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DC Field | Value | Language |
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dc.contributor.author | Molina Ortiz, JP | - |
dc.contributor.author | Read, MN | - |
dc.contributor.author | McClure, DD | - |
dc.contributor.author | Holmes, A | - |
dc.contributor.author | Dehghani, F | - |
dc.contributor.author | Shanahan, ER | - |
dc.date.accessioned | 2022-12-19T12:32:07Z | - |
dc.date.available | 2022-12-19T12:32:07Z | - |
dc.date.issued | 2022-09-08 | - |
dc.identifier | ORCID iD: Juan P. Molina Ortiz https://orcid.org/0000-0003-4432-6689; Dale McClure https://orcid.org/0000-0001-6790-5179. | - |
dc.identifier | e2118831 | - |
dc.identifier.citation | Molina Ortiz, J.P. et al. (2022) 'High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure', Gut Microbes, 14 (1), e2118831, pp. 1 - 21. doi: 10.1080/19490976.2022.2118831. | en_US |
dc.identifier.issn | 1949-0976 | - |
dc.identifier.uri | https://bura.brunel.ac.uk/handle/2438/25656 | - |
dc.description | Data availability statement: All data generated or analyzed during this study are included in this published article and its supplementary information files. | en_US |
dc.description.abstract | Copyright © 2022 The Author(s). Human gut microbiome structure and emergent metabolic outputs impact health outcomes. However, what drives such community characteristics remains underexplored. Here, we rely on high throughput genomic reconstruction modeling, to infer the metabolic attributes and nutritional requirements of 816 gut strains, via a framework termed GEMNAST. This has been performed in terms of a group of human vitamins to examine the role vitamin exchanges have at different levels of community organization. We find that only 91 strains can satisfy their vitamin requirements (prototrophs) while the rest show various degrees of auxotrophy/specialization, highlighting their dependence on external sources, such as other members of the microbial community. Further, 79% of the strains in our sample were mapped to 11 distinct vitamin requirement profiles with low phylogenetic consistency. Yet, we find that human gut microbial community enterotype indicators display marked metabolic differences. Prevotella strains display a metabolic profile that can be complemented by strains from other genera often associated with the Prevotella enterotype and agrarian diets, while Bacteroides strains occupy a prototrophic profile. Finally, we identify pre-defined interaction modules (IMs) of gut species from human and mice predicted to be driven by, or highly independent of vitamin exchanges. Our analysis provides mechanistic grounding to gut microbiome stability and to co-abundance-based observations, a fundamental step toward understanding emergent processes that influence health outcomes. Further, our work opens a path to future explorations in the field through applications of GEMNAST to additional nutritional dimensions. | en_US |
dc.description.sponsorship | University of Sydney (PhD scholarship and à Beckett Cancer Research Trust Fellowship). | en_US |
dc.format.extent | 1 - 21 | - |
dc.format.medium | Print-Electronic | - |
dc.language.iso | en_US | en_US |
dc.publisher | Taylor & Francis Group | en_US |
dc.rights | Copyright © 2022 The Author(s). Published with license by Taylor & Francis Group, LLC. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. | - |
dc.rights.uri | https://creativecommons.org/licenses/by/4.0/ | - |
dc.subject | gut microbiome | en_US |
dc.subject | genome scale modeling | en_US |
dc.subject | computational biology | en_US |
dc.subject | networks | en_US |
dc.subject | interactions | en_US |
dc.subject | cofactors | en_US |
dc.subject | vitamins | en_US |
dc.subject | enterotypes | en_US |
dc.title | High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure | en_US |
dc.type | Article | en_US |
dc.identifier.doi | https://doi.org/10.1080/19490976.2022.2118831 | - |
dc.relation.isPartOf | Gut Microbes | - |
pubs.issue | 1 | - |
pubs.publication-status | Published | - |
pubs.volume | 14 | - |
dc.identifier.eissn | 1949-0984 | - |
dc.rights.holder | The Author(s) | - |
Appears in Collections: | Dept of Chemical Engineering Research Papers |
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