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John F. Rawls

James B. Duke Distinguished Professor of Molecular Genetics and Microbiology
Molecular Genetics and Microbiology
323A CARL Building, Box 3580, Durham, NC 27710
323A CARL Building Box 3580, 213 Research Drive, Durham, NC 27710

Overview


We seek to understand how the intestinal microbiome contributes to vertebrate physiology and disease. To that end, we leverage complementary zebrafish and mouse models to study the integrative physiology of host-microbiome interactions. This work has identified novel and conserved mechanisms by which intestinal bacteria regulate dietary fat metabolism and systemic innate immunity. We also apply genomic approaches in these animal models to understand the transcriptional regulatory pathways utilized by the intestinal epithelium to mediate host responses to the microbiome. Using this approach, we have identified mechanisms of transcriptional and chromatin regulation that have been conserved during vertebrate evolution and also contribute to modern human diseases such as the inflammatory bowel diseases, obesity, and diabetes. To further advance our understanding of obesity pathophysiology, we developed the zebrafish as a model system for studying adipose tissues and identifying new environmental and genetic regulators of adiposity. We are also engaged in translational research in humans and animal models to define microbial and metabolic determinants of obesity and efficacy of weight loss intervention. Grounded in comparative and integrative physiology, our research program has been effective in discovering ancient mechanisms of host-microbiome interaction that are conserved across animal taxa and contribute to the etiology of modern human diseases. These insights are advancing our understanding of host-microbiome relationships in vertebrate physiology and identifying novel therapeutic targets for human diseases ranging from inflammatory bowel disease to obesity to neurological disorders.

Current Appointments & Affiliations


James B. Duke Distinguished Professor of Molecular Genetics and Microbiology · 2023 - Present Molecular Genetics and Microbiology, Basic Science Departments
Professor of Molecular Genetics and Microbiology · 2020 - Present Molecular Genetics and Microbiology, Basic Science Departments
Professor in Medicine · 2020 - Present Medicine, Gastroenterology, Medicine
Professor of Cell Biology · 2022 - Present Cell Biology, Basic Science Departments
Member of the Duke Cancer Institute · 2013 - Present Duke Cancer Institute, Institutes and Centers

In the News


Published June 27, 2023
DNA Barcoding Identifies the Plants a Person Has Eaten
Published May 4, 2023
Duke Awards 44 Distinguished Professorships
Published May 13, 2022
Microbes Help Orchestrate How the Gut Uses its Genes

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Recent Publications


Protein absorption in the zebrafish gut is regulated by interactions between lysosome rich enterocytes and the microbiome.

Journal Article Elife · March 13, 2025 Dietary protein absorption in neonatal mammals and fishes relies on the function of a specialized and conserved population of highly absorptive lysosome-rich enterocytes (LREs). The gut microbiome has been shown to enhance absorption of nutrients, such as ... Full text Link to item Cite

Branched chain amino acid metabolism and microbiome in adolescents with obesity during weight loss therapy.

Journal Article medRxiv · February 4, 2025 BACKGROUND: Towards improving outcomes for adolescents with obesity, we aimed to define metabolic and microbiome phenotypes at baseline and post-weight loss intervention. METHODS: The Pediatric Obesity Microbiome and Metabolism Study enrolled 220 adolescen ... Full text Link to item Cite

Early subclinical stages of the inflammatory bowel diseases: insights from human and animal studies.

Journal Article Am J Physiol Gastrointest Liver Physiol · January 1, 2025 The inflammatory bowel diseases (IBD) occur in genetically susceptible individuals that mount inappropriate immune responses to their microbiota leading to chronic intestinal inflammation. The natural history of IBD progression begins with early subclinica ... Full text Link to item Cite
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Recent Grants


Tri-Institutional Molecular Mycology and Pathogenesis Training Program

Inst. Training Prgm or CMEMentor · Awarded by National Institutes of Health · 2024 - 2029

Gut-intrinsic mechanisms of gut dysmotility in animal models of autism

ResearchPrincipal Investigator · Awarded by Simons Foundation · 2025 - 2028

Microbial regulation of intestinal epithelial gene expression

ResearchPrincipal Investigator · Awarded by National Institute of Diabetes and Digestive and Kidney Diseases · 2024 - 2028

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Education, Training & Certifications


Washington University in St. Louis · 2001 Ph.D.
Emory University · 1996 B.S.