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Noecker C, Turnbaugh PJ. Emerging tools and best practices for studying gut microbial community metabolism. Nat Metab 2024:10.1038/s42255-024-01074-z. [PMID: 38961185 DOI: 10.1038/s42255-024-01074-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 05/30/2024] [Indexed: 07/05/2024]
Abstract
The human gut microbiome vastly extends the set of metabolic reactions catalysed by our own cells, with far-reaching consequences for host health and disease. However, our knowledge of gut microbial metabolism relies on a handful of model organisms, limiting our ability to interpret and predict the metabolism of complex microbial communities. In this Perspective, we discuss emerging tools for analysing and modelling the metabolism of gut microorganisms and for linking microorganisms, pathways and metabolites at the ecosystem level, highlighting promising best practices for researchers. Continued progress in this area will also require infrastructure development to facilitate cross-disciplinary synthesis of scientific findings. Collectively, these efforts can enable a broader and deeper understanding of the workings of the gut ecosystem and open new possibilities for microbiome manipulation and therapy.
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Affiliation(s)
- Cecilia Noecker
- Department of Biological Sciences, Minnesota State University, Mankato, Mankato, MN, USA
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Peter J Turnbaugh
- Department of Microbiology & Immunology, University of California, San Francisco, San Francisco, CA, USA.
- Chan Zuckerberg Biohub-San Francisco, San Francisco, CA, USA.
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2
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Gao Y, Wu J, Xia Q, Liu J, Zhu JJ, Zhang JR, Chen X, Zhu W, Chen Z. Operando Spectroscopic Elucidation of the Bubble Sunshade Effect in Inorganic-Biological Hybrids for Photosynthetic Hydrogen Production. ACS NANO 2024; 18:14546-14557. [PMID: 38776420 DOI: 10.1021/acsnano.4c02264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Hydrogen production by photosynthetic hybrid systems (PBSs) offers a promising avenue for renewable energy. However, the light-harvesting efficiency of PBSs remains constrained due to unclear intracellular kinetic factors. Here, we present an operando elucidation of the sluggish light-harvesting behavior for existing PBSs and strategies to circumvent them. By quantifying the spectral shift in the structural color scattering of individual PBSs during the photosynthetic process, we observe the accumulation of product hydrogen bubbles on their outer membrane. These bubbles act as a sunshade and inhibit light absorption. This phenomenon elucidates the intrinsic constraints on the light-harvesting efficiency of PBSs. The introduction of a tension eliminator into the PBSs effectively improves the bubble sunshade effect and results in a 4.5-fold increase in the light-harvesting efficiency. This work provides valuable insights into the dynamics of transmembrane transport gas products and holds the potential to inspire innovative designs for improving the light-harvesting efficiency of PBSs.
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Affiliation(s)
- Yan Gao
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jingyu Wu
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Qing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Juan Liu
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jun-Jie Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Jian-Rong Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Xueqin Chen
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Wenlei Zhu
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
| | - Zixuan Chen
- State Key Laboratory of Pollution Control and Resource Reuse, State Key Laboratory of Analytical Chemistry for Life Science, the Frontiers Science Center for Critical Earth Material Cycling, School of the Environment, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People's Republic of China
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3
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Kesharwani A, Gujrati V. Multimodal techniques and strategies for chemical and metabolic imaging at the single-cell level. Curr Opin Biotechnol 2024; 88:103149. [PMID: 38810301 DOI: 10.1016/j.copbio.2024.103149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 05/13/2024] [Accepted: 05/13/2024] [Indexed: 05/31/2024]
Abstract
Single-cell chemical and metabolic imaging technologies provide unprecedented insights into individual cell dynamics, advancing our understanding of cellular processes, molecular interactions, and metabolic activities. Advances in fluorescence, Raman, optoacoustic (photoacoustic), or mass spectrometry methods have paved the way to characterize metabolites, signaling molecules, and other moieties within individual cells. These modalities can also lead to single-cell imaging capabilities by targeting endogenous cell contrast or by employing exogenous contrast generation techniques, including contrast agents that target specific cell structure or function. In this review, we present key developments, summarize recent applications in single-cell interrogation and imaging, and illustrate their advantages, limitations, and outlook.
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Affiliation(s)
- Ajay Kesharwani
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine and Health, Technical University of Munich, Munich, Germany
| | - Vipul Gujrati
- Institute of Biological and Medical Imaging, Helmholtz Zentrum München, Neuherberg, Germany; Chair of Biological Imaging at the Central Institute for Translational Cancer Research (TranslaTUM), School of Medicine and Health, Technical University of Munich, Munich, Germany.
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4
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Abstract
Biogeography is the study of species distribution and diversity within an ecosystem and is at the core of how we understand ecosystem dynamics and interactions at the macroscale. In gut microbial communities, a historical reliance on bulk sequencing to probe community composition and dynamics has overlooked critical processes whereby microscale interactions affect systems-level microbiota function and the relationship with the host. In recent years, higher-resolution sequencing and novel single-cell level data have uncovered an incredible heterogeneity in microbial composition and have enabled a more nuanced spatial understanding of the gut microbiota. In an era when spatial transcriptomics and single-cell imaging and analysis have become key tools in mammalian cell and tissue biology, many of these techniques are now being applied to the microbiota. This fresh approach to intestinal biogeography has given important insights that span temporal and spatial scales, from the discovery of mucus encapsulation of the microbiota to the quantification of bacterial species throughout the gut. In this Review, we highlight emerging knowledge surrounding gut biogeography enabled by the observation and quantification of heterogeneity across multiple scales.
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Affiliation(s)
- Giselle McCallum
- Department of Biology, Concordia University, Montreal, Quebec, Canada
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Carolina Tropini
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada.
- School of Biomedical Engineering, University of British Columbia, Vancouver, British Columbia, Canada.
- Humans and the Microbiome Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada.
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5
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Bai Y, Camargo CM, Glasauer SMK, Gifford R, Tian X, Longhini AP, Kosik KS. Single-cell mapping of lipid metabolites using an infrared probe in human-derived model systems. Nat Commun 2024; 15:350. [PMID: 38191490 PMCID: PMC10774263 DOI: 10.1038/s41467-023-44675-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 12/20/2023] [Indexed: 01/10/2024] Open
Abstract
Understanding metabolic heterogeneity is the key to uncovering the underlying mechanisms of metabolic-related diseases. Current metabolic imaging studies suffer from limitations including low resolution and specificity, and the model systems utilized often lack human relevance. Here, we present a single-cell metabolic imaging platform to enable direct imaging of lipid metabolism with high specificity in various human-derived 2D and 3D culture systems. Through the incorporation of an azide-tagged infrared probe, selective detection of newly synthesized lipids in cells and tissue became possible, while simultaneous fluorescence imaging enabled cell-type identification in complex tissues. In proof-of-concept experiments, newly synthesized lipids were directly visualized in human-relevant model systems among different cell types, mutation status, differentiation stages, and over time. We identified upregulated lipid metabolism in progranulin-knockdown human induced pluripotent stem cells and in their differentiated microglia cells. Furthermore, we observed that neurons in brain organoids exhibited a significantly lower lipid metabolism compared to astrocytes.
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Affiliation(s)
- Yeran Bai
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
- Photothermal Spectroscopy Corp., Santa Barbara, CA, USA.
| | - Carolina M Camargo
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Stella M K Glasauer
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Raymond Gifford
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Xinran Tian
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Andrew P Longhini
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA
| | - Kenneth S Kosik
- Neuroscience Research Institute, Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, USA.
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6
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Lo HY, Wink K, Nitz H, Kästner M, Belder D, Müller JA, Kaster AK. scMAR-Seq: a novel workflow for targeted single-cell genomics of microorganisms using radioactive labeling. mSystems 2023; 8:e0099823. [PMID: 37982643 PMCID: PMC10734494 DOI: 10.1128/msystems.00998-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/09/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE A central question in microbial ecology is which member of a community performs a particular metabolism. Several sophisticated isotope labeling techniques are available for analyzing the metabolic function of populations and individual cells in a community. However, these methods are generally either insufficiently sensitive or throughput-limited and thus have limited applicability for the study of complex environmental samples. Here, we present a novel approach that combines highly sensitive radioisotope tracking, microfluidics, high-throughput sorting, and single-cell genomics to simultaneously detect and identify individual microbial cells based solely on their in situ metabolic activity, without prior information on community structure.
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Affiliation(s)
- Hao-Yu Lo
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Konstantin Wink
- Institute for Analytical Chemistry, Leipzig University, Leipzig, Germany
| | - Henrike Nitz
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Matthias Kästner
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Detlev Belder
- Institute for Analytical Chemistry, Leipzig University, Leipzig, Germany
| | - Jochen A. Müller
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Environmental Biotechnology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Anne-Kristin Kaster
- Institute for Biological Interfaces (IBG-5), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
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7
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Xu FX, Wu R, Hu K, Fu D. Measuring Drug Response with Single-Cell Growth Rate Quantification. Anal Chem 2023; 95:18114-18121. [PMID: 38016067 PMCID: PMC11016461 DOI: 10.1021/acs.analchem.3c03434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2023]
Abstract
Intratumoral heterogeneity is a substantial cause of drug resistance development during chemotherapy or other drug treatments for cancer. Therefore, monitoring and measuring cell exposure and response to drugs at the single-cell level are crucial. Previous research suggested that the single-cell growth rate can be used to investigate drug-cell interactions. However, currently established methods for quantifying single-cell growth are limited to isolated or monolayer cells. Here, we introduce a technique that accurately measures both 2D and 3D cell growth rates using label-free ratiometric stimulated Raman scattering (SRS) microscopy. We use deuterated amino acids, leucine, isoleucine, and valine, as tracers and measure the C-D SRS signal from deuterium-labeled proteins and the C-H SRS signal from unlabeled proteins simultaneously to determine the cell growth rate at the single-cell level. The technique offers single-cell level drug sensitivity measurement with a shorter turnaround time (within 12 h) than most traditional assays. The submicrometer resolution of the imaging technique allows us to examine the effects of chemotherapeutic drugs, including kinase inhibitors, mitotic inhibitors, and topoisomerase II inhibitors, on both the cell growth rate and morphology. The capability of quantifying 3D cell growth rates provides insight into a deeper understanding of the cell-drug interaction in the actual tumor environment.
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Affiliation(s)
- Fiona Xi Xu
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Ruibing Wu
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Kailun Hu
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
| | - Dan Fu
- Department of Chemistry, University of Washington, Seattle, WA 98195, United States
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8
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Wu J, Fang H, Li F, Fu H, Lin F, Li J, Huang Y, Yu Q, Song S, Xu X, Xu Y, Wang W, Wang L, Lu S, Li H, Huang S, Lu Z, Ou C, Wei X, Liu B, Kobbi R, Tang X, Lin L, Zhou Q, Hu Q, Bogunović H, Orlando JI, Zhang X, Xu Y. GAMMA challenge: Glaucoma grAding from Multi-Modality imAges. Med Image Anal 2023; 90:102938. [PMID: 37806020 DOI: 10.1016/j.media.2023.102938] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/04/2023] [Accepted: 08/16/2023] [Indexed: 10/10/2023]
Abstract
Glaucoma is a chronic neuro-degenerative condition that is one of the world's leading causes of irreversible but preventable blindness. The blindness is generally caused by the lack of timely detection and treatment. Early screening is thus essential for early treatment to preserve vision and maintain life quality. Colour fundus photography and Optical Coherence Tomography (OCT) are the two most cost-effective tools for glaucoma screening. Both imaging modalities have prominent biomarkers to indicate glaucoma suspects, such as the vertical cup-to-disc ratio (vCDR) on fundus images and retinal nerve fiber layer (RNFL) thickness on OCT volume. In clinical practice, it is often recommended to take both of the screenings for a more accurate and reliable diagnosis. However, although numerous algorithms are proposed based on fundus images or OCT volumes for the automated glaucoma detection, there are few methods that leverage both of the modalities to achieve the target. To fulfil the research gap, we set up the Glaucoma grAding from Multi-Modality imAges (GAMMA) Challenge to encourage the development of fundus & OCT-based glaucoma grading. The primary task of the challenge is to grade glaucoma from both the 2D fundus images and 3D OCT scanning volumes. As part of GAMMA, we have publicly released a glaucoma annotated dataset with both 2D fundus colour photography and 3D OCT volumes, which is the first multi-modality dataset for machine learning based glaucoma grading. In addition, an evaluation framework is also established to evaluate the performance of the submitted methods. During the challenge, 1272 results were submitted, and finally, ten best performing teams were selected for the final stage. We analyse their results and summarize their methods in the paper. Since all the teams submitted their source code in the challenge, we conducted a detailed ablation study to verify the effectiveness of the particular modules proposed. Finally, we identify the proposed techniques and strategies that could be of practical value for the clinical diagnosis of glaucoma. As the first in-depth study of fundus & OCT multi-modality glaucoma grading, we believe the GAMMA Challenge will serve as an essential guideline and benchmark for future research.
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Affiliation(s)
- Junde Wu
- South China University of Technology, Guangzhou, China; Pazhou Lab, Guangzhou, China
| | - Huihui Fang
- South China University of Technology, Guangzhou, China; Pazhou Lab, Guangzhou, China
| | - Fei Li
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Huazhu Fu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Fengbin Lin
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China
| | - Jiongcheng Li
- School of Informatics, Xiamen University, Xiamen, China
| | - Yue Huang
- School of Informatics, Xiamen University, Xiamen, China
| | - Qinji Yu
- Shanghai Jiao Tong University, Shanghai, China
| | - Sifan Song
- Xi'an Jiaotong-Liverpool University, Suzhou, China
| | - Xinxing Xu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yanyu Xu
- Institute of High Performance Computing (IHPC), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wensai Wang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Lingxiao Wang
- Institute of Biomedical Engineering, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin, China
| | - Shuai Lu
- School of Medical Technology, Beijing Institute of Technology, Beijing, China
| | - Huiqi Li
- School of Medical Technology, Beijing Institute of Technology, Beijing, China; School of Information and Electronics, Beijing Institute of Technology, Beijing, China
| | - Shihua Huang
- Department of Computing, Hong Kong Polytechnic University, Hong Kong, China
| | - Zhichao Lu
- Department of Computer Science and Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Chubin Ou
- Weizhi Medical Technology Company, Suzhou, China
| | - Xifei Wei
- Weizhi Medical Technology Company, Suzhou, China
| | - Bingyuan Liu
- École de technologie supérieure, Montreal, Montreal, Canada
| | | | - Xiaoying Tang
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Li Lin
- Department of Electrical and Electronic Engineering, Southern University of Science and Technology, Shenzhen, China; Department of Electrical and Electronic Engineering, The University of Hong Kong, Hong Kong, China
| | - Qiang Zhou
- Suixin (Shanghai) Technology Co., Ltd., Shanghai, China
| | - Qiang Hu
- Suixin (Shanghai) Technology Co., Ltd., Shanghai, China
| | - Hrvoje Bogunović
- Christian Doppler Lab for Artificial Intelligence in Retina, Department of Ophthalmology, Medical University of Vienna, Austria
| | | | - Xiulan Zhang
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Ophthalmology and Visual Science, Guangzhou, China.
| | - Yanwu Xu
- South China University of Technology, Guangzhou, China; Pazhou Lab, Guangzhou, China.
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Pereira FC, Ge X, Kristensen JM, Kirkegaard RH, Maritsch K, Zhu Y, Decorte M, Hausmann B, Berry D, Wasmund K, Schintlmeister A, Boettcher T, Cheng JX, Wagner M. The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.12.566429. [PMID: 38014294 PMCID: PMC10680583 DOI: 10.1101/2023.11.12.566429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single cell chemical imaging to investigate the impact of two widely prescribed nervous system targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.
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10
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Zhu Y, Ge X, Ni H, Yin J, Lin H, Wang L, Tan Y, Prabhu Dessai CV, Li Y, Teng X, Cheng JX. Stimulated Raman photothermal microscopy toward ultrasensitive chemical imaging. SCIENCE ADVANCES 2023; 9:eadi2181. [PMID: 37889965 PMCID: PMC10610916 DOI: 10.1126/sciadv.adi2181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy has shown enormous potential in revealing molecular structures, dynamics, and couplings in complex systems. However, the sensitivity of SRS is fundamentally limited to the millimolar level due to shot noise and the small modulation depth. To overcome this barrier, we revisit SRS from the perspective of energy deposition. The SRS process pumps molecules to their vibrationally excited states. The subsequent relaxation heats up the surroundings and induces refractive index changes. By probing the refractive index changes with a laser beam, we introduce stimulated Raman photothermal (SRP) microscopy, where a >500-fold boost of modulation depth is achieved. The versatile applications of SRP microscopy on viral particles, cells, and tissues are demonstrated. SRP microscopy opens a way to perform vibrational spectroscopic imaging with ultrahigh sensitivity.
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Affiliation(s)
- Yifan Zhu
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Xiaowei Ge
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Hongli Ni
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Jiaze Yin
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Haonan Lin
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Le Wang
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Yuying Tan
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | | | - Yueming Li
- Department of Mechanical Engineering, Boston University, Boston, MA 02215, USA
| | - Xinyan Teng
- Department of Chemistry, Boston University, Boston, MA 02215, USA
| | - Ji-Xin Cheng
- Department of Chemistry, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
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11
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Cao J, Mou T, Mei B, Yao P, Han C, Gong X, Song P, Jiang Z, Frauenheim T, Xiao J, Xu W. Improved Electrocatalytic Activity and Stability by Single Iridium Atoms on Iron-based Layered Double Hydroxides for Oxygen Evolution. Angew Chem Int Ed Engl 2023; 62:e202310973. [PMID: 37667678 DOI: 10.1002/anie.202310973] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 08/28/2023] [Accepted: 09/04/2023] [Indexed: 09/06/2023]
Abstract
Full understanding to the origin of the catalytic performance of a supported nanocatalyst from the points of view of both the active component and support is significant for the achievement of high performance. Herein, based on a model electrocatalyst of single-iridium-atom-doped iron (Fe)-based layered double hydroxides (LDH) for oxygen evolution reaction (OER), we reveal the first completed origin of the catalytic performance of such supported nanocatalysts. Specially, besides the activity enhancement of Ir sites by LDH support, the stability of surface Fe sites is enhanced by doped Ir sites: DFT calculation shows that the Ir sites can reduce the activity and enhance the stability of the nearby Fe sites; while further finite element simulations indicate, the stability enhancement of distant Fe sites could be attributed to the much low concentration of OER reactant (hydroxyl ions, OH- ) around them induced by the much fast consumption of OH- on highly active Ir sites. These new findings about the interaction between the main active components and supports are applicable in principle to other heterogeneous nanocatalysts and provide a completed understanding to the catalytic performance of heterogeneous nanocatalysts.
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Affiliation(s)
- Jing Cao
- State Key Laboratory of Electroanalytical Chemistry and Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Science and Technology of China, Anhui, 230026, China
| | - Tong Mou
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, 116023, P. R. China
- Beijing Computational Science Research Center, Beijing, 100193, P. R. China
| | - Bingbao Mei
- Shanghai Synchrotron Radiation Facility, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201800, P. R. China
| | - Pengfei Yao
- State Key Laboratory of Electroanalytical Chemistry and Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Science and Technology of China, Anhui, 230026, China
| | - Ce Han
- State Key Laboratory of Electroanalytical Chemistry and Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Science and Technology of China, Anhui, 230026, China
| | - Xue Gong
- State Key Laboratory of Electroanalytical Chemistry and Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Science and Technology of China, Anhui, 230026, China
| | - Ping Song
- State Key Laboratory of Electroanalytical Chemistry and Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Science and Technology of China, Anhui, 230026, China
| | - Zheng Jiang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, 230026, China
| | - Thomas Frauenheim
- Shenzhen JL Computational and Applied Research Institute, Shenzhen, 518131, P. R. China
- Bremen Center for Computational Materials Science, University of Bremen, 28359, Bremen, Germany
- Beijing Computational Science Research Center, Beijing, 100193, P. R. China
| | - Jianping Xiao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Dalian National Laboratory for Clean Energy, Chinese Academy of Sciences, Dalian, 116023, P. R. China
- Beijing Computational Science Research Center, Beijing, 100193, P. R. China
| | - Weilin Xu
- State Key Laboratory of Electroanalytical Chemistry and Jilin Province Key Laboratory of Low Carbon Chemical Power, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- University of Science and Technology of China, Anhui, 230026, China
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12
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Zhu Y, Ge X, Ni H, Yin J, Lin H, Wang L, Tan Y, Prabhu Dessai CV, Li Y, Teng X, Cheng JX. Stimulated Raman Photothermal Microscopy towards Ultrasensitive Chemical Imaging. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.06.531387. [PMID: 36945642 PMCID: PMC10028842 DOI: 10.1101/2023.03.06.531387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Stimulated Raman scattering (SRS) microscopy has shown enormous potential in revealing molecular structures, dynamics and coupling in a complex system. However, the bond-detection sensitivity of SRS microscopy is fundamentally limited to milli-molar level due to the shot noise and the small modulation depth in either pump or Stokes beam4. Here, to overcome this barrier, we revisit SRS from the perspective of energy deposition. The SRS process pumps molecules to their vibrational excited states. The thereafter relaxation heats up the surrounding and induces a change in refractive index. By probing the refractive index change with a continuous wave beam, we introduce stimulated Raman photothermal (SRP) microscopy, where a >500-fold boost of modulation depth is achieved on dimethyl sulfide with conserved average power. Versatile applications of SRP microscopy on viral particles, cells, and tissues are demonstrated. With much improved signal to noise ratio compared to SRS, SRP microscopy opens a new way to perform vibrational spectroscopic imaging with ultrahigh sensitivity and minimal water absorption.
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13
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Zhang C, Le Dévédec SE, Ali A, Hankemeier T. Single-cell metabolomics by mass spectrometry: ready for primetime? Curr Opin Biotechnol 2023; 82:102963. [PMID: 37356380 DOI: 10.1016/j.copbio.2023.102963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 04/17/2023] [Accepted: 05/23/2023] [Indexed: 06/27/2023]
Abstract
Single-cell metabolomics (SCMs) is a powerful tool for studying cellular heterogeneity by providing insight into the differences between individual cells. With the development of a set of promising SCMs pipelines, this maturing technology is expected to be widely used in biomedical research. However, before SCMs is ready for primetime, there are some challenges to overcome. In this review, we summarize the trends and challenges in the development of SCMs. We also highlight the latest methodologies, applications, and sketch the perspective for integration with other omics and imaging approaches.
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Affiliation(s)
- Congrou Zhang
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands
| | - Ahmed Ali
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands.
| | - Thomas Hankemeier
- Metabolomics and Analytics Center, Leiden Academic Centre of Drug Research, Leiden University, Leiden, the Netherlands.
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14
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Sawers RG. Perspective elucidating the physiology of a microbial cell: Neidhardt's Holy Grail. Mol Microbiol 2023; 120:54-59. [PMID: 36855806 DOI: 10.1111/mmi.15051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/02/2023]
Abstract
A living microbial cell represents a system of high complexity, integration, and extreme order. All processes within that cell interconvert free energy through a multitude of interconnected metabolic reactions that help to maintain the cell in a state of low entropy, which is a characteristic of all living systems. The study of macromolecular interactions outside this cellular environment yields valuable information about the molecular function of macromolecules but represents a system in comparative disorder. Consequently, care must always be taken in interpreting the information gleaned from such studies and must be compared with how the same macromolecules function in vivo, otherwise, discrepancies can arise. The importance of combining reductionist approaches with the study of whole-cell microbial physiology is discussed regarding the long-term aim of understanding how a cell functions in its entirety. This can only be achieved by the continued development of high-resolution structural and multi-omic technologies. It is only by studying the whole cell that we can ever hope to understand how living systems function.
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Affiliation(s)
- R Gary Sawers
- Institute of Microbiology, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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15
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Bai Y, Guo Z, Pereira FC, Wagner M, Cheng JX. Mid-Infrared Photothermal-Fluorescence In Situ Hybridization for Functional Analysis and Genetic Identification of Single Cells. Anal Chem 2023; 95:2398-2405. [PMID: 36652555 PMCID: PMC9893215 DOI: 10.1021/acs.analchem.2c04474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Simultaneous identification and metabolic analysis of microbes with single-cell resolution and high throughput are necessary to answer the question of "who eats what, when, and where" in complex microbial communities. Here, we present a mid-infrared photothermal-fluorescence in situ hybridization (MIP-FISH) platform that enables direct bridging of genotype and phenotype. Through multiple improvements of MIP imaging, the sensitive detection of isotopically labeled compounds incorporated into proteins of individual bacterial cells became possible, while simultaneous detection of FISH labeling with rRNA-targeted probes enabled the identification of the analyzed cells. In proof-of-concept experiments, we showed that the clear spectral red shift in the protein amide I region due to incorporation of 13C atoms originating from 13C-labeled glucose can be exploited by MIP-FISH to discriminate and identify 13C-labeled bacterial cells within a complex human gut microbiome sample. The presented methods open new opportunities for single-cell structure-function analyses for microbiology.
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Affiliation(s)
- Yeran Bai
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States,Photonics
Center, Boston University, Boston, Massachusetts 02215, United States
| | - Zhongyue Guo
- Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States,Photonics
Center, Boston University, Boston, Massachusetts 02215, United States
| | - Fátima C. Pereira
- Centre
for Microbiology and Environmental Systems Science, Department of
Microbiology and Ecosystem Science, University
of Vienna, Vienna 1030, Austria
| | - Michael Wagner
- Centre
for Microbiology and Environmental Systems Science, Department of
Microbiology and Ecosystem Science, University
of Vienna, Vienna 1030, Austria,Department
of Chemistry and Bioscience, Aalborg University, Aalborg 9220, Denmark,
| | - Ji-Xin Cheng
- Department
of Electrical and Computer Engineering, Boston University, Boston, Massachusetts 02215, United States,Department
of Biomedical Engineering, Boston University, Boston, Massachusetts 02215, United States,Photonics
Center, Boston University, Boston, Massachusetts 02215, United States,
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16
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Alcolombri U, Pioli R, Stocker R, Berry D. Single-cell stable isotope probing in microbial ecology. ISME COMMUNICATIONS 2022; 2:55. [PMID: 37938753 PMCID: PMC9723680 DOI: 10.1038/s43705-022-00142-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 05/10/2022] [Accepted: 06/09/2022] [Indexed: 05/30/2023]
Abstract
Environmental and host-associated microbiomes are typically diverse assemblages of organisms performing myriad activities and engaging in a network of interactions that play out in spatially structured contexts. As the sum of these activities and interactions give rise to overall microbiome function, with important consequences for environmental processes and human health, elucidating specific microbial activities within complex communities is a pressing challenge. Single-cell stable isotope probing (SC-SIP) encompasses multiple techniques that typically utilize Raman microspectroscopy or nanoscale secondary ion mass spectrometry (NanoSIMS) to enable spatially resolved tracking of isotope tracers in cells, cellular components, and metabolites. SC-SIP techniques are uniquely suited for illuminating single-cell activities in microbial communities and for testing hypotheses about cellular functions generated for example from meta-omics datasets. Here, we illustrate the insights enabled by SC-SIP techniques by reviewing selected applications in microbiology and offer a perspective on their potential for future research.
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Affiliation(s)
- Uria Alcolombri
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roberto Pioli
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland.
| | - David Berry
- Division of Microbial Ecology, Department of Microbiology and Ecosystem Science, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria.
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