John Franklin Rawls

John Franklin Rawls

Professor of Molecular Genetics and Microbiology

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.

Appointments and Affiliations

  • Professor of Molecular Genetics and Microbiology
  • Professor in Medicine
  • Member of the Duke Cancer Institute

Contact Information

  • Office Location: 323A CARL Building Box 3580, 213 Research Drive, Durham, NC 27710
  • Office Phone: (919) 613-7212
  • Email Address:
  • Websites:


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

Awards, Honors, and Distinctions

  • Fellow. American Academy of Microbiology. 2021
  • Fellow. American Association for the Advancement of Science. 2016
  • Kavli Fellow. Kavli Frontiers of Science Program. 2009
  • Pew Scholar in the Biomedical Sciences. Pew Charitable Trust. 2008
  • Mentored Research Scientist Development Award. National Institutes of Health. 2006
  • Ruth L. Kirschstein Individual National Research Service Award. National Institutes of Health. 2002
  • Spencer T. and Ann W. Olin Medical Scientist Fellow. Washington University School of Medicine. 2001
  • Victor Hamburger Prize in Developmental Biology. Washington University School of Medicine. 2001

Courses Taught

  • BIOLOGY 728F: University Program in Genetics and Genomics Biological Solutions Module VI
  • CMB 778F: University Program in Genetics and Genomics Biological Solutions Module VI
  • MGM 593: Research Independent Study
  • MGM 778F: University Program in Genetics and Genomics Biological Solutions Module VI
  • UPGEN 778A: University Program in Genetics and Genomics Biological Solutions Module I
  • UPGEN 778E: University Program in Genetics and Genomics Biological Solutions Module V
  • UPGEN 778F: University Program in Genetics and Genomics Biological Solutions Module VI

In the News

Representative Publications

  • Yan, C; Yang, Q; Zhang, S; Millar, DG; Alpert, EJ; Do, D; Veloso, A; Brunson, DC; Drapkin, BJ; Stanzione, M; Scarfò, I; Moore, JC; Iyer, S; Qin, Q; Wei, Y; McCarthy, KM; Rawls, JF; Dyson, NJ; Cobbold, M; Maus, MV; Langenau, DM, Single-cell imaging of T cell immunotherapy responses in vivo., J Exp Med, vol 218 no. 10 (2021) [10.1084/jem.20210314] [abs].
  • Kelly, MS; Plunkett, C; Yu, Y; Aquino, JN; Patel, SM; Hurst, JH; Young, RR; Smieja, M; Steenhoff, AP; Arscott-Mills, T; Feemster, KA; Boiditswe, S; Leburu, T; Mazhani, T; Patel, MZ; Rawls, JF; Jawahar, J; Shah, SS; Polage, CR; Cunningham, CK; Seed, PC, Non-diphtheriae Corynebacterium species are associated with decreased risk of pneumococcal colonization during infancy., Isme J (2021) [10.1038/s41396-021-01108-4] [abs].
  • Wen, J; Mercado, GP; Volland, A; Doden, HL; Lickwar, CR; Crooks, T; Kakiyama, G; Kelly, C; Cocchiaro, JL; Ridlon, JM; Rawls, JF, Fxr signaling and microbial metabolism of bile salts in the zebrafish intestine., Science Advances, vol 7 no. 30 (2021) [10.1126/sciadv.abg1371] [abs].
  • McCann, JR; Bihlmeyer, NA; Roche, K; Catherine, C; Jawahar, J; Kwee, LC; Younge, NE; Silverman, J; Ilkayeva, O; Sarria, C; Zizzi, A; Wootton, J; Poppe, L; Anderson, P; Arlotto, M; Wei, Z; Granek, JA; Valdivia, RH; David, LA; Dressman, HK; Newgard, CB; Shah, SH; Seed, PC; Rawls, JF; Armstrong, SC, The Pediatric Obesity Microbiome and Metabolism Study (POMMS): Methods, Baseline Data, and Early Insights., Obesity (Silver Spring), vol 29 no. 3 (2021), pp. 569-578 [10.1002/oby.23081] [abs].
  • Chen, C; Gu, Y; Philippe, J; Zhang, P; Bachman, H; Zhang, J; Mai, J; Rufo, J; Rawls, JF; Davis, EE; Katsanis, N; Huang, TJ, Acoustofluidic rotational tweezing enables high-speed contactless morphological phenotyping of zebrafish larvae., Nature Communications, vol 12 no. 1 (2021) [10.1038/s41467-021-21373-3] [abs].