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Ge X, Pereira FC, Mitteregger M, Berry D, Zhang M, Hausmann B, Zhang J, Schintlmeister A, Wagner M, Cheng JX. SRS-FISH: A high-throughput platform linking microbiome metabolism to identity at the single-cell level. Proc Natl Acad Sci U S A 2022; 119:e2203519119. [PMID: 35727976 PMCID: PMC9245642 DOI: 10.1073/pnas.2203519119] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022] Open
Abstract
One of the biggest challenges in microbiome research in environmental and medical samples is to better understand functional properties of microbial community members at a single-cell level. Single-cell isotope probing has become a key tool for this purpose, but the current detection methods for determination of isotope incorporation into single cells do not allow high-throughput analyses. Here, we report on the development of an imaging-based approach termed stimulated Raman scattering-two-photon fluorescence in situ hybridization (SRS-FISH) for high-throughput metabolism and identity analyses of microbial communities with single-cell resolution. SRS-FISH offers an imaging speed of 10 to 100 ms per cell, which is two to three orders of magnitude faster than achievable by state-of-the-art methods. Using this technique, we delineated metabolic responses of 30,000 individual cells to various mucosal sugars in the human gut microbiome via incorporation of deuterium from heavy water as an activity marker. Application of SRS-FISH to investigate the utilization of host-derived nutrients by two major human gut microbiome taxa revealed that response to mucosal sugars tends to be dominated by Bacteroidales, with an unexpected finding that Clostridia can outperform Bacteroidales at foraging fucose. With high sensitivity and speed, SRS-FISH will enable researchers to probe the fine-scale temporal, spatial, and individual activity patterns of microbial cells in complex communities with unprecedented detail.
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Affiliation(s)
- Xiaowei Ge
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Fátima C. Pereira
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Matthias Mitteregger
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - David Berry
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Meng Zhang
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
| | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, 1030 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Jing Zhang
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
| | - Arno Schintlmeister
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
| | - Michael Wagner
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, 1030 Vienna, Austria
- Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark
| | - Ji-Xin Cheng
- Department of Electrical & Computer Engineering, Boston University, Boston, MA 02215
- Department of Biomedical Engineering, Photonics Center, Boston University, Boston, MA 02215
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2
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Liu Y, Ziatdinov M, Kalinin SV. Exploring Causal Physical Mechanisms via Non-Gaussian Linear Models and Deep Kernel Learning: Applications for Ferroelectric Domain Structures. ACS Nano 2022; 16:1250-1259. [PMID: 34964598 DOI: 10.1021/acsnano.1c09059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Rapid emergence of multimodal imaging in scanning probe, electron, and optical microscopies has brought forth the challenge of understanding the information contained in these complex data sets, targeting the intrinsic correlations between different channels, and further exploring the underpinning causal physical mechanisms. Here, we develop such an analysis framework for Piezoresponse Force Microscopy. We argue that under certain conditions, we can bootstrap experimental observations with the prior knowledge of materials structure to get information on certain nonobserved properties, and demonstrate linear causal analysis for PFM observables. We further demonstrate that the strength of individual causal links between complex descriptors can be ascertained using the deep kernel learning (DKL) model. In this DKL analysis, we use the prior information on domain structure within the image to predict the physical properties. This analysis demonstrates the correlative relationships between morphology, piezoresponse, elastic property, etc., at nanoscale. The prediction of morphology and other physical parameters illustrates a mutual interaction between surface condition and physical properties in ferroelectric materials. This analysis is universal and can be extended to explore the correlative relationships of other multichannel data sets, and allow for high-fidelity reconstruction of underpinning functionalities and physical mechanisms.
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Affiliation(s)
- Yongtao Liu
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Maxim Ziatdinov
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sergei V Kalinin
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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3
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Bower AJ, Mahmassani Z, Zhao Y, Chaney EJ, Marjanovic M, Lee MK, Graf BW, De Lisio M, Kong H, Boppart MD, Boppart SA. In Vivo Assessment of Engineered Skin Cell Delivery with Multimodal Optical Microscopy. Tissue Eng Part C Methods 2018; 23:434-442. [PMID: 28605991 DOI: 10.1089/ten.tec.2017.0185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The healing process is often significantly impaired under conditions of chronic or large area wounds, which are often treated clinically using autologous split-thickness skin grafts. However, in many cases, harvesting of donor tissue presents a serious problem such as in the case of very large area burns. In response to this, engineered biomaterials have emerged that attempt to mimic the natural skin environment or deliver a suitable therapy to assist in the healing process. In this study, a custom-built multimodal optical microscope capable of noninvasive structural and functional imaging is used to investigate both the engineered tissue microenvironment and the in vivo wound healing process. Investigation of various engineered scaffolds show the strong relationship among the microenvironment of the scaffold, the organization of the cells within the scaffold, and the delivery pattern of these cells onto the healing wound. Through noninvasive tracking of these processes and parameters, multimodal optical microscopy provides an important tool in the assessment of engineered scaffolds both in vitro and in vivo.
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Affiliation(s)
- Andrew J Bower
- 1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois.,2 Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Ziad Mahmassani
- 1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois.,3 Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Youbo Zhao
- 1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Eric J Chaney
- 1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Marina Marjanovic
- 1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois.,4 Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Min Kyung Lee
- 5 Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Benedikt W Graf
- 1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois.,2 Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Michael De Lisio
- 3 Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign , Urbana, Illinois.,6 School of Human Kinetics, Brain and Mind Research Institute and Centre for Neuromuscular Disease, University of Ottawa , Ottawa, Canada
| | - Hyunjoon Kong
- 5 Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Marni D Boppart
- 1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois.,3 Department of Kinesiology and Community Health, University of Illinois at Urbana-Champaign , Urbana, Illinois
| | - Stephen A Boppart
- 1 Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois.,2 Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign , Urbana, Illinois.,4 Department of Bioengineering, University of Illinois at Urbana-Champaign , Urbana, Illinois.,7 Department of Internal Medicine, University of Illinois at Urbana-Champaign , Urbana, Illinois
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Balu M, Saytashev I, Hou J, Dantus M, Tromberg BJ. Sub-40 fs, 1060-nm Yb-fiber laser enhances penetration depth in nonlinear optical microscopy of human skin. J Biomed Opt 2015; 20:120501. [PMID: 26641198 PMCID: PMC4671301 DOI: 10.1117/1.jbo.20.12.120501] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2015] [Accepted: 10/30/2015] [Indexed: 05/03/2023]
Abstract
Advancing the practical utility of nonlinear optical microscopy requires continued improvement in imaging depth and contrast. We evaluated second-harmonic generation (SHG) and third-harmonic generation images from ex vivo human skin and showed that a sub-40 fs, 1060-nm Yb-fiber laser can enhance SHG penetration depth by up to 80% compared to a >100 fs, 800 nm Ti:sapphire source. These results demonstrate the potential of fiber-based laser systems to address a key performance limitation related to nonlinear optical microscopy (NLOM) technology while providing a low-barrier-to-access alternative to Ti:sapphire sources that could help accelerate the movement of NLOM into clinical practice.
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Affiliation(s)
- Mihaela Balu
- University of California, Irvine, Beckman Laser Institute, Laser Microbeam and Medical Program, 1002 Health Sciences Road, Irvine, California 92612, United States
- Address all correspondence to: Mihaela Balu, E‐mail:
| | - Ilyas Saytashev
- Michigan State University, Department of Chemistry, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Jue Hou
- University of California, Irvine, Beckman Laser Institute, Laser Microbeam and Medical Program, 1002 Health Sciences Road, Irvine, California 92612, United States
| | - Marcos Dantus
- Michigan State University, Department of Chemistry, 578 South Shaw Lane, East Lansing, Michigan 48824, United States
| | - Bruce J. Tromberg
- University of California, Irvine, Beckman Laser Institute, Laser Microbeam and Medical Program, 1002 Health Sciences Road, Irvine, California 92612, United States
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5
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Piper T, Piper J. Variable multimodal light microscopy with interference contrast and phase contrast; dark or bright field. J Microsc 2014; 255:30-41. [PMID: 24832212 DOI: 10.1111/jmi.12134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Accepted: 04/09/2014] [Indexed: 11/28/2022]
Abstract
Using the optical methods described, specimens can be observed with modified multimodal light microscopes based on interference contrast combined with phase contrast, dark- or bright-field illumination. Thus, the particular visual information associated with interference and phase contrast, dark- and bright-field illumination is joined in real-time composite images appearing in enhanced clarity and purified from typical artefacts, which are apparent in standard phase contrast and dark-field illumination. In particular, haloing and shade-off are absent or significantly reduced as well as marginal blooming and scattering. The background brightness and thus the range of contrast can be continuously modulated and variable transitions can be achieved between interference contrast and complementary illumination techniques. The methods reported should be of general interest for all disciplines using phase and interference contrast microscopy, especially in biology and medicine, and also in material sciences when implemented in vertical illuminators.
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Affiliation(s)
- T Piper
- Department of Light Microscopy, Laboratory for Applied Microscopy Research, Marienburgstr. 23, Bullay, Rheinland-Pfalz, Germany
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6
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Graf BW, Boppart SA. Multimodal In Vivo Skin Imaging with Integrated Optical Coherence and Multiphoton Microscopy. IEEE J Sel Top Quantum Electron 2012; 18:1280-1286. [PMID: 25673966 PMCID: PMC4321748 DOI: 10.1109/jstqe.2011.2166377] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
In this paper, we demonstrate high-resolution, multimodal in vivo imaging of human skin using optical coherence (OCM) and multiphoton microscopy (MPM). These two modalities are integrated into a single instrument to enable simultaneous acquisition and coregistration. The system design and the OCM image processing architecture enable sufficient performance of both modalities for in vivo imaging of human skin. Examples of multimodal in vivo imaging are presented as well as time lapse imaging of blood flow in single capillary loops. By making use of multiple intrinsic contrast mechanisms this integrated technique improves the ability to noninvasively visualize living tissue. Integrated OCM and MPM has potential applications for in vivo diagnosis of various pathological skin conditions, such as skin cancer, as well as potential pharmaceutical and cosmetic research applications.
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Affiliation(s)
- Benedikt W. Graf
- Department of Electrical and Computer Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Stephen A. Boppart
- Departments of Electrical and Computer Engineering, Bioengineering, and Internal Medicine, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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7
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Smith ZJ, Wang JCE, Quataert SA, Berger AJ. Integrated Raman and angular scattering microscopy reveals chemical and morphological differences between activated and nonactivated CD8+ T lymphocytes. J Biomed Opt 2010; 15:036021. [PMID: 20615023 PMCID: PMC2903831 DOI: 10.1117/1.3443794] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2009] [Revised: 02/22/2010] [Accepted: 04/21/2010] [Indexed: 05/29/2023]
Abstract
Integrated Raman and angular-scattering microscopy (IRAM) is a multimodal platform capable of noninvasively probing both the chemistry and morphology of a single cell without prior labeling. Using this system, we are able to detect activation-dependent changes in the Raman and elastic-scattering signals from CD8+ T cells stimulated with either Staphylococcal enterotoxin B (SEB) or phorbol myristate acetate (PMA). In both cases, results obtained from the IRAM instrument correlate well with results obtained from traditional fluorescence-based flow cytometry for paired samples. SEB-mediated activation was distinguished from resting state in CD8+ T cells by an increase in the number and mean size of small ( approximately 500-nm) elastic scatterers as well as a decrease in Raman bands, indicating changes in nuclear content. PMA-mediated activation induced a different profile in CD8+ T cells from SEB, showing a similar increase in small elastic scatterers but a different Raman change, with elevation of cellular protein and lipid bands. These results suggest the potential of this multimodal, label-free optical technique for studying processes in single cells.
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Affiliation(s)
- Zachary J Smith
- University of Rochester, The Institute of Optics, 275 Hutchison Road, Rochester, New York 14627, USA
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