Browsing by Author "Letourneau, Jeffrey"
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Item Open Access Ecological memory of prior nutrient exposure in the human gut microbiome.(The ISME journal, 2022-07-23) Letourneau, Jeffrey; Holmes, Zachary C; Dallow, Eric P; Durand, Heather K; Jiang, Sharon; Carrion, Verónica M; Gupta, Savita K; Mincey, Adam C; Muehlbauer, Michael J; Bain, James R; David, Lawrence AMany 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.Item Open Access Modulation of microbial community dynamics by spatial partitioning.(Nature chemical biology, 2022-04) Wu, Feilun; Ha, Yuanchi; Weiss, Andrea; Wang, Meidi; Letourneau, Jeffrey; Wang, Shangying; Luo, Nan; Huang, Shuquan; Lee, Charlotte T; David, Lawrence A; You, LingchongMicrobial communities inhabit spatial architectures that divide a global environment into isolated or semi-isolated local environments, which leads to the partitioning of a microbial community into a collection of local communities. Despite its ubiquity and great interest in related processes, how and to what extent spatial partitioning affects the structures and dynamics of microbial communities are poorly understood. Using modeling and quantitative experiments with simple and complex microbial communities, we demonstrate that spatial partitioning modulates the community dynamics by altering the local interaction types and global interaction strength. Partitioning promotes the persistence of populations with negative interactions but suppresses those with positive interactions. For a community consisting of populations with both positive and negative interactions, an intermediate level of partitioning maximizes the overall diversity of the community. Our results reveal a general mechanism underlying the maintenance of microbial diversity and have implications for natural and engineered communities.Item Open Access Variation and Stability in Gut Microbial Ecology Assessed Through Multi-Omics Time-Series Analysis(2022) Letourneau, JeffreyThe gut microbiome is a complex ecosystem of hundreds of species that is constantly subject to perturbations as a result of day-to-day dietary variation, among other factors. In some cases, disturbances to microbial communities have been associated with lasting impacts on microbiome structure. While much research has been done to uncover sources of inter-individual variation in the gut microbiome, less focus has been given to understanding the ecological mechanisms governing intra¬-individual variation. To address this, we carried out dietary intervention studies in human cohorts and analyzed microbiome composition, metabolism, and physical particulate structure. We also employed in vitro models of the gut microbiome to manipulate variables difficult to modulate in vivo, and to collect samples with a greater temporal resolution. As discussed in more detail in Chapter 2, we found that bacterial communities retain an “ecological memory” of past prebiotic exposures, which is encoded within one day by changes to the abundance and transcriptional state of primary degraders. Chapter 3 details findings from an investigation into fecal particle size, in which we found this metric to correlate with microbiome diversity and to be stable within individuals. Together, the results presented in this dissertation present fundamental new insights into the ecology of the gut microbiome.