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ToolsWatson, Andrea R., Füssel, Jessika, Veseli, Iva, DeLongchamp, Johanna Zaal, Silva, Marisela, Trigodet, Florian, Lolans, Karen, Shaiber, Alon, Fogarty, Emily, Runde, Joseph M., Quince, Christopher, Yu, Michael K., Söylev, Arda, Morrison, Hilary G., Lee, Sonny T. M., Kao, Dina, Rubin, David T., Jabri, Bana, Louie, Thomas and Eren, A. Murat (2023) Metabolic independence drives gut microbial colonization and resilience in health and disease. Genome Biology, 24. ISSN 1474-7596
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Abstract
Background: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge. Results: Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients. Conclusions: These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of “dysbiosis” that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.
| Item Type: | Article |
|---|---|
| Additional Information: | Availability of data and materials: Raw sequencing data for donor and recipient metagenomes are stored under the NCBI BioProject PRJNA701961 (see Additional file 1 for accession numbers for each sample) [89]. The geographically distributed human gut metagenomes were obtained from previously published datasets (Additional file 5) [44, 90,91,92,93,94,95,96,97,98,99,100,101,102,103,104]. The URL https://merenlab.org/data/fmt-gut-colonization [105] serves a reproducible bioinformatics workflow and gives access to ad hoc scripts, usage instructions, and intermediate data objects to reproduce findings in our study. All ad hoc scripts also available under CC-BY 4.0 International license on Figshare (https://doi.org/10.6084/m9.figshare.22352989) [106]. Funding Information: This project was supported by the GI Research Foundation (GIRF) and the Mutchnik Family Fund. Additionally, ARW acknowledges support from the Robert C. and Mary Jane Gallo Scholarship Fund; JF acknowledges support from the Alissa and Gianna Carlino Fellowship in Celiac Disease Research; BJ acknowledges support from the Cancer Center Support grant P30CA014599 and Digestive Diseases Research Core Center P30 DK42086; AME acknowledges support from the NIH NIDDK grant (RC2 DK122394); and IV acknowledges support from the National Science Foundation Graduate Research Fellowship (1746045). |
| Uncontrolled Keywords: | fecal microbiota transplantation,human gut microbiome,metabolic independence,microbial colonization,microbial metabolism,ecology, evolution, behavior and systematics,genetics,cell biology,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1100/1105 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 23 Oct 2024 15:30 |
| Last Modified: | 01 Nov 2024 12:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97159 |
| DOI: | 10.1186/s13059-023-02924-x |
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