Ecological memory of prior nutrient exposure in the human gut microbiome.

Autor: Letourneau J; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA., Holmes ZC; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA., Dallow EP; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA., Durand HK; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA., Jiang S; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA., Carrion VM; Duke Office of Clinical Research, Duke University School of Medicine, Durham, NC, USA., Gupta SK; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA., Mincey AC; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA., Muehlbauer MJ; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA., Bain JR; Duke Molecular Physiology Institute, Duke University School of Medicine, Durham, NC, USA.; Department of Medicine (Endocrinology), Duke University School of Medicine, Durham, NC, USA., David LA; Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, USA. lawrence.david@duke.edu.; Program in Computational Biology and Bioinformatics, Duke University School of Medicine, Durham, NC, USA. lawrence.david@duke.edu.
Jazyk: angličtina
Zdroj: The ISME journal [ISME J] 2022 Nov; Vol. 16 (11), pp. 2479-2490. Date of Electronic Publication: 2022 Jul 23.
DOI: 10.1038/s41396-022-01292-x
Abstrakt: Many ecosystems have been shown to retain a memory of past conditions, which in turn affects how they respond to future stimuli. In microbial ecosystems, community disturbance has been associated with lasting impacts on microbiome structure. However, whether microbial communities alter their response to repeated stimulus remains incompletely understood. Using the human gut microbiome as a model, we show that bacterial communities retain an "ecological memory" of past carbohydrate exposures. Memory of the prebiotic inulin was encoded within a day of supplementation among a cohort of human study participants. Using in vitro gut microbial models, we demonstrated that the strength of ecological memory scales with nutrient dose and persists for days. We found evidence that memory is seeded by transcriptional changes among primary degraders of inulin within hours of nutrient exposure, and that subsequent changes in the activity and abundance of these taxa are sufficient to enhance overall community nutrient metabolism. We also observed that ecological memory of one carbohydrate species impacts microbiome response to other carbohydrates, and that an individual's habitual exposure to dietary fiber was associated with their gut microbiome's efficiency at digesting inulin. Together, these findings suggest that the human gut microbiome's metabolic potential reflects dietary exposures over preceding days and changes within hours of exposure to a novel nutrient. The dynamics of this ecological memory also highlight the potential for intra-individual microbiome variation to affect the design and interpretation of interventions involving the gut microbiome.
(© 2022. The Author(s), under exclusive licence to International Society for Microbial Ecology.)
Databáze: MEDLINE
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