Multi-omic approaches to exploring the gut microbiome and metabolic dysfunction-associated steatotic liver disease (MASLD) - PROJECT SUMMARY While gut microbial communities are implicated in the development and progression of metabolic dysfunction- associated steatotic liver disease (MASLD), formerly known as non-alcoholic fatty liver disease, significant gaps remain in translating this knowledge into patient benefits. Prior studies have focused on species-level data and bacterial presence, largely overlooking strain-level heterogeneity, gut viral contributions, microbial transcription, and biochemical activity. These limitations hinder our ability to understand microbial mechanisms and ultimately identify therapeutic targets aimed at microbiome modulation. The overall objective of this proposal is to comprehensively investigate gut microbial communities by leveraging the largest compiled cohort to date and using a multi-omic framework to gain deeper insights into microbial genetics and molecular functions in MASLD. This project will integrate metagenomic, metabolomic, and metatranscriptomic analyses to explore microbial functional roles in MASLD and identify metabolic pathways linked to disease etiopathogenesis. Specifically, we will conduct a metagenomic systematic review and meta-analysis of internal and publicly available datasets to identify harmonized strain-level and viral signatures associated with MASLD. This will allow us to assess strain- specific differences and viral determinants in the gut microbiome that may contribute to MASLD, uncovering key microbial factors involved in disease modulation. Further, we will leverage stool metagenomic, metabolomic, and metatranscriptomic collections from the MICRObiome Among Nurses (MICRO-N), a subcohort from the Nurses’ Health Study II, which includes decades of longitudinal dietary and lifestyle data, and confirm findings using the Human Microbiome and Cardiometabolic Health Consortium (MicroCardio) and publicly available datasets. Using novel yet established computational tools, we will generate a prioritized list of microbial candidates based on transcriptional and metabolic activity, focusing on functional relevance rather than simple presence or abundance. To validate these findings, we will conduct in vitro experiments to characterize microbial metabolism and provide mechanistic insights, facilitating the discovery of microbial enzymes involved in MASLD metabolism and highlighting novel bacterial contributions to disease etiopathogenesis. This integrated multi-omic and experimental approach will greatly advance MASLD microbiome research, laying the foundation for future translational studies, including gnotobiotic experiments and clinical trials to validate microbially-driven targets contributing to MASLD. This project aligns with the National Institute of Diabetes and Digestive and Kidney Diseases' (NIDDK) mission and vision, addressing the rising burden of MASLD, which is closely linked to obesity and increases the risk of hepatocellular carcinoma (HCC). Under the mentorship of a multidisciplinary research advisory committee, the candidate will develop expertise in multi-omic computational methodologies and microbiology, establishing a unique independent research program positioning the candidate to lead future interdisciplinary investigations in microbiome science and chronic liver disease epidemiology.
