Scott Handley, PhD

Scott Handley, PhD

Professor, Pathology & Immunology



  • BS: Missouri State University, Springfield, MO (1998)
  • PhD: Washington University, St. Louis, MO (2006)

Research Interests

For the past 15 years, I have been involved in projects devoted to the advanced understanding of how microbial ecology and invasive pathogens operate and impact human health. My view of how microbial ecology can contribute to disease comes in two forms. The first is more traditional in which the introduction of an invasive organism (pathogen) negatively impacts either the host or the other members of the microbial community. The second form is when an imbalance in the community itself leads to disease (dysbiosis). My overall research goal is to better classify and test how alterations in community membership and function contribute to disease. To do this, I utilize high-throughput sequencing technologies, computational tools and community ecology analysis. Most of this research occurs in the mammalian gastrointestinal tract, however, lessons learned should be broadly applicable to studies at other sites.

Selected Publications

PubMed Search

Gosmann C, Anahtar MN, Handley SA, Farcasanu M, Abu-Ali G, Bowman BA, Padavattan N, Desai C, Droit L, Moodley A, Dong M, Chen Y, Ismail N, Ndung’u T, Ghebremichael MS, Wesemann DR, Mitchell C, Dong KL, Huttenhower C, Walker BD, Virgin HW, Kwon DS. Lactobacillus-Deficient Cervicovaginal Bacterial Communities Are Associated with Increased HIV Acquisition in Young South African Women. Immunity. 2017 Jan 9. pii: S1074-7613(16)30519-2. doi: 10.1016/j.immuni.2016.12.013. PMID: 28087240
Handley SA, Desai C, Zhao G, Droit L, Monaco CL, Schroeder AC, Nkolola JP, Norman ME, Miller AD, Wang D, Barouch DH, Virgin HW. SIV Infection-Mediated Changes in Gastrointestinal Bacterial Microbiome and Virome Are Associated with Immunodeficiency and Prevented by Vaccination. Cell Host Microbe. 2016 Mar 9;19(3):323-35. PMID: 26962943.
Monaco CL, Gootenberg DB, Zhao G, Handley SA, Ghebremichael MS, Lim ES, Lankowski A, Baldridge MT, Wilen CB, Flagg M, Norman JM, Keller BC, Luévano JM, Wang D, Boum Y, Martin JN, Hunt PW, Bangsberg DR, Siedner MJ, Kwon DS, Virgin HW. Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome. Cell Host Microbe. 2016 Mar 9;19(3):311-22. PMID: 26962942.
Park S, Buck MD, Desai C, Zhang X, Loginicheva E, Martinez J, Freeman ML, Saitoh T, Akira S, Guan JL, He YW, Blackman MA, Handley SA, Levine B, Green DR, Reese TA, Artyomov MN, Virgin HW. Autophagy Genes Enhance Murine Gammaherpesvirus 68 Reactivation from Latency by Preventing Virus-Induced Systemic Inflammation. Cell Host Microbe. 2016 Jan 13;19(1):91-101. PMID: 26764599.
Barouch DH, Alter G, Broge T, Linde C, Ackerman ME, Brown EP, Borducchi EN, Smith KM, Nkolola JP, Liu J, Shields J, Parenteau L, Whitney JB, Abbink P, Ng’ang’a DM, Seaman MS, Lavine CL, Perry JR, Li W, Colantonio AD, Lewis MG, Chen B, Wenschuh H, Reimer U, Piatak M, Lifson JD, Handley SA, Virgin HW, Koutsoukos M, Lorin C, Voss G, Weijtens M, Pau MG, Schuitemaker H. Protective efficacy of adenovirus/protein vaccines against SIV challenges in rhesus monkeys. Science. 2015 Jul 17;349(6245):320-4. PMID: 26138104
Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DP, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015 Jan 29;160(3):447-60. PMID: 25619688.
Abbink P, Maxfield LF, Ng’ang’a D, Borducchi EN, Iampietro MJ, Bricault CA, Teigler JE, Blackmore S, Parenteau L, Wagh K, Handley SA, Zhao G, Virgin HW, Korber B, Barouch DH. Construction and Evaluation of Novel Rhesus Monkey Adenovirus Vaccine Vectors. J Virol. 2014 Nov 19. PMID: 25410856
Taube, S., Kolawole, A.O., Hohne, M., Wilkinson, J.E., Handley, S.A., Perry, J.W., Thackray, L.B., Akkina, R., Wobus, C.E. A mouse model of human norovirus. Mbio 2013; Jul 16;4(4). PMCID: PMC3735125.
Handley S.A., Thackray L.B., Zhao G., Presti R., Miller A.D., Droit L., Abbink P., Maxfield L.F., Kambal A., Duan E., Stanley K., Kramer J., Macri S.C., Permar S.R., Schmitz J.E., Mansfield K., Brenchley J.M., Veazey R.S., Stappenbeck T.S., Wang D., Barouch D.H., Virgin H.W. Pathogenic simian immunodeficiency virus infection is associated with expansion of the enteric virome. Cell. 2012; Oct 12;151(2):253-66.
Loh, J., G. Zhao, C. A. Nelson, P. Coder, L. Droit, Handley, S.A., L. S. Johnson, P. Vachharajani, H. Guzman, R. B. Tesh, D. Wang, D. H. Fremont, and H. W. Virgin. Identification and Sequencing of a Novel Rodent γ-herpesvirus that Establishes Acute and Latent Infection in Laboratory Mice. J Virol. 2010. J Virol. Mar;85(6):2642-56.
Handley, S.A. and V.L. Miller. General and specific host responses to bacterial infection in Peyer’s patches: A role for matrix metalloproteinase 3 during S. typhimurium infection. Mol Microbiol. 2007 Apr;64(1):94-110.
Lawlor, M.L., Handley, S.A. and V.L. Miller. 2006. Comparison of the host response to wild type and cps mutant Klebsiella pneumonia infections. Infect Immun. 2006 Sep; 74(9):5402-7.
Handley, S.A., Dube, P.H. and V.L. Miller. 2006. Histamine signaling through the H2 receptor in the Peyer’s patches is important for controlling Yersinia enterocolitica infection. Proc. Natl. Acad. Sci. USA. Jun 13;103(24): 9268-73.
Handley, S.A., Newberry, R.D. and V.L. Miller. 2005. Yersinia enterocolitica invasion-dependent and invasion-independent mechanisms of systemic dissemination. Infect. Immun. Dec;73(12):8453-5.
Hambuch, T.M., Handley, S.A., Ellis, B., Chamberlin, J., Romero, S., and R. Regnery. 2004. Population genetic analysis of Bartonella bacilliformis isolates from areas of Peru where Carrion’s disease is endemic and epidemic. J. Clin. Microbiol. Aug;42(8):3675-80.
Alsmark, C.M., Frank, A.C., Karlberg, E.O., Legault, B., Ardell, D.H., Canbäck, B., Eriksson, A., Näslund, A.K., Handley, S.A., Huvet, M., La Scola, B., Holmberg, M., and S.G.E. Andersson. 2004. The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae. Proc. Natl. Acad. Sci. USA. Jun 29;101(26):9716-21.
Dube, P.H., Handley, S.A., Lewis, J., and V.L. Miller. 2004. Protective role of IL-6 during Yersinia enterocolitica infection is mediated through the modulation of inflammatory cytokines. Infect. Immun. Jun;72(6):3561-70.
 Handley, S.A., Dube, P.H., Revell, P.A., and V.L. Miller. 2004. Characterization of oral Yersinia enterocolitica infection in three different strains of inbred mice. Infect. Immun. Mar;72(3):1645-56.
Cummings, M.P., Handley, S.A., Myers, D.S., Reed, D.L., Rokas, A., and K. Winka. 2003. Comparing bootstrap and posterior probability values in the four-taxon case. Syst. Biol. Aug; 52(4):477-87.
Ehrenborg, C., Handley, S., Ellis, B., Mills, J., and M. Holmberg. 2003. Bartonella grahamii infecting rodents display high genetic diversity over short geographic distances. Ann. NY Acad. Sci. Jun; 990:233-5.
Dube, P.H., Handley, S.A., Revell, P.A., and V.L. Miller. 2003. The rovA mutant of Yersinia enterocolitica displays differential degrees of virulence depending on the route of infection. Infect. Immun. Jun; 71(6):3512-20.
Handley, S.A., and R.L. Regnery. 2000. Differentiation of pathogenic Bartonella species by IRS-PCR. J. Clin. Micro. Aug;38(8):3010-5.

Lab Phone: 314-479-3830
Office Location: CSRB, Room 8851