1
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Vibrational spectroscopy for decoding cancer microbiota interactions: Current evidence and future perspective. Semin Cancer Biol 2022; 86:743-752. [PMID: 34273519 DOI: 10.1016/j.semcancer.2021.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 01/27/2023]
Abstract
The role of human microbiota in cancer initiation and progression is recognized in recent years. In order to investigate the interactions between cancer cells and microbes, a systematic analysis using various emerging techniques is required. Owing to the label-free, non-invasive and molecular fingerprinting characteristics, vibrational spectroscopy is uniquely suited to decode and understand the relationship and interactions between cancer and the microbiota at the molecular level. In this review, we first provide a quick overview of the fundamentals of vibrational spectroscopic techniques, namely Raman and infrared spectroscopy. Next, we discuss the emerging evidence underscoring utilities of these spectroscopic techniques to study cancer or microbes separately, and share our perspective on how vibrational spectroscopy can be employed at the intersection of the two fields. Finally, we envision the potential opportunities in exploiting vibrational spectroscopy not only in basic cancer-microbiome research but also in its clinical translation, and discuss the challenges in the bench to bedside translation.
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2
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Wang Y, Xu J, Kong L, Liu T, Yi L, Wang H, Huang WE, Zheng C. Raman-deuterium isotope probing to study metabolic activities of single bacterial cells in human intestinal microbiota. Microb Biotechnol 2019; 13:572-583. [PMID: 31821744 PMCID: PMC7017835 DOI: 10.1111/1751-7915.13519] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/15/2019] [Indexed: 12/22/2022] Open
Abstract
Human intestinal microbiota is important to host health and is associated with various diseases. It is a challenge to identify the functions and metabolic activity of microorganisms at the single-cell level in gut microbial community. In this study, we applied Raman microspectroscopy and deuterium isotope probing (Raman-DIP) to quantitatively measure the metabolic activities of intestinal bacteria from two individuals and analysed lipids and phenylalanine metabolic pathways of functional microorganisms in situ. After anaerobically incubating the human faeces with heavy water (D2 O), D2 O with specific substrates (glucose, tyrosine, tryptophan and oleic acid) and deuterated glucose, the C-D band in single-cell Raman spectra appeared in some bacteria in faeces, due to the Raman shift from the C-H band. Such Raman shift was used to indicate the general metabolic activity and the activities in response to the specific substrates. In the two individuals' intestinal microbiota, the structures of the microbial communities were different and the general metabolic activities were 76 ± 1.0% and 30 ± 2.0%. We found that glucose, but not tyrosine, tryptophan and oleic acid, significantly stimulated metabolic activity of the intestinal bacteria. We also demonstrated that the bacteria within microbiota preferably used glucose to synthesize fatty acids in faeces environment, whilst they used glucose to synthesize phenylalanine in laboratory growth environment (e.g. LB medium). Our work provides a useful approach for investigating the metabolic activity in situ and revealing different pathways of human intestinal microbiota at the single-cell level.
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Affiliation(s)
- Yi Wang
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China.,Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.,Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Jiabao Xu
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Lingchao Kong
- School of Environment, Harbin Institute of Technology, Harbin, 150090, China
| | - Tang Liu
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lingbo Yi
- Health Time Gene Institute, Shenzhen, 518000, China
| | | | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
| | - Chunmiao Zheng
- Guangdong Provincial Key Laboratory of Soil and Groundwater Pollution Control, School of Environmental Science and Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
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3
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Alunni Cardinali M, Casagrande Pierantoni D, Caponi S, Corte L, Fioretto D, Cardinali G. Meso-Raman approach for rapid yeast cells identification. Biophys Chem 2019; 254:106249. [DOI: 10.1016/j.bpc.2019.106249] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 08/13/2019] [Accepted: 08/13/2019] [Indexed: 01/28/2023]
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4
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Xu J, Potter M, Tomas C, Elson JL, Morten KJ, Poulton J, Wang N, Jin H, Hou Z, Huang WE. A new approach to find biomarkers in chronic fatigue syndrome/myalgic encephalomyelitis (CFS/ME) by single-cell Raman micro-spectroscopy. Analyst 2019; 144:913-920. [DOI: 10.1039/c8an01437j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Single-cell Raman microspectroscopy to detect phenylalanine as a potential biomarker for mitochondrial dysfunction and chronic fatigue syndrome.
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5
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Noirot-Gros MF, Shinde S, Larsen PE, Zerbs S, Korajczyk PJ, Kemner KM, Noirot PH. Dynamics of Aspen Roots Colonization by Pseudomonads Reveals Strain-Specific and Mycorrhizal-Specific Patterns of Biofilm Formation. Front Microbiol 2018; 9:853. [PMID: 29774013 PMCID: PMC5943511 DOI: 10.3389/fmicb.2018.00853] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Accepted: 04/13/2018] [Indexed: 12/20/2022] Open
Abstract
Rhizosphere-associated Pseudomonas fluorescens are known plant growth promoting (PGP) and mycorrhizal helper bacteria (MHB) of many plants and ectomycorrhizal fungi. We investigated the spatial and temporal dynamics of colonization of mycorrhizal and non-mycorrhizal Aspen seedlings roots by the P. fluorescens strains SBW25, WH6, Pf0-1, and the P. protegens strain Pf-5. Seedlings were grown in laboratory vertical plates systems, inoculated with a fluorescently labeled Pseudomonas strain, and root colonization was monitored over a period of 5 weeks. We observed unexpected diversity of bacterial assemblies on seedling roots that changed over time and were strongly affected by root mycorrhization. P. fluorescens SBW25 and WH6 stains developed highly structured biofilms with internal void spaces forming channels. On mycorrhizal roots bacteria appeared encased in a mucilaginous substance in which they aligned side by side in parallel arrangements. The different phenotypic classes of bacterial assemblies observed for the four Pseudomonas strains were summarized in a single model describing transitions between phenotypic classes. Our findings also reveal that bacterial assembly phenotypes are driven by interactions with mucilaginous materials present at roots.
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Affiliation(s)
| | - Shalaka Shinde
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Peter E Larsen
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Sarah Zerbs
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Peter J Korajczyk
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Kenneth M Kemner
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
| | - Philippe H Noirot
- Biosciences Division, Argonne National Laboratory, Lemont, IL, United States
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6
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Koza A, Kusmierska A, McLaughlin K, Moshynets O, Spiers AJ. Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation. FEMS Microbiol Lett 2018; 364:3850210. [PMID: 28535292 DOI: 10.1093/femsle/fnx109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022] Open
Abstract
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function.
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Affiliation(s)
- Anna Koza
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kusmierska
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Kimberley McLaughlin
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Olena Moshynets
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kiev 03143, Ukraine
| | - Andrew J Spiers
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
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7
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Abstract
Biofilms are a communal way of living for microorganisms in which microorganism cells are surrounded by extracellular polymeric substances (EPS). Most microorganisms can live in biofilm form. Since microorganisms are everywhere, understanding biofilm structure and composition is crucial for making the world a better place to live, not only for humans but also for other living creatures. Raman spectroscopy is a nondestructive technique and provides fingerprint information about an analyte of interest. Surface-enhanced Raman spectroscopy is a form of this technique and provides enhanced scattering of the analyte that is in close vicinity of a nanostructured noble metal surface such as silver or gold. In this review, the applications of both techniques and their combination with other biofilm analysis techniques for characterization of composition and structure of biofilms are discussed.
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8
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Song Y, Cui L, López JÁS, Xu J, Zhu YG, Thompson IP, Huang WE. Raman-Deuterium Isotope Probing for in-situ identification of antimicrobial resistant bacteria in Thames River. Sci Rep 2017; 7:16648. [PMID: 29192181 PMCID: PMC5709456 DOI: 10.1038/s41598-017-16898-x] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 11/10/2017] [Indexed: 11/09/2022] Open
Abstract
The emergence and widespread distribution of antimicrobial resistant (AMR) bacteria has led to an increasing concern with respect to potential environmental and public health risks. Culture-independent and rapid identification of AMR bacteria in-situ in complex environments is important in understanding the role of viable but non-culturable and antibiotic persistent bacteria and in revealing potential pathogens without waiting for colony formation. In this study, a culture-independent and non-destructive phenotyping approach, so called Raman Deuterium Stable Isotope Probing (Raman-DIP), was developed to identify AMR bacteria in the River Thames. It is demonstrated that Raman-DIP was able to accurately identify resistant and susceptible bacteria within 24 hours. The work shows that, in the River Thames, the majority of the bacteria (76 ± 2%) were metabolically active, whilst AMR bacteria to carbenicillin, kanamycin and both two antibiotics were 35 ± 5%, 28 ± 3%, 25 ± 1% of the total bacterial population respectively. Raman activated cell ejection (RACE) was applied to isolate single AMR bacteria for the first time, linking AMR phenotype (reistance to antibiotics) and genotype (DNA sequence). The sequences of the RACE sorted cells indicate that they were potential human pathogens Aeromonas sp., Stenotrophomonas sp. and an unculturable bacterium. This work demonstrates Raman-DIP and RACE are effective culture-independent approach for rapid identification of AMR bacteria at the single cell level in their natural conditions.
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Affiliation(s)
- Yizhi Song
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ, Oxford, United Kingdom
| | - Li Cui
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ, Oxford, United Kingdom
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - José Ángel Siles López
- Chemical Engineering Department, University of Córdoba, Campus Universitario de Rabanales, Ctra. N-IV, km 396, building Marie Curie (C-3), CP/14071, Córdoba, Spain
| | - Jiabao Xu
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ, Oxford, United Kingdom
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Ian P Thompson
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ, Oxford, United Kingdom
| | - Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, OX1 3PJ, Oxford, United Kingdom.
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9
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Raman microspectroscopy, surface-enhanced Raman scattering microspectroscopy, and stable-isotope Raman microspectroscopy for biofilm characterization. Anal Bioanal Chem 2017; 409:4353-4375. [DOI: 10.1007/s00216-017-0303-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 01/31/2017] [Accepted: 03/08/2017] [Indexed: 12/27/2022]
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10
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New Insights into the Effects of Several Environmental Parameters on the Relative Fitness of a Numerically Dominant Class of Evolved Niche Specialist. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2016; 2016:4846565. [PMID: 28101396 PMCID: PMC5214101 DOI: 10.1155/2016/4846565] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2016] [Accepted: 11/24/2016] [Indexed: 11/17/2022]
Abstract
Adaptive radiation in bacteria has been investigated using Wrinkly Spreaders (WS), a morphotype which colonises the air-liquid (A-L) interface of static microcosms by biofilm formation with a significant fitness advantage over competitors growing lower down in the O2-limited liquid column. Here, we investigate several environmental parameters which impact the ecological opportunity that the Wrinkly Spreaders exploit in this model system. Manipulation of surface area/volume ratios suggests that the size of the WS niche was not as important as the ability to dominate the A-L interface and restrict competitor growth. The value of this niche to the Wrinkly Spreaders, as determined by competitive fitness assays, was found to increase as O2 flux to the A-L interface was reduced, confirming that competition for O2 was the main driver of WS fitness. The effect of O2 on fitness was also found to be dependent on the availability of nutrients, reflecting the need to take up both for optimal growth. Finally, the meniscus trap, a high-O2 region formed by the interaction of the A-L interface with the vial walls, was also important for fitness during the early stages of biofilm formation. These findings reveal the complexity of this seemingly simple model system and illustrate how changes in environmental physicality alter ecological opportunity and the fitness of the adaptive morphotype.
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11
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Huang WE, Song Y, Xu J. Single cell biotechnology to shed a light on biological 'dark matter' in nature. Microb Biotechnol 2015; 8:15-6. [PMID: 25627841 PMCID: PMC4321360 DOI: 10.1111/1751-7915.12249] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 11/04/2014] [Indexed: 11/30/2022] Open
Affiliation(s)
- Wei E Huang
- Department of Engineering Science, University of Oxford, Parks Road, Oxford, OX1 3PJ, UK
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12
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Udall YC, Deeni Y, Hapca SM, Raikes D, Spiers AJ. The evolution of biofilm-forming Wrinkly Spreaders in static microcosms and drip-fed columns selects for subtle differences in wrinkleality and fitness. FEMS Microbiol Ecol 2015; 91:fiv057. [DOI: 10.1093/femsec/fiv057] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/20/2015] [Indexed: 12/30/2022] Open
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13
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Fahs A, Quilès F, Jamal D, Humbert F, Francius G. In Situ Analysis of Bacterial Extracellular Polymeric Substances from a Pseudomonas fluorescens Biofilm by Combined Vibrational and Single Molecule Force Spectroscopies. J Phys Chem B 2014; 118:6702-13. [DOI: 10.1021/jp5030872] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ahmad Fahs
- Université de Lorraine, Laboratoire de Chimie Physique
et Microbiologie pour l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour
l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
| | - Fabienne Quilès
- Université de Lorraine, Laboratoire de Chimie Physique
et Microbiologie pour l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour
l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
| | - Dima Jamal
- Université de Lorraine, Laboratoire de Chimie Physique
et Microbiologie pour l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour
l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
| | - François Humbert
- Université de Lorraine, Laboratoire de Chimie Physique
et Microbiologie pour l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour
l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
| | - Grégory Francius
- Université de Lorraine, Laboratoire de Chimie Physique
et Microbiologie pour l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
- CNRS, Laboratoire de Chimie Physique et Microbiologie pour
l’Environnement, UMR 7564, Villers-lès-Nancy, F-54600, France
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14
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Nikel PI, Silva-Rocha R, Benedetti I, de Lorenzo V. The private life of environmental bacteria: pollutant biodegradation at the single cell level. Environ Microbiol 2014; 16:628-42. [DOI: 10.1111/1462-2920.12360] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 11/23/2013] [Accepted: 12/10/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Pablo Iván Nikel
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Madrid 28049 Spain
| | - Rafael Silva-Rocha
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Madrid 28049 Spain
| | - Ilaria Benedetti
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Madrid 28049 Spain
| | - Víctor de Lorenzo
- Systems and Synthetic Biology Program; Centro Nacional de Biotecnología (CNB-CSIC); Madrid 28049 Spain
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15
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A mechanistic explanation linking adaptive mutation, niche change, and fitness advantage for the wrinkly spreader. INTERNATIONAL JOURNAL OF EVOLUTIONARY BIOLOGY 2014; 2014:675432. [PMID: 24551477 PMCID: PMC3914426 DOI: 10.1155/2014/675432] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 11/08/2013] [Indexed: 11/17/2022]
Abstract
Experimental evolution studies have investigated adaptive radiation in static liquid microcosms using the environmental bacterium Pseudomonas fluorescens SBW25. In evolving populations a novel adaptive mutant known as the Wrinkly Spreader arises within days having significant fitness advantage over the ancestral strain. A molecular investigation of the Wrinkly Spreader has provided a mechanistic explanation linking mutation with fitness improvement through the production of a cellulose-based biofilm at the air-liquid interface. Colonisation of this niche provides greater access to oxygen, allowing faster growth than that possible for non-biofilm-forming competitors located in the lower anoxic region of the microcosm. Cellulose is probably normally used for attachment to plant and soil aggregate surfaces and to provide protection in dehydrating conditions. However, the evolutionary innovation of the Wrinkly Spreader in static microcosms is the use of cellulose as the matrix of a robust biofilm, and is achieved through mutations that deregulate multiple diguanylate cyclases leading to the over-production of cyclic-di-GMP and the stimulation of cellulose expression. The mechanistic explanation of the Wrinkly Spreader success is an exemplar of the modern evolutionary synthesis, linking molecular biology with evolutionary ecology, and provides an insight into the phenomenal ability of bacteria to adapt to novel environments.
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16
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Chien CC, Lin BC, Wu CH. Biofilm formation and heavy metal resistance by an environmental Pseudomonas sp. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.01.014] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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17
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Advanced Microscopy of Microbial Cells. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2010; 124:21-54. [DOI: 10.1007/10_2010_83] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/26/2023]
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18
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Andrews JS, Rolfe SA, Huang WE, Scholes JD, Banwart SA. Biofilm formation in environmental bacteria is influenced by different macromolecules depending on genus and species. Environ Microbiol 2010; 12:2496-507. [PMID: 20406292 DOI: 10.1111/j.1462-2920.2010.02223.x] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The formation of biofilms by diverse bacteria isolated from contaminated soil and groundwater on model substrata with different surface properties was assessed in a multifactorial screen. Diverse attachment phenotypes were observed as measured by crystal violet dye retention and confocal laser scanning microscopy (CLSM). Bulk measurements of cell hydrophobicity had little predictive ability in determining whether biofilms would develop on hydrophobic or hydrophilic substrata. Therefore selected pairs of bacteria from the genera Rhodococcus, Pseudomonas and Sphingomonas that exhibited different attachment phenotypes were examined in more detail using CLSM and the lipophilic dye, Nile Red. The association of Rhodococcus sp. cell membranes with lipids was shown to influence the attachment properties of these cells, but this approach was not informative for Pseudomonas and Sphingomonas sp. Confocal Raman Microspectroscopy of Rhodococcus biofilms confirmed the importance of lipids in their formation and indicated that in Pseudomonas and Sphingomonas biofilms, nucleic acids and proteins, respectively, were important in identifying the differences in attachment phenotypes of the selected strains. Treatment of biofilms with DNase I confirmed a determining role for nucleic acids as predicted for Pseudomonas. This work demonstrates that the attachment phenotypes of microbes from environmental samples to different substrata varies markedly, a diverse range of macromolecules may be involved and that these differ significantly between genera. A combination of CLSM and Raman spectroscopy distinguished between phenotypes and could be used to identify the key macromolecules involved in cell attachment to surfaces for the specific cases studied.
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Affiliation(s)
- Johanna S Andrews
- The Cell-Mineral Research Centre, Kroto Research Institute, University of Sheffield, Broad Lane, Sheffield S3 7HQ, UK
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19
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Huang WE, Li M, Jarvis RM, Goodacre R, Banwart SA. Shining light on the microbial world the application of Raman microspectroscopy. ADVANCES IN APPLIED MICROBIOLOGY 2010; 70:153-86. [PMID: 20359457 DOI: 10.1016/s0065-2164(10)70005-8] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Raman microspectroscopy is a noninvasive, label-free, and single-cell technology for biochemical analysis of individual mammalian cells, organelles, bacteria, viruses, and nanoparticles. Chemical information derived from a Raman spectrum provides comprehensive and intrinsic information (e.g., nucleic acids, protein, carbohydrates, and lipids) of single cells without the need of any external labeling. A Raman spectrum functions as a molecular "fingerprint" of single cells, which enables the differentiation of cell types, physiological states, nutrient condition, and variable phenotypes. Raman microspectroscopy combined with stable isotope probing, fluorescent in situ hybridization, and optical tweezers offers a culture-independent approach to study the functions and physiology of unculturable microorganisms in the ecosystem. Here, we review the application of Raman microspectroscopy to microbiology research with particular emphasis on single bacterial cells.
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Affiliation(s)
- Wei E Huang
- Department of Civil and Structural Engineering, Kroto Research Institute, University of Sheffield, Sheffield, United Kingdom.
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20
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Harz M, Rösch P, Popp J. Vibrational spectroscopy--a powerful tool for the rapid identification of microbial cells at the single-cell level. Cytometry A 2009; 75:104-13. [PMID: 19156822 DOI: 10.1002/cyto.a.20682] [Citation(s) in RCA: 161] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Rapid microbial detection and identification with a high grade of sensitivity and selectivity is a great and challenging issue in many fields, primarily in clinical diagnosis, pharmaceutical, or food processing technology. The tedious and time-consuming processes of current microbiological approaches call for faster ideally on-line identification techniques. The vibrational spectroscopic techniques IR absorption and Raman spectroscopy are noninvasive methods yielding molecular fingerprint information; thus, allowing for a fast and reliable analysis of complex biological systems such as bacterial or yeast cells. In this short review, we discuss recent vibrational spectroscopic advances in microbial identification of yeast and bacterial cells for bulk environment and single-cell analysis. IR absorption spectroscopy enables a bulk analysis whereas micro-Raman-spectroscopy with excitation in the near infrared or visible range has the potential for the analysis of single bacterial and yeast cells. The inherently weak Raman signal can be increased up to several orders of magnitude by applying Raman signal enhancement methods such as UV-resonance Raman spectroscopy with excitation in the deep UV region, surface enhanced Raman scattering, or tip-enhanced Raman scattering.
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Affiliation(s)
- M Harz
- Institute of Physical Chemistry, Friedrich-Schiller-Universität Jena, Helmholtzweg 4, Jena 07743, Germany
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21
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Huang WE, Ward AD, Whiteley AS. Raman tweezers sorting of single microbial cells. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:44-9. [PMID: 23765719 DOI: 10.1111/j.1758-2229.2008.00002.x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
We have selectively isolated microbial cells by identifying and then manipulating cells using a combination of Raman microspectroscopy and optical trapping. The criterion for cell discrimination is based on spectral peak shifts within the Raman spectrum of individual cells. A specific shift in the phenylalanine peak position from 1001 rel. cm(-1) to 965 rel. cm(-1) is utilized to indicate the uptake of (13) C within the cell that utilized (13) C-substrate. Cells were captured and manipulated using an infrared (1064 nm) laser while Raman spectra were acquired over shorter timescales (30 s) using a co-aligned 514.5 nm laser beam. Selected cells were manoeuvred to a clean part of a capillary tube and the tubes were cleaved to physically separate the cells. The technique was tested for cell viability and cross-contamination effects using 70 single yeast cells (Saccharomyces cerevisia). Following these tests, 58 single bacterial cells (Escherichia coli DH5α, and Pseudomonas fluorescens SBW25::Km-RFP) that exhibited (13) C uptake were sorted from bacterial populations. Among those isolated cells, 11 out of 18 yeast cells and 7 out of 18 single SBW25::Km-RFP cells were recovered by incubation; 2 out of 7 sorted yeast cells and 3 out of 8 sorted bacterial cells (single SBW25::Km-RFP) were genome amplified correctly. We show that the Raman tweezers approach has the potential to open a new frontier to study unculturable microorganisms, which account for more than 99% microbes in natural environment.
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Affiliation(s)
- Wei E Huang
- Molecular Microbial Ecology, CEH-Oxford, Mansfield Road, Oxford OX1 3SR, UK. Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Science and Innovation Campus, Didcot OX11 0QX, UK
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