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Enabling rational gut microbiome manipulations by understanding gut ecology through experimentally-evidenced in silico models
Authors
F Dehghani
AJ Holmes
+4 more
DD McClure
JP Molina Ortiz
MN Read
ER Shanahan
Publication date
1 January 2021
Publisher
'Informa UK Limited'
Doi
Abstract
© 2021 The Author(s). 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.University of Sydney’s Centre for Advanced Food and Engineering; JPMO acknowledges a PhD scholarship from the Faculty of Engineering at the University of Sydney. ERS acknowledges the financial support from the à Beckett Cancer Research Trust (University of Sydney Fellowship)
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Last time updated on 13/12/2021
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Last time updated on 30/11/2021