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Melnik AV, Vázquez-Baeza Y, Aksenov AA, Hyde E, McAvoy AC, Wang M, da Silva RR, Protsyuk I, Wu JV, Bouslimani A, Lim YW, Luzzatto-Knaan T, Comstock W, Quinn RA, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC, Garg N. Molecular and Microbial Microenvironments in Chronically Diseased Lungs Associated with Cystic Fibrosis. mSystems 2019; 4:e00375-19. [PMID: 31551401 PMCID: PMC6759567 DOI: 10.1128/msystems.00375-19] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 09/02/2019] [Indexed: 02/07/2023] Open
Abstract
To visualize the personalized distributions of pathogens and chemical environments, including microbial metabolites, pharmaceuticals, and their metabolic products, within and between human lungs afflicted with cystic fibrosis (CF), we generated three-dimensional (3D) microbiome and metabolome maps of six explanted lungs from three cystic fibrosis patients. These 3D spatial maps revealed that the chemical environments differ between patients and within the lungs of each patient. Although the microbial ecosystems of the patients were defined by the dominant pathogen, their chemical diversity was not. Additionally, the chemical diversity between locales in the lungs of the same individual sometimes exceeded interindividual variation. Thus, the chemistry and microbiome of the explanted lungs appear to be not only personalized but also regiospecific. Previously undescribed analogs of microbial quinolones and antibiotic metabolites were also detected. Furthermore, mapping the chemical and microbial distributions allowed visualization of microbial community interactions, such as increased production of quorum sensing quinolones in locations where Pseudomonas was in contact with Staphylococcus and Granulicatella, consistent with in vitro observations of bacteria isolated from these patients. Visualization of microbe-metabolite associations within a host organ in early-stage CF disease in animal models will help elucidate the complex interplay between the presence of a given microbial structure, antibiotics, metabolism of antibiotics, microbial virulence factors, and host responses.IMPORTANCE Microbial infections are now recognized to be polymicrobial and personalized in nature. Comprehensive analysis and understanding of the factors underlying the polymicrobial and personalized nature of infections remain limited, especially in the context of the host. By visualizing microbiomes and metabolomes of diseased human lungs, we reveal how different the chemical environments are between hosts that are dominated by the same pathogen and how community interactions shape the chemical environment or vice versa. We highlight that three-dimensional organ mapping methods represent hypothesis-building tools that allow us to design mechanistic studies aimed at addressing microbial responses to other microbes, the host, and pharmaceutical drugs.
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Affiliation(s)
- Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yoshiki Vázquez-Baeza
- Jacobs School of Engineering, University of California, San Diego, La Jolla, California, USA
- UC San Diego Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
| | - Alexander A Aksenov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Embriette Hyde
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Andrew C McAvoy
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Mingxun Wang
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Ivan Protsyuk
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jason V Wu
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Yan Wei Lim
- Biology Department, San Diego State University, San Diego, California, USA
| | - Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - William Comstock
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Robert A Quinn
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Richard Wong
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
| | - Timothy Spivey
- Department of Radiology, University of California, San Diego, La Jolla, California, USA
| | - Sharon S Brouha
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Nuno Bandeira
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
| | - Grace Y Lin
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Forest Rohwer
- Biology Department, San Diego State University, San Diego, California, USA
| | - Douglas J Conrad
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Rob Knight
- Department of Pediatrics, University of California, San Diego, La Jolla, California, USA
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, California, USA
- UC San Diego Center for Microbiome Innovation, University of California, San Diego, La Jolla, California, USA
- Department of Bioengineering, University of California, San Diego, La Jolla, California, USA
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
| | - Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California, USA
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia, USA
- Emory-Children's Center for Cystic Fibrosis and Airways Disease Research, Atlanta, Georgia, USA
- Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, Georgia, USA
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Garg N, Wang M, Hyde E, da Silva RR, Melnik AV, Protsyuk I, Bouslimani A, Lim YW, Wong R, Humphrey G, Ackermann G, Spivey T, Brouha SS, Bandeira N, Lin GY, Rohwer F, Conrad DJ, Alexandrov T, Knight R, Dorrestein PC. Three-Dimensional Microbiome and Metabolome Cartography of a Diseased Human Lung. Cell Host Microbe 2017; 22:705-716.e4. [PMID: 29056429 DOI: 10.1016/j.chom.2017.10.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 07/12/2017] [Accepted: 09/14/2017] [Indexed: 12/12/2022]
Abstract
Our understanding of the spatial variation in the chemical and microbial makeup of an entire human organ remains limited, in part due to the size and heterogeneity of human organs and the complexity of the associated metabolome and microbiome. To address this challenge, we developed a workflow to enable the cartography of metabolomic and microbiome data onto a three-dimensional (3D) organ reconstruction built off radiological images. This enabled the direct visualization of the microbial and chemical makeup of a human lung from a cystic fibrosis patient. We detected host-derived molecules, microbial metabolites, medications, and region-specific metabolism of medications and placed it in the context of microbial distributions in the lung. Our tool further created browsable maps of a 3D microbiome/metabolome reconstruction map on a radiological image of a human lung and forms an interactive resource for the scientific community.
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Affiliation(s)
- Neha Garg
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mingxun Wang
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Embriette Hyde
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ricardo R da Silva
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Alexey V Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ivan Protsyuk
- Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Amina Bouslimani
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Yan Wei Lim
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Richard Wong
- Department of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Greg Humphrey
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Gail Ackermann
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA
| | - Timothy Spivey
- Department of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Sharon S Brouha
- Department of Radiology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Nuno Bandeira
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Grace Y Lin
- Department of Pathology, University of California, San Diego Health, San Diego, CA 92103, USA
| | - Forest Rohwer
- Biology Department, San Diego State University, San Diego, CA, USA
| | - Douglas J Conrad
- Department of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Theodore Alexandrov
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Structural and Computational Biology, European Molecular Biology Laboratory, Heidelberg 69117, Germany.
| | - Rob Knight
- Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Pieter C Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Department of Computer Science & Engineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 92093, USA.
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