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Decoding Microbial Diversity in the Human Gut Microbiome

Award Number: R35GM151045
ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
OPDIV: NIH
AWARD CLASS: DISCRETIONARY
AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)
PERIOD OF PERFORMANCE START DATE: 08/01/2023
PERIOD OF PERFORMANCE END DATE: 05/31/2028

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Decoding Microbial Diversity in the Human Gut Microbiome - PROJECT SUMMARY / ABSTRACT The ecological concept of diversity is deceptively simple: what organisms are present and how are they distributed. The advent of high-throughput sequencing enabled more than a decade of observational human microbiome studies; however, these studies frequently established correlation, but not causation, between microbial diversity and health. Through mechanistic research, I and others have shown the significance of strain variation, i.e. phenotypic and genotypic variation within a species, in host-microbiome interactions; however, most of our understanding comes from a limited range of model organisms which poorly represent the large diversity observed in the human gastrointestinal tract. Rather than view strain diversity as a limitation and caveat in microbiome research, my group takes a fundamentally different approach: we exploit it as a tool for mechanistic research. The mission of my research program is to understand how our microbial communities shape human health and physiology. We do this through leveraging computational biology and big data with wet lab experiments including gnotobiotic animal models to balance reductionism and biological relevance. The research themes in this proposal ask discrete questions about the interface of host and microbe but are unified in their approach of using naturally occurring strain variation coupled to comparative genomics as a tool for gene discovery in a reference panel of >300 genome sequenced bacterial isolates. Theme I will ask a fundamental question: can we leverage 10 years of publicly available data to rationally design functional synthetic communities? These consortia will act as both tools for understanding the assembly and function of complex communities, and will have translational applications as alternatives to human fecal transplant therapy. Theme II will focus on deconvoluting the shared host and microbial metabolism of bile acids (BAs), a family of compounds with broad relevance to infectious and autoimmune diseases, cancer, and metabolic health. Despite their importance, the microbial metabolic pathways of BA metabolism and their phylogenetic distribution are poorly characterized. Through comprehensive analysis of our strain library and synthetic communities derived thereof, we will determine the origins of biologically significant BAs. Understanding these trans-species pathways will address an important question: can we predict the metabolic output of a community based on the sum of its parts? Theme III addresses an urgent question in medicine: how does microbial strain-variation contribute to interpersonal variation in drug response? We are now working on a new class of important orally administered drugs which were not previously known to interact with the gut microbiome: antimalarials. Building on preliminary data demonstrating off-target strain-variable antibacterial effects, we will characterize how bacterial interactions with antimalarials affect therapeutic efficiency. These themes have a shared and unified goal: to generate both resources and fundamental understanding of host-microbe interactions leading to translational applications.


Issue Date FY	Funding FY	Legal Entity Name	Legal Entity Address	Legal Entity City	Legal Entity State	Legal Entity Zip Code	Legal Entity COUNTY	Legal Entity COUNTRY	Assistance Listing	Award Code	Budget Year	Action Date	Action Type	Action Amount

Issue Date FY: 2025 ( Subtotal = $377,103 )
2025	2025	THE PENNSYLVANIA STATE UNIVERSITY	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Biomedical Research and Research Training	000	3	5/16/2025	NON-COMPETING CONTINUATION	$377,103
														Subtotal = $377,103

Issue Date FY: 2024 ( Subtotal = $377,983 )
2024	2024	THE PENNSYLVANIA STATE UNIVERSITY	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Biomedical Research and Research Training	000	2	5/27/2024	NON-COMPETING CONTINUATION	$377,983
														Subtotal = $377,983

Issue Date FY: 2023 ( Subtotal = $383,000 )
2023	2023	PENNSYLVANIA STATE UNIVERSITY, THE	201 OLD MAIN	UNIVERSITY PARK	PA	16802	CENTRE	USA	Biomedical Research and Research Training	000	1	7/22/2023	NEW	$383,000
														Subtotal = $383,000

Grand Total All Awards = $1,138,086

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Decoding Microbial Diversity in the Human Gut Microbiome

Award Number: R35GM151045

ORGANIZATION: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES

OPDIV: NIH

AWARD CLASS: DISCRETIONARY

AWARD ACTIVITY TYPE: SCIENTIFIC/HEALTH RESEARCH (INCLUDES SURVEYS)

PERIOD OF PERFORMANCE START DATE: 08/01/2023

PERIOD OF PERFORMANCE END DATE: 05/31/2028

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