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ToolsWang, Tong, Li, Leyuan, Figeys, Daniel and Liu, Yang-Yu (2024) Pairing metagenomics and metaproteomics to characterize ecological niches and metabolic essentiality of gut microbiomes. ISME Communications, 4 (1). ycae063. ISSN 2730-6151
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Abstract
The genome of a microorganism encodes its potential functions that can be implemented through expressed proteins. It remains elusive how a protein's selective expression depends on its metabolic essentiality to microbial growth or its ability to claim resources as ecological niches. To reveal a protein's metabolic or ecological role, we developed a computational pipeline, which pairs metagenomics and metaproteomics data to quantify each protein's gene-level and protein-level functional redundancy simultaneously. We first illustrated the idea behind the pipeline using simulated data of a consumer-resource model. We then validated it using real data from human and mouse gut microbiome samples. In particular, we analyzed ABC-type transporters and ribosomal proteins, confirming that the metabolic and ecological roles predicted by our pipeline agree well with prior knowledge. Finally, we performed in vitro cultures of a human gut microbiome sample and investigated how oversupplying various sugars involved in ecological niches influences the community structure and protein abundance. The presented results demonstrate the performance of our pipeline in identifying proteins' metabolic and ecological roles, as well as its potential to help us design nutrient interventions to modulate the human microbiome.
| Item Type: | Article |
|---|---|
| Additional Information: | Data and code availability: All code for simulations used in this manuscript can be found at https://github.com/wt1005203/ecological_niches. Funding information: D.F. acknowledges grants from Natural Sciences and Engineering Research Council of Canada (NSERC), and the Government of Canada through Genome Canada and the Ontario Genomics Institute (OGI-114 and OGI-149). D.F. acknowledges a Distinguished Research Chair from the University of Ottawa. Y.-Y.L. is supported by grants R01AI141529, R01HD093761, RF1AG067744, UH3OD023268, U19AI095219, and U01HL089856 from the National Institutes of Health, USA; a pilot grant from the Biology of Trauma Initiative of Broad Institute, USA; and the Office of the Assistant Secretary of Defense for Health Affairs, through the Traumatic Brain Injury and Psychological Health Research Program (Focused Program Award) under award no. (W81XWH-22-S-TBIPH2), endorsed by the Department of Defense, USA. |
| Uncontrolled Keywords: | ecological niche functional redundancy gut microbiome metabolic essentiality metagenomics metaproteomics,metaproteomics,functional redundancy,gut microbiome,metagenomics,metabolic essentiality,ecological niche,microbiology ,/dk/atira/pure/subjectarea/asjc/2400/2404 |
| 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: | 08 Sep 2025 09:30 |
| Last Modified: | 08 Sep 2025 09:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/100290 |
| DOI: | 10.1093/ismeco/ycae063 |
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