Variation and Stability in Gut Microbial Ecology Assessed Through Multi-Omics Time-Series Analysis

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The 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.





Letourneau, Jeffrey (2022). Variation and Stability in Gut Microbial Ecology Assessed Through Multi-Omics Time-Series Analysis. Dissertation, Duke University. Retrieved from


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