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Molina Ortiz JP, McClure DD, Shanahan ER, Dehghani F, Holmes AJ, Read MN. Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models. Gut Microbes 2021; 13:1965698. [PMID: 34455914 PMCID: PMC8432618 DOI: 10.1080/19490976.2021.1965698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 07/01/2021] [Accepted: 07/27/2021] [Indexed: 02/04/2023] Open
Abstract
The gut microbiome has emerged as a contributing factor in non-communicable disease, rendering it a target of health-promoting interventions. Yet current understanding of the host-microbiome dynamic is insufficient to predict the variation in intervention outcomes across individuals. We explore the mechanisms that underpin the gut bacterial ecosystem and highlight how a more complete understanding of this ecology will enable improved intervention outcomes. This ecology varies within the gut over space and time. Interventions disrupt these processes, with cascading consequences throughout the ecosystem. In vivo studies cannot isolate and probe these processes at the required spatiotemporal resolutions, and in vitro studies lack the representative complexity required. However, we highlight that, together, both approaches can inform in silico models that integrate cellular-level dynamics, can extrapolate to explain bacterial community outcomes, permit experimentation and observation over ecological processes at high spatiotemporal resolution, and can serve as predictive platforms on which to prototype interventions. Thus, it is a concerted integration of these techniques that will enable rational targeted manipulations of the gut ecosystem.
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Affiliation(s)
- Juan P. Molina Ortiz
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Dale D. McClure
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Erin R. Shanahan
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Fariba Dehghani
- School of Chemical and Biomolecular Engineering, Faculty of Engineering, The University of Sydney, Sydney, Australia
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
| | - Andrew J. Holmes
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- School of Life and Environmental Sciences, Faculty of Science, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - Mark N. Read
- Faculty of Engineering, Centre for Advanced Food Engineering, The University of Sydney, Sydney, Australia
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
- School of Computer Science, Faculty of Engineering, The University of Sydney, Sydney, Australia
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Effect of heat on antigenicity and immunogenicity of the antigenic determinant shared by Haemophilus influenzae type b and Escherichia coli K100. Infect Immun 1977; 18:68-72. [PMID: 71269 PMCID: PMC421194 DOI: 10.1128/iai.18.1.68-72.1977] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Escherichia coli K100 produces an antigenic determinant similar to, or identical with, the capsular antigen of Haemophilus influenzae type b. Studies of the effects of heat on the immunogenicity, erythrocyte-modifying capacity, and antigenicity of this cross-reacting antigen (CRA) revealed the following findings. Immunization of rabbits with viable or formaldehyde-killed suspensions of E. coli K100, producing CRA, engendered CRA antibodies in significant titers, as demonstrated by hemagglutination of erythrocytes modified by H. influenzae type b antigen. Heating of the suspensions for 1 h at 56 or 100 degrees C destroyed the immunogenicity of CRA, and the heated suspensions did not prime for a secondary antibody response. Supernatants of heated suspensions also were non-immunogenic. Repeated freezing and thawing of heated suspensions of E. coli K100 or their supernatants did not restore immunogenicity. Heat also abolished the immunogenicity of H. influenzae type b. The loss of immunogenicity of CRA of E. coli K100 by heat was not due to alteration of the antigenic determinant, since heated suspensions and supernatants thereof modified erythrocytes for agglutination by H. influenzae type b antiserum. The latter supernatants also inhibited hemagglutination by H. influenzae type b antibodies and absorbed the latter. We conclude that striking differences exist in the effects of heat on CRA on the one hand and of enterobacterial common antigen and lipopolysaccharide O antigen of enteric bacteria on the other. Heating of the latter two antigens does not abolish their priming effect, and repeated freezing and thawing restores the immunogenicity of heated antigens.
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