John Franklin Rawls

John Franklin Rawls

Associate Professor of Molecular Genetics and Microbiology

Our research uses multiple complementary approaches to understand how host-microbe interactions in the intestine regulate digestive physiology and energy balance. First, my lab uses genetic, gnotobiotic, and in vivo imaging approaches to determine how commensal microorganisms (microbiota) interact with vertebrate hosts to regulate their nutrition and immunity, as well as the mechanisms underlying assembly of intestinal microbial communities. We utilize the zebrafish as a host model in which host and microbial cells can be viewed and manipulated a transparent living vertebrate. We have pioneered the use of germ-free or gnotobiotic zebrafish to investigate the roles of microorganisms in vertebrate biology, and we are using these methods to investigate the bacterial signals and responsive host pathways that regulate host immunity, nutrition, and gene expression. Second, my laboratory is utilizing the zebrafish system to investigate mechanisms underlying the formation and function of adipose tissues. We have developed methods for in vivo imaging of zebrafish adipose tissue, and we are currently using these techniques to explore the developmental and environmental processes regulating adipose tissue growth and physiology. In both of these fields, we have effectively used zebrafish and mice to model key aspects of human physiology and pathophysiology, and to gain new insights into underlying mechanisms.

Appointments and Affiliations

  • Associate Professor of Molecular Genetics and Microbiology
  • Associate 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, 2001
  • B.S. Emory University, 1996

Awards, Honors, and Distinctions

  • 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

  • MGM 593: Research Independent Study
  • UPGEN 778B: University Program in Genetics and Genomics Biological Solutions Module Il

In the News

Representative Publications

  • King, J; Foster, J; Davison, JM; Rawls, JF; Breton, G, Zebrafish Transcription Factor ORFeome for Gene Discovery and Regulatory Network Elucidation., Zebrafish, vol 15 no. 2 (2018), pp. 202-205 [10.1089/zeb.2017.1486] [abs].
  • Minchin, JEN; Rawls, JF, Elucidating the role of plexin D1 in body fat distribution and susceptibility to metabolic disease using a zebrafish model system., Adipocyte, vol 6 no. 4 (2017), pp. 277-283 [10.1080/21623945.2017.1356504] [abs].
  • Phelps, D; Brinkman, NE; Keely, SP; Anneken, EM; Catron, TR; Betancourt, D; Wood, CE; Espenschied, ST; Rawls, JF; Tal, T, Microbial colonization is required for normal neurobehavioral development in zebrafish., Scientific Reports, vol 7 no. 1 (2017) [10.1038/s41598-017-10517-5] [abs].
  • Kelly, MS; Surette, MG; Smieja, M; Pernica, JM; Rossi, L; Luinstra, K; Steenhoff, AP; Feemster, KA; Goldfarb, DM; Arscott-Mills, T; Boiditswe, S; Rulaganyang, I; Muthoga, C; Gaofiwe, L; Mazhani, T; Rawls, JF; Cunningham, CK; Shah, SS; Seed, PC, The Nasopharyngeal Microbiota of Children With Respiratory Infections in Botswana., Pediatric Infectious Disease Journal, vol 36 no. 9 (2017), pp. e211-e218 [10.1097/inf.0000000000001607] [abs].
  • Lickwar, CR; Camp, JG; Weiser, M; Cocchiaro, JL; Kingsley, DM; Furey, TS; Sheikh, SZ; Rawls, JF, Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells., PLoS biology, vol 15 no. 8 (2017) [10.1371/journal.pbio.2002054] [abs].