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Ellie Margolis, MD, PhD
Ellie Margolis, MD, PhD

Ellie Margolis, MD, PhD

Assistant Member, St. Jude Faculty



MD - Emory School of Medicine, Atlanta GA
PhD - Emory University, Atlanta GA
ScB - Brown University, Providence RI

Research Interests

  • Microbiome dynamics in immunocompromised and neonate hosts
  • Ecological processes that determine the composition of human microbiota
  • Commensal microbes that limit Clostridium difficile toxin expression
  • Techniques to improve the reliability of microbiome dynamical analysis
  • Development of assays to determine microbiome resilience and response to disturbances

Selected Publications

Funk A, Jia Q, Janke L, Crawford A, Iverson A, Rosch J, Emmons J, Savage C, Glasgow H, Hayden R, Margolis E, Pisharath H. Isolation and characterization of a novel alpha-hemolytic Streptococcus spp. from the oral cavity and blood of septicemic periparturient immunodeficient mice. Comp Med Sep 11, 2023.

Margolis EB, Alfaro GM, Sun Y, Dallas RH, Allison KJ, Ferrolino J, Ross HS, Davis AE, Jia Q, Turner P, Mackay V, Morin CE, Triplett BM, Klein EJ, Englund JA, Tang L, Hayden RT. Microbiota predict infections and acute graft-versus-host disease after pediatric allogeneic hematopoietic stem cell transplantation. J Infect Dis 228(5):627-636, 2023.

Berryhill BA, Gil-Gil T, Manuel JA, Smith AP, Margolis E, Baquero F, Levin BR. What's the matter with MICs: Bacterial nutrition, limiting resources, and antibiotic pharmacodynamics. Microbiol Spectr 11(3): e0409122, 2023.

Kohler CM, Quintanar Alfaro AG, Hayden RT, Margolis EB. Real-time quantitative PCR method for detection and quantification of Clostridioides difficile cells and spores. J Microbiol Methods 196; 106458, 2022.

Margolis EB, Hakim H, Dallas RH, Allison KJ, Ferrolino J, Sun Y, Pui CH, Yao J, Chang TC, Hayden RT, Jeha S, Tuomanen EI, Tang L, Rosch JW, Wolf J. Antibiotic prophylaxis and the gastrointestinal resistome in paediatric patients with acute lymphoblastic leukaemia: A cohort study with metagenomic sequencing analysis. Lancet Microbe 2(4):e159-e167, 2021.

Dao TH, Alsallaq R, Parsons JB, Ferrolino J, Hayden RT, Rubnitz JE, Rafiqullah IM, Robinson DA, Margolis EB, Rosch JW, Wolf J. Vancomycin heteroresistance and clinical outcomes in bloodstream infections caused by coagulase-negative staphylococci. Antimicrob Agents Chemother 64(11), 2020.

Rowe HM, Livingston B, Margolis E, Davis A, Meliopoulos VA, Echlin H, Schultz-Cherry S, Rosch JW. Respiratory bacteria stabilize and promote airborne transmission of influenza A virus. mSystems 5(5), 2020.

Cortez V, Boyd DF, Crawford JC, Sharp B, Livingston B, Rowe HM, Davis A, Alsallaq R, Robinson CG, Vogel P, Rosch JW, Margolis E, Thomas PG, Schultz-Cherry S. Astrovirus infects actively secreting goblet cells and alters the gut mucus barrier. Nat Commun 11(1):2097, 2020.

Wolf J, Margolis E. Effect of antimicrobial stewardship on outcomes in patients with cancer or undergoing hematopoietic stem cell transplantation. Clin Infect Dis 71(4):068-970, 2019.

Cortez V, Margolis E, Schultz-Cherry S. Astrovirus and the microbiome. Curr Opin Virol 37:10-15, 2019.

Davis A, Kohler C, Alsallaq R, Hayden R, Maron G, Margolis E. Improved yield and accuracy for DNA extraction in microbiome studies with variation in microbial biomass. Biotechniques 66(6): 285-290, 2019.

Margolis E, Rosch JW. Fitness landscape of the immune compromised favors the emergence of antibiotic resistance. ACS Infect Dis 4(9):1275-1277, 2018.

Cortez V, Canal E, Dupont-Turkowsky JC, Quevedo T, Albujar C, Chang TC, Salmon-Mulanovich G, Guezala-Villavicencio MC, Simons MP, Margolis E, Schultz-Cherry S, Pacheco V, Bausch DG. Identification of Leptospira and Bartonella among rodents collected across a habitat disturbance gradient along the Inter-Oceanic Highway in the southern Amazon Basin of Peru. PLoS One 13(10): e0205068, 2018.

Golob JL, Margolis E, Hoffman N, Fredricks DN. Evaluating the Accuracy of Amplicon–Based Microbiome Computational Pipelines on Simulated Human Gut Microbial Communities. BMC Bioinformatics 18:283, 2017. PMID 28558684

Margolis E, Yates A, Levin BR. The ecology of nasal colonization of Streptococcus pneumoniae, Haemophilus influenzae and Staphylococcus aureus. BMC Microbiology 10:59, 2010. PMID 20178591

Margolis E. Hydrogen peroxide mediated interference competition by Streptococcus pneumoniae has no significant effect on Staphylococcus aureus nasal colonization of neonatal rats. Journal of Bacteriology 191:571-5, 2009. PMID 19011027

Handel A, Margolis E, Levin BR. Exploring the role of the immune response in preventing antibiotic resistance. Journal of Theoretical Biology 256:655-62, 2009. PMID 19056402

Margolis E, Levin BR. Within–Host Evolution for the Invasiveness of Commensal Bacteria: an Experimental Study of Bacteremias Resulting from Haemophilus influenzae Nasal Carriage. Journal of Infectious Diseases 196:1068-75, 2007. PMID 17763330

Last update: November 2023