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ToolsLi, Leyuan, Ryan, James, Ning, Zhibin, Zhang, Xu, Mayne, Janice, Lavallée-Adam, Mathieu, Stintzi, Alain and Figeys, Daniel (2020) A functional ecological network based on metaproteomics responses of individual gut microbiomes to resistant starches. Computational and Structural Biotechnology Journal, 18. pp. 3833-3842. ISSN 2001-0370
Full text not available from this repository. (Request a copy)Abstract
Resistant starches (RS) are dietary compounds processed by the gut microbiota into metabolites, such as butyrate, that are beneficial to the host. The production of butyrate by the microbiome appears to be affected by the plant source and type of RS as well as the individual's microbiota. In this study, we used in vitro culture and metaproteomic methods to explore individual microbiome's functional responses to RS2 (enzymatically-resistant starch), RS3 (retrograded starch) and RS4 (chemically-modified starch). Results showed that RS2 and RS3 significantly altered the protein expressions in the individual gut microbiomes, while RS4 did not result in significant protein changes. Significantly elevated protein groups were enriched in carbohydrate metabolism and transport functions of families Eubacteriaceae, Lachnospiraceae and Ruminococcaceae. In addition, Bifidobacteriaceae was significantly increased in response to RS3. We also observed taxon-specific enrichments of starch metabolism and pentose phosphate pathways corresponding to this family. Functions related to starch utilization, ABC transporters and pyruvate metabolism pathways were consistently increased in the individual microbiomes in response to RS2 and RS3. Given that these taxon-specific responses depended on the type of carbohydrate sources, we constructed a functional ecological network to gain a system-level insight of functional organization. Our results suggest that while some microbes tend to be functionally independent, there are subsets of microbes that are functionally co-regulated by environmental changes, potentially by alterations of trophic interactions.
| Item Type: | Article |
|---|---|
| Additional Information: | Data availability: The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD017907. There were 21 additional samples in the same database search task that was not involved in this study (three other compounds tested with the same microbiomes). To ensure data analysis reproducibility, we uploaded all these 157 raw files to the Pride Database. |
| Uncontrolled Keywords: | functional network,gut microbiome,metaproteomics,resistant starch,biotechnology,biophysics,structural biology,biochemistry,genetics,computer science applications ,/dk/atira/pure/subjectarea/asjc/1300/1305 |
| Faculty \ School: | Faculty of Medicine and Health Sciences > Norwich Medical School |
| UEA Research Groups: | Faculty of Medicine and Health Sciences > Research Centres > Metabolic Health |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 19 Mar 2026 09:33 |
| Last Modified: | 19 Mar 2026 09:33 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/102474 |
| DOI: | 10.1016/j.csbj.2020.10.042 |
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