I am an Assistant Project Scientist in the Gilbert Lab, housed between the University of California San Diego School of Medicine and Scripps Intitution of Oceanography. I am interested in exploring how we can harness microbiome research to support environmental sustainability as well as safe and productive food systems. To address growing challenges, such as the presence of emerging contaminants and increasing climate variability, I believe that interdisciplinary collaboration and stakeholder engagement will be essential.

I began my research career as an undergraduate, investigating the pollination efficiency and diversity of native bees on watermelon fields in the Mid-Atlantic. After receiving my B.A. in Biology from Haverford College in 2009, I began an ORISE fellowship in the Division of Microbiology at the FDA’s Center for Food Safety and Applied Nutrition. At FDA, I participated in environmental sampling for foodborne pathogens, evaluation of a food safety biological control agent, and optimization of Salmonella detection methods from environmental samples. As a graduate student in Plant Science at the University of Maryland, I studied the influence of farming practices and environmental conditions on plant microbiomes in the complex agricultural environment. As part of the CONSERVE team based in the UMD School of Public Health, I worked as a postdoctoral fellow and Assistant Program Manager, primarily working to characterize the microbiomes of nontraditional irrigation water sources including surface water and reclaimed wastewater. I actively participated in farmer and community outreach and directed the CONSERVE Summer Intern Program.

In addition to science, I am passionate about music, cooking, hiking, and my scruffy rescue dog, Joni.

The illustration of me that you see above was made by friend Meredith Jensen.


  • University of Maryland: PhD in Plant Science, GPA 3.96.
  • Haverford College: Bachelor of Arts in Biology, GPA 3.5.

Professional Experience

University of California San Diego School of Medicine

La Jolla, CA (2019 - Present)

Assistant Project Scientist with Dr. Jack Gilbert.

  • Supervise and conduct research related to environmental, medical, and built environment microbiomes.
  • Develop interdisciplinary educational programming focused on microbiomes.

University of Maryland School of Public Health

College Park, MD (2018 - 2019)

Assistant Program Manager for CONSERVE.

  • Facilitate collaboration, communication, data sharing for team located across multiple institutions.
  • Direct CONSERVE Summer Internship Program for undergraduate students, including overseeing candidate selection, leading professional development seminars, and evaluating program efficacy.
  • Organize and lead interdisciplinary CONSERVE Scholars educational trip to Israel/West Bank.

University of Maryland School of Public Health

College Park, MD (2016 - 2018)

Postdoctoral Fellow with Dr. Amy Sapkota.

  • Coordinated and participated in on-farm sampling of nontraditional irrigation water in the Mid-Atlantic.
  • Described water microbiomes through DNA extractions, PCR assays, and bioinformatic analysis of 16S rRNA and shotgun sequencing data.
  • Collaborated extensively with multidisciplinary team located across multiple institutions and states.

University of Maryland Department of Plant Science

College Park, MD (2013 - 2016)

Graduate Research Assistant to Dr. Shirley Micallef.

  • Assessed the influence of on-farm conditions on the microbial ecology of tomato and cucumber plants in the agricultural environment through standard microbiological analysis as well as 16S rRNA sequencing and bioinformatic analysis.
  • Completed dissertation: Bacterial communities of the tomato phyllosphere: response to soil amendment application, rainfall, and insect visitation.

FDA Center for Food Safety and Applied Nutrition

College Park, MD (2009 - 2013)

ORISE Fellow in the Division of Microbiology

  • Evaluated reservoirs of Salmonella in agricultural environments on Virginia’s Eastern Shore.
  • Compared efficacy of molecular and microbiological methods of Salmonella detection from farm- fresh and store-bought tomatoes.
  • Conducted field, growth chamber, and high tunnel studies to investigate the potential of Paenibacillus alvei TS-15 as a food safety biological control agent.

Bryn Mawr College Department of Biology

Bryn Mawr, PA (2008 - 2009)

Research Assistant to Dr. Neal Williams.

  • Conducted fieldwork investigating the relationship between bee biodiversity and pollination function on watermelon plants at several farms in the Delaware Valley.


  • S. Allard and S. Micallef (2019). The Plant Microbiome: Diversity, Dynamics, and Role in Food Safety (Chapter 11). In: Biswas, D. and Micallef, S., editors. Safety and Practice for Organic Food. Academic Press. ISBN: 9780128120606.
  • S. Allard, M.T. Callahan, A. Bui, A.M. Ferelli, J. Chopyk, E.F. Mongodin, S.A. Micallef, A.R. Sapkota (2019). Creek to Table: Investigating the movement of fecal indicators, bacterial pathogens, and total bacterial communities through creek water irrigation of kale and radishes. Science of the Total Environment 666: 461-471. publication online.
  • S. Allard, S. Solaiman, M.T. Callahan, A. Bui, H. Craddock, J. Haymaker, D. Foust, E. Smyth, E.F. Mongodin, F. Hashem, E. May, S.A. Micallef, A.R. Sapkota (2019). Quenching by sodium thiosulfate does not influence 16S rRNA gene sequencing profiles of reclaimed water from three sites in Maryland, United States. Environmental Research 172: 296-300. publication online.
  • S. Panthi, G. Raspanti, S. Allard, A. Bui, M.T. Callahan, H. Craddock, R. Murray, C. East, E. Handy, B. Anderson, S. Craighead, S. Gartley, A. Vanore, E. May, M. Taabodi, R. Duncan, D. Foust, J. Haymaker, W. Betancourt, A.R. Sapkota, M. Sharma, K. Kniel, S.A. Micallef, F. Hashem, C. Gerba, S. Ravishankar, M. Pop, S. Parveen, E. May, A. Sapkota (2019). Pharmaceuticals, herbicides, and disinfectants in agricultural water sources. Environmental Research 174: 1-8. publication online.
  • J. Haymaker, M. Sharma, S. Parveen, F. Hashem, E.B. May, E.T. Handy, C. White, C. East, R. Bradshaw, S.A. Micallef, M.T. Callahan, S. Allard, B. Anderson, S. Craighead, S. Gartley, A. Vanore, K.E. Kniel, S. Solaiman, A. Bui, R.T. Murray, H.A. Craddock, P. Kulkarni, D. Foust, R. Duncan, M. Taabodi, A.R. Sapkota (2019). Prevalence of Shiga-toxigenic and Atypical Enteropathogenic Escherichia coli in Untreated Surface Water and Reclaimed Water in the Mid-Atlantic U.S. Environmental Research 172: 630-636. publication online.
  • S. Allard, A. Ottesen, E. Brown, S. Micallef (2018). Insect exclusion limits variation in tomato flower and fruit microbiomes. Journal of Applied Microbiology 125(6): 1749-1760. publication online.
  • J.S. Meisel, D.J. Nasko, B. Brubach, V.C. Espinoza, J. Chopyk, H. Corrada-Bravo, M. Fedarko, J. Ghurye, K. Javkar, N.D. Olson, N. Shah, S.M. Allard, A.L. Bazinet, N.H. Bergman, A. Brown, J.G. Caporaso, S. Conlan, J. DiRuggiero, S.P. Forry, N.A. Hasan, J. Kralj, P.M. Luethy, D.K. Milton, B. Ondov, S. Preheim, S. Ratnayake, S.M. Rogers, M.J. Rosovitz, E.G. Sakowski, N.O. Schliebs, D.D. Sommer, K.L. Ternus, G. Uritskiy, S.X. Zhang, M. Pop, T. Treangen (2018). Current progress and future opportunities in applications of bioinformatics for biodefense and pathogen detection: Report from the Winter Mid-Atlantic Microbiome Meet-up, College Park, MD January 10th, 2018. Microbiome 6: 197. publication online.
  • J. Chopyk, S. Allard, D.J. Nasko, A. Bui, E.F. Mongodin, A.R. Sapkota (2018). Agricultural freshwater pond supports diverse and dynamic bacterial and viral populations. Frontiers in Microbiology 9(792). publication online.
  • S. Allard, C. Walsh, A. Wallis, A. Ottesen, E. Brown, S. Micallef (2016). Solanum lycopersicum (tomato) hosts robust phyllosphere and rhizosphere bacterial communities when grown in soil amended with various organic and synthetic fertilizers. Science of the Total Environment 573: 555-563. publication online.
  • R. Bell, J. Zheng, E. Burrows, S. Allard, C. Wang, C. Keys, D. Melka, E. Strain, Y. Luo, M. Allard, S. Rideout, E. Brown (2015). Ecological prevalence, genetic diversity, and epidemiological aspects of Salmonella isolated from tomato agricultural regions of the Virginia Eastern Shore. Frontiers in Microbiology 6(415). publication online.
  • S. Allard, A. Enurah, E. Strain, R. Blodgett, P. Millner, S. Rideout, E. Brown, J. Zheng (2014). In situ evaluation of Paenibacillus alvei in reducing carriage of Salmonella Newport on whole tomato plants. Applied and Environmental Microbiology 80(13): 3842:3849. publication online.
  • Y. Luo, C. Wang, S. Allard, E. Strain, M. Allard, E. Brown, and J. Zheng (2013). Draft Genome Sequences of Paenibacillus alvei. Genome Announcements 1(5): e00673-13. publication online.
  • A. Ottesen, A. Gonzalez, J. White, J. Pettengill, C. Li, S. Allard, S. Rideout, M. Allard, T. Hill, P. Evans, E. Strain, S. Musser, R. Knight, E. Brown (2013). Baseline survey of the anatomical microbial ecology of an important food plant: Solanum lycopersicum (tomato). BMC Microbiology 13(1): 114. publication online.
  • J. Zheng, S. Allard, S. Reynolds, P. Millner, G. Arce, R. Blodgett, E. Brown (2013). Colonization and Internalization of Salmonella enterica in Tomato Plants. Applied and Environmental Microbiology 79: 2494-502. publication online.