
of Life Sciences, The University of Manchester, The Michael Smith Building, Oxford
Road, Manchester, M13 9PT, United Kingdom
| | - Peter March
- Faculty
of Life Sciences, The University of Manchester, The Michael Smith Building, Oxford
Road, Manchester, M13 9PT, United Kingdom
| | - Royston Goodacre
- School
of Chemistry, Manchester Institute of Biotechnology, University of Manchester, 131 Princess Street, Manchester, M1 7DN, United Kingdom
| | - Jian Xu
- Single-cell
Center, CAS Key Laboratory of Biofuels, and Shandong Key Laboratory
of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess
Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, P. R. China
| | - Wei E. Huang
- Kroto
Research Institute, The University of Sheffield, Broad Lane, Sheffield, South Yorkshire, S3 7HQ, United Kingdom
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116
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Klepárník K, Foret F. Recent advances in the development of single cell analysis--a review. Anal Chim Acta 2013; 800:12-21. [PMID: 24120162 DOI: 10.1016/j.aca.2013.09.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2013] [Revised: 08/23/2013] [Accepted: 09/05/2013] [Indexed: 01/12/2023]
Abstract
Development of techniques for the analysis of the content of individual cells represents an important direction in modern bioanalytical chemistry. While the analysis of chromosomes, organelles, or location of selected proteins has been traditionally the domain of microscopic techniques, the advances in miniaturized analytical systems bring new possibilities for separations and detections of molecules inside the individual cells including smaller molecules such as hormones or metabolites. It should be stressed that the field of single cell analysis is very broad, covering advanced optical, electrochemical and mass spectrometry instrumentation, sensor technology and separation techniques. The number of papers published on single cell analysis has reached several hundred in recent years. Thus a complete literature coverage is beyond the limits of a journal article. The following text provides a critical overview of some of the latest developments with the main focus on mass spectrometry, microseparation methods, electrophoresis in capillaries and microfluidic devices and respective detection techniques for performing single cell analyses.
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Affiliation(s)
- Karel Klepárník
- Institute of Analytical Chemistry, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
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117
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Gérard E, Ménez B, Couradeau E, Moreira D, Benzerara K, Tavera R, López-García P. Specific carbonate-microbe interactions in the modern microbialites of Lake Alchichica (Mexico). ISME JOURNAL 2013; 7:1997-2009. [PMID: 23804151 DOI: 10.1038/ismej.2013.81] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2012] [Revised: 03/22/2013] [Accepted: 04/17/2013] [Indexed: 02/02/2023]
Abstract
The role of microorganisms in microbialite formation remains unresolved: do they induce mineral precipitation (microbes first) or do they colonize and/or entrap abiotic mineral precipitates (minerals first)? Does this role vary from one species to another? And what is the impact of mineral precipitation on microbial ecology? To explore potential biogenic carbonate precipitation, we studied cyanobacteria-carbonate assemblages in modern hydromagnesite-dominated microbialites from the alkaline Lake Alchichica (Mexico), by coupling three-dimensional imaging of molecular fluorescence emitted by microorganisms, using confocal laser scanning microscopy, and Raman scattering/spectrometry from the associated minerals at a microscale level. Both hydromagnesite and aragonite precipitate within a complex biofilm composed of photosynthetic and other microorganisms. Morphology and pigment-content analysis of dominant photosynthetic microorganisms revealed up to six different cyanobacterial morphotypes belonging to Oscillatoriales, Chroococcales, Nostocales and Pleurocapsales, as well as several diatoms and other eukaryotic microalgae. Interestingly, one of these morphotypes, Pleurocapsa-like, appeared specifically associated with aragonite minerals, the oldest parts of actively growing Pleurocapsa-like colonies being always aragonite-encrusted. We hypothesize that actively growing cells of Pleurocapsales modify local environmental conditions favoring aragonite precipitation at the expense of hydromagnesite, which precipitates at seemingly random locations within the biofilm. Therefore, at least part of the mineral precipitation in Alchichica microbialites is most likely biogenic and the type of biominerals formed depends on the nature of the phylogenetic lineage involved. This observation may provide clues to identify lineage-specific biosignatures in fossil stromatolites from modern to Precambrian times.
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Affiliation(s)
- Emmanuelle Gérard
- Géobiosphère Actuelle et Primitive, Institut de Physique du Globe de Paris, CNRS UMR 7154, Université Paris Diderot, Sorbonne Paris Cité, Paris, France
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118
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Li M, Huang WE, Gibson CM, Fowler PW, Jousset A. Stable Isotope Probing and Raman Spectroscopy for Monitoring Carbon Flow in a Food Chain and Revealing Metabolic Pathway. Anal Chem 2013; 85:1642-9. [DOI: 10.1021/ac302910x] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mengqiu Li
- Department of Civil and Structural
Engineering, Kroto Research Institute, North Campus, The University of Sheffield, Broad Lane, Sheffield
S3 7HQ, U.K
| | - Wei E. Huang
- Department of Civil and Structural
Engineering, Kroto Research Institute, North Campus, The University of Sheffield, Broad Lane, Sheffield
S3 7HQ, U.K
| | | | - Patrick W. Fowler
- Department
of Chemistry, The University of Sheffield, Sheffield S3 7HF, U.K
| | - Alexandre Jousset
- J.F. Blumenbach Institute of Zoology
and Anthropology, University of Göttingen, Berliner Str. 28, 37073 Göttingen, Germany
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119
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Infectious Diseases, Vibrational Spectroscopic Approaches to Rapid Diagnostics. Infect Dis (Lond) 2013. [DOI: 10.1007/978-1-4614-5719-0_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
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120
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Evidence for phenotypic plasticity among multihost Campylobacter jejuni and C. coli lineages, obtained using ribosomal multilocus sequence typing and Raman spectroscopy. Appl Environ Microbiol 2012. [PMID: 23204423 DOI: 10.1128/aem.02521-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Closely related bacterial isolates can display divergent phenotypes. This can limit the usefulness of phylogenetic studies for understanding bacterial ecology and evolution. Here, we compare phenotyping based on Raman spectrometric analysis of cellular composition to phylogenetic classification by ribosomal multilocus sequence typing (rMLST) in 108 isolates of the zoonotic pathogens Campylobacter jejuni and C. coli. Automatic relevance determination (ARD) was used to identify informative peaks in the Raman spectra that could be used to distinguish strains in taxonomic and host source groups (species, clade, clonal complex, and isolate source/host). Phenotypic characterization based on Raman spectra showed a degree of agreement with genotypic classification using rMLST, with segregation accuracy between species (83.95%), clade (in C. coli, 98.41%), and, to some extent, clonal complex (86.89% C. jejuni ST-21 and ST-45 complexes) being achieved. This confirmed the utility of Raman spectroscopy for lineage classification and the correlation between genotypic and phenotypic classification. In parallel analysis, relatively distantly related isolates (different clonal complexes) were assigned the correct host origin irrespective of the clonal origin (74.07 to 96.97% accuracy) based upon different Raman peaks. This suggests that the phenotypic characteristics, from which the phenotypic signal is derived, are not fixed by clonal descent but are influenced by the host environment and change as strains move between hosts.
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121
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Barnett MJ, Pearce DA, Cullen DC. Advances in the in-field detection of microorganisms in ice. ADVANCES IN APPLIED MICROBIOLOGY 2012; 81:133-67. [PMID: 22958529 DOI: 10.1016/b978-0-12-394382-8.00004-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The historic view of ice-bound ecosystems has been one of a predominantly lifeless environment, where microorganisms certainly exist but are assumed to be either completely inactive or in a state of long-term dormancy. However, this standpoint has been progressively overturned in the past 20years as studies have started to reveal the importance of microbial life in the functioning of these environments. Our present knowledge of the distribution, taxonomy, and metabolic activity of such microbial life has been derived primarily from laboratory-based analyses of collected field samples. To date, only a restricted range of life detection and characterization techniques have been applied in the field. Specific examples include direct observation and DNA-based techniques (microscopy, specific stains, and community profiling based on PCR amplification), the detection of biomarkers (such as adenosine triphosphate), and measurements of metabolism [through the uptake and incorporation of radiolabeled isotopes or chemical alteration of fluorescent substrates (umbelliferones are also useful here)]. On-going improvements in technology mean that smaller and more robust life detection and characterization systems are continually being designed, manufactured, and adapted for in-field use. Adapting technology designed for other applications is the main source of new methodology, and the range of techniques is currently increasing rapidly. Here we review the current use of technology and techniques to detect and characterize microbial life within icy environments and specifically its deployment to in-field situations. We discuss the necessary considerations, limitations, and adaptations, review emerging technologies, and highlight the future potential. Successful application of these new techniques to in-field studies will certainly generate new insights into the way ice bound ecosystems function.
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Affiliation(s)
- Megan J Barnett
- Cranfield Health, Vincent Building, Cranfield University, Cranfield, Bedfordshire MK43 0AL, UK
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122
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Li M, Ashok PC, Dholakia K, Huang WE. Raman-Activated Cell Counting for Profiling Carbon Dioxide Fixing Microorganisms. J Phys Chem A 2012; 116:6560-3. [DOI: 10.1021/jp212619n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mengqiu Li
- Kroto Research Institute, The University of Sheffield, Broad Lane, Sheffield
S3 7HQ, United Kingdom
| | - Praveen C. Ashok
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
| | - Kishan Dholakia
- SUPA, School of Physics & Astronomy, University of St Andrews, North Haugh, St Andrews KY16 9SS, United Kingdom
| | - Wei E. Huang
- Kroto Research Institute, The University of Sheffield, Broad Lane, Sheffield
S3 7HQ, United Kingdom
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123
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Fuchs TM, Eisenreich W, Heesemann J, Goebel W. Metabolic adaptation of human pathogenic and related nonpathogenic bacteria to extra- and intracellular habitats. FEMS Microbiol Rev 2012; 36:435-62. [DOI: 10.1111/j.1574-6976.2011.00301.x] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 07/21/2011] [Indexed: 01/02/2023] Open
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124
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Zhang L, Xu J, Mi L, Gong H, Jiang S, Yu Q. Multifunctional magnetic–plasmonic nanoparticles for fast concentration and sensitive detection of bacteria using SERS. Biosens Bioelectron 2012; 31:130-6. [DOI: 10.1016/j.bios.2011.10.006] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Revised: 10/03/2011] [Accepted: 10/04/2011] [Indexed: 11/24/2022]
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125
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Driskell JD, Tripp RA. Infectious Diseases, Vibrational Spectroscopic Approaches to Rapid Diagnostics. Infect Dis (Lond) 2012. [DOI: 10.1007/978-1-0716-2463-0_532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
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126
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Paret ML, Sharma SK, Alvarez AM. Characterization of biofumigated Ralstonia solanacearum cells using micro-Raman spectroscopy and electron microscopy. PHYTOPATHOLOGY 2012; 102:105-13. [PMID: 21899389 DOI: 10.1094/phyto-12-10-0330] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Essential oils of palmarosa, lemongrass, and eucalyptus have shown promise as biofumigants for control of the bacterial wilt disease of edible ginger (Zingiber officinale) caused by Ralstonia solanacearum race 4 in previous potting medium studies. Biochemical changes in R. solanacearum cells were evaluated with micro-Raman spectroscopy following treatment with essential oils at different concentrations (0.04, 0.07, and 0.14% [vol/vol] of culture medium) and changes in cell structure were observed using electron microscopy. All treatments except palmarosa oil at 0.04% caused significant reductions in levels of amino acids, purine and pyrimidine bases of nucleic acids, carbohydrates, and lipids, as indicated by significant reduction in Raman peak heights at 621, 1,003, and 1,031 inverse centimeters (cm(-1)) (phenylalanine); 643, 827, 852, 1,158, and 1,172 cm(-1) (tyrosine); 758 cm(-1) (tryptophan); 725, 782, 1,337, and 1,578 cm(-1) (adenine, cytosine plus uracil, adenine, and adenine plus guanine, respectively); 1,097 cm(-1) (carbohydrates); and 1,127, 1,450, and 2,932 cm(-1) (lipids) compared with untreated controls. Lemongrass oil treatments were the most effective in degrading cellular components. Scanning electron microscopy of palmarosa and lemongrass-oil-treated cells showed rupture of cell walls and cell debris but no degradation was noted for eucalyptus-oil-treated cells. Palmarosa- and lemongrass-oil-treated cells were positively stained with uranyl acetate when viewed by transmission electron microscopy whereas controls and eucalyptus-oil-treated cells were negatively stained, indicating that the cell membranes were intact. The viability of eucalyptus-oil-treated cells was confirmed by cell culture following treatment. Micro-Raman spectroscopy is a powerful tool which can be further employed to better understand effects of fumigants and other bactericides on bacterial cells.
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Affiliation(s)
- Mathews L Paret
- Department of Plant and Environmental Protection Services, University of Hawaii, Honolulu, HI, USA
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127
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Culture-independent methods for studying environmental microorganisms: methods, application, and perspective. Appl Microbiol Biotechnol 2011; 93:993-1003. [DOI: 10.1007/s00253-011-3800-7] [Citation(s) in RCA: 131] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 11/23/2011] [Accepted: 11/27/2011] [Indexed: 01/29/2023]
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128
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Rapid resonance Raman microspectroscopy to probe carbon dioxide fixation by single cells in microbial communities. ISME JOURNAL 2011; 6:875-85. [PMID: 22113377 DOI: 10.1038/ismej.2011.150] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Photosynthetic microorganisms play crucial roles in aquatic ecosystems and are the major primary producers in global marine ecosystems. The discovery of new bacteria and microalgae that play key roles in CO(2) fixation is hampered by the lack of methods to identify hitherto-unculturable microorganisms. To overcome this problem we studied single microbial cells using stable-isotope probing (SIP) together with resonance Raman (RR) microspectroscopy of carotenoids, the light-absorbing pigments present in most photosynthetic microorganisms. We show that fixation of (13)CO(2) into carotenoids produces a red shift in single-cell RR (SCRR) spectra and that this SCRR-SIP technique is sufficiently sensitive to detect as little as 10% of (13)C incorporation. Mass spectrometry (MS) analysis of labelled cellular proteins verifies that the red shift in carotenoid SCRR spectra acts as a reporter of the (13)C content of single cells. Millisecond Raman imaging of cells in mixed cultures and natural seawater samples was used to identify cells actively fixing CO(2), demonstrating that the SCRR-SIP is a noninvasive method for the rapid and quantitative detection of CO(2) fixation at the single cell level in a microbial community. The SCRR-SIP technique may provide a direct method for screening environmental samples, and could help to reveal the ecophysiology of hitherto-unculturable microorganisms, linking microbial species to their ecological function in the natural environment.
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129
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Ashton L, Lau K, Winder CL, Goodacre R. Raman spectroscopy: lighting up the future of microbial identification. Future Microbiol 2011; 6:991-7. [DOI: 10.2217/fmb.11.89] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Over the last decade Raman spectroscopy has become established as a physicochemical technique for the rapid identification of microbes. This powerful analytical method generates a spectroscopic fingerprint from the microbial sample, which provides quantitative and qualitative information that can be used to characterize, discriminate and identify microorganisms, in both bacteria slurry and at the single-cell level. Recent developments in Raman spectroscopy have dramatically increased in recent years due to the enhancement of the signal by techniques including tip-enhanced Raman spectroscopy and coherent anti-Stokes Raman spectroscopy and due to the availability of user-friendly instrumentation and software. The result of this has been reduced cost and rapid collection time, and it has allowed the nonspecialist access to this physical sciences approach for biological applications. In this article, we will briefly explain the technique of Raman spectroscopy and discuss enhancement techniques, including the recent application of tip-enhanced Raman spectroscopy to microbiology, as well as the move towards rapid microbial identification with Raman spectroscopy. Furthermore, recent studies have combined Raman spectroscopy with microfluidic devices, giving greater control of sample conditions, which will no doubt have an important impact in the future development of Raman spectroscopy for microbial identification.
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Affiliation(s)
| | - Katherine Lau
- Spectroscopy Products Division, Renishaw plc, Old Town, Wotton-Under-Edge, Gloucestershire, GL12 7DW, UK
| | - Catherine L Winder
- School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
| | - Royston Goodacre
- School of Chemistry, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
- Manchester Centre for Integrative Systems Biology, Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess Street, Manchester, M1 7DN, UK
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130
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Maturation of released spores is necessary for acquisition of full spore heat resistance during Bacillus subtilis sporulation. Appl Environ Microbiol 2011; 77:6746-54. [PMID: 21821751 DOI: 10.1128/aem.05031-11] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The first ∼10% of spores released from sporangia (early spores) during Bacillus subtilis sporulation were isolated, and their properties were compared to those of the total spores produced from the same culture. The early spores had significantly lower resistance to wet heat and hypochlorite than the total spores but identical resistance to dry heat and UV radiation. Early and total spores also had the same levels of core water, dipicolinic acid, and Ca and germinated similarly with several nutrient germinants. The wet heat resistance of the early spores could be increased to that of total spores if early spores were incubated in conditioned sporulation medium for ∼24 h at 37°C (maturation), and some hypochlorite resistance was also restored. The maturation of early spores took place in pH 8 buffer with Ca(2+) but was blocked by EDTA; maturation was also seen with early spores of strains lacking the CotE protein or the coat-associated transglutaminase, both of which are needed for normal coat structure. Nonetheless, it appears to be most likely that it is changes in coat structure that are responsible for the increased resistance to wet heat and hypochlorite upon early spore maturation.
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132
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Meisel S, Stöckel S, Elschner M, Rösch P, Popp J. Assessment of two isolation techniques for bacteria in milk towards their compatibility with Raman spectroscopy. Analyst 2011; 136:4997-5005. [DOI: 10.1039/c1an15761b] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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133
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Label-free screening assays: a strategy for finding better drug candidates. Future Med Chem 2010; 2:1703-16. [DOI: 10.4155/fmc.10.246] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The last 10 years have seen advances in automation and high-throughput biochemistry in the drug-discovery arena. However, these advances have not led to improvements in drug-discovery success. Drug programs must find new ways to identify superior compounds. Advances in label-free assay technologies may provide advantages needed for improved drug discovery. In this article, we will discuss high-throughput MS, a technology that allows screening with native substrates and with targets inaccessible to standard assay formats. We will then discuss cell-based label-free biosensors, focusing on the increased information content available when using these platforms. We will conclude with speculation on the future and ways to obtain relevant biological information early in development to ensure the best compounds are promoted to medicinal chemistry campaigns.
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134
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Yuen JM, Shah NC, Walsh JT, Glucksberg MR, Van Duyne RP. Transcutaneous glucose sensing by surface-enhanced spatially offset Raman spectroscopy in a rat model. Anal Chem 2010; 82:8382-5. [PMID: 20845919 PMCID: PMC3031996 DOI: 10.1021/ac101951j] [Citation(s) in RCA: 149] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This letter presents the first quantitative, in vivo, transcutaneous glucose measurements using surface enhanced Raman spectroscopy (SERS). Silver film over nanosphere (AgFON) surfaces were functionalized with a mixed self-assembled monolayer (SAM) and implanted subcutaneously in a Sprague-Dawley rat. The glucose concentration was monitored in the interstitial fluid. SER spectra were collected from the sensor chip through the skin using spatially offset Raman spectroscopy (SORS). The combination of SERS and SORS is a powerful new approach to the challenging problem of in vivo metabolite and drug sensing.
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Affiliation(s)
- Jonathan M. Yuen
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208
| | - Nilam C. Shah
- Chemistry Department, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208
| | - Joseph T. Walsh
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208
| | - Matthew R. Glucksberg
- Department of Biomedical Engineering, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208
| | - Richard P. Van Duyne
- Chemistry Department, Northwestern University, 2145 Sheridan Rd, Evanston, Illinois 60208
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135
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Lidstrom ME, Konopka MC. The role of physiological heterogeneity in microbial population behavior. Nat Chem Biol 2010; 6:705-12. [PMID: 20852608 DOI: 10.1038/nchembio.436] [Citation(s) in RCA: 207] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
As the ability to analyze individual cells in microbial populations expands, it is becoming apparent that isogenic microbial populations contain substantial cell-to-cell differences in physiological parameters such as growth rate, resistance to stress and regulatory circuit output. Subpopulations exist that are manyfold different in these parameters from the population average, and these differences arise by stochastic processes. Such differences can dramatically affect the response of cells to perturbations, especially stress, which in turn dictates overall population response. Defining the role of cell-to-cell heterogeneity in population behavior is important for understanding population-based research problems, including those involving infecting populations, normal flora and bacterial populations in water and soils. Emerging technological breakthroughs are poised to transform single-cell analysis and are critical for the next phase of insights into physiological heterogeneity in the near future. These include technologies for multiparameter analysis of live cells, with downstream processing and analysis.
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Affiliation(s)
- Mary E Lidstrom
- Department of Chemical Engineering, University of Washington, Seattle, Washington, USA.
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