Wednesday, February 5, 2025
2/5/2025
PROJECT SUMMARY In Inflammatory Bowel Disease (IBD), the gut microbiome demonstrates reduced species diversity that can then be reversed following FMT. However, no study has identified a common pattern of microbiome alteration that is causally related to IBD nor has any study elucidated the mechanisms underlying FMT success in the subset of individuals with IBD that respond. In FMT, both species and strain diversity are increasing but currently studies only track changes in species diversity, resulting in a fundamental feature of the microbiome that is changing but not measured in trials or in cross sectional studies of comparing with healthy and IBD microbiomes. Thus, it is unclear whether it is the increase in species or strain diversity that is critical to FMT success or if there are unique differences in the strain-level structure of the IBD microbiome. Since microbial functional variation is found at the strain level, a functional understanding of microbiome composition in IBD may lie at the strain level. However, no studies so far have systematically characterized the strain-level microbiome structure in health or disease. This proposal aims to define strain count—the number of unique strains each bacterial species stably maintains in an individual—in healthy and IBD microbiomes and to further investigate the functional impact of strain count in disease. We will quantify strain count by employing a high- throughput culturing technique to isolate and sequence thousands of gut bacterial isolates for all culturable species in a breadth-focused manner and validate our breadth-focused quantifications by using a depth- focused approach to intensely sequence more genomes from ten of the most common gut species. For our depth-sequencing, we will use gnotobiotic mice fed different diets to enrich for low abundance strains. This experimental approach allows us to increase the efficiency by which we capture the strains of a particular species and achieve a more accurate quantification of strain count. Aim 1—Based on our preliminary findings, we anticipate that there is a limited number of strains each species can maintain in the gut microbiota and that our method sequences a sufficient number of genomes to quantify strain count. We aim to define strain count in healthy and IBD microbiomes which will allow for higher resolution, functional investigations into microbiome composition in disease. In Aim 2—we will investigate the effect of increasing strain count on colitis severity. We will combine defined communities of strains isolated from an IBD and healthy microbiota in a gnotobiotic T cell transfer colitis model. The defined communities will allow us to specifically increase strain count while holding species diversity stable. By studying the functional role of strain count, we can uncover the potential contributions of microbiome strain-level architecture to the disease process and identify appropriate targets for optimizing FMT for the treatment of IBD.
HHS’ Tracking Accountability in Government Grants System (TAGGS) website provides access to detailed descriptions of grants, loans, aggregated direct payments and other types of financial assistance awarded by the HHS Operating Divisions (OPDIVs) and the Office of the Secretary Staff Divisions (STAFFDIVs).