About

I am an Associate 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 recovery after disturbance, safe and productive food systems, and human health. To address growing challenges, such as the presence of emerging contaminants and increasing climate variability, I believe that interdisciplinary collaboration and community engagement are 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. As a Project Scientist at UCSD’s Scripps Institution for Oceanography and School of Medicine, my research is highly interdisciplinary, examining complex relationships between microbiomes, the environment, and human health. In addition to research, I coordinate a Research Experience and Mentoring program designed to build a robust mentoring environment and facilitate hands-on training for local undergraduate students interested in pursuing STEM careers.

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

Education

  • University of Maryland: PhD in Plant Science
  • Haverford College: Bachelor of Arts in Biology

Professional Experience

University of California San Diego School of Medicine

La Jolla, CA (2019 - Present)

Associate Project Scientist (2023-Present) and Assistant Project Scientist (2019-2023) with Dr. Jack Gilbert.

  • Supervise and conduct research related to 1) the human microbiome in nutrition, disease, and mental health; 2) microbial ecology of the built environment; and 3) host-microbe-environment interactions in aquaculture and agriculture
  • Mentor undergraduate and graduate students, postdoctoral fellows, and laboratory staff
  • Manage data systems for storage, remote computing, and bioinformatic workflows
  • Develop interdisciplinary educational programming focused on microbiomes.
  • Diversity Coordinator for UCSD Microbiome and Metagenomics Center, part of the NIH Nutrition for Precision Health Consortium
  • Director of Research Experience and Mentoring (REM) program – includes writing grant proposals, managing the budget, recruiting and selecting candidates, leading professional development programming, and evaluating program efficacy

Bioinformatics Consultant

La Jolla, CA (2019 - 2022)

  • Create custom databases from publicly available genomic data
  • Provide expertise for microbiome-related product development

University of Maryland School of Public Health

College Park, MD (2018 - 2019)

Assistant Program Manager for CONSERVE.

  • Facilitated collaboration, communication, data sharing for team located across multiple institutions.
  • Directed CONSERVE Summer Internship Program for undergraduate students, including overseeing candidate selection, leading professional development seminars, and evaluating program efficacy.
  • Organized and led 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 gene 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 with Dr. Eric Brown

  • 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.

Select Publications

Full list: Google scholar

  • R. Diner, S.M. Allard, J.A. Gilbert (2024). Host-associated microbes mitigate the negative impacts of aquatic pollution. mSystems 0:e00868-24. publication online.
  • K. Schulkers Escalante, S.S. Bai-Tong, S.M. Allard, G. Ecklu-Mensah, C. Sanchez, S.J. Song, J. Gilbert, L. Bode, P. Dorrestein, R. Knight, D.J. Gonzalez, S.A. Leibel, S.L. Leibel (2024). The impact of breastfeeding on the preterm infant’s microbiome and metabolome: a pilot study. Pediatric Research. publication online.
  • E. Kunselman, D. Manrique, C. Burge, S. Allard, Z. Daniel, G. Mitta, B. Petton, J. Gilbert (2024). Temperature and microbe mediated impacts of the San Diego Bay ostreid herpesvirus (OsHV-1) microvariant on juvenile Pacific oysters. Sustainable Microbiology 1:1. publication online.
  • E. Kunselman, S. Allard, C. Burge, B. Marshman, A. Frederick, J. Gilbert (2024). Metagenome-assembled genome of withering syndrome causative agent, ‘Candidatus Xenohaliotis californiensis’, from endangered white abalone (Haliotis sorenseni). Microbial Resource Announcements. publication online.
  • B.K. Linnehan, S.M. Kodera, S.M. Allard, E.C. Brodie, C. Allaband, R. Knight, H.L. Lutz, M.C. Carroll, J.M. Meegan, E.D. Jensen, J.A. Gilbert (2024). Evaluation of the safety and efficacy of fecal microbiota transplantations in bottlenose dolphins (Tursiops truncatus) using metagenomic sequencing. Journal of Applied Microbiology 135:2. publication online.
  • E. Kunselman, K. Wiggin, R.E. Diner, J.A. Gilbert, S.M. Allard (2024). Microbial threats and sustainable solutions for molluscan aquaculture. Sustainable Microbiology. publication online.
  • N.R. Gottel, M.S. Hill, M.J. Neal, S.M. Allard, K. Zengler, J.A. Gilbert (2024). Biocontrol in built environments to reduce pathogen exposure and infection risk. The ISME Journal 18:1. publication online.
  • M.I. Dothard, S.M. Allard, J.A. Gilbert (2023). The effects of hormone replacement therapy on the microbiomes of postmenopausal women. Climacteric: 1-11. publication online.
  • R.E. Diner, A. Zimmer-Faust, E. Cooksey, S. Allard, S.M. Kodera, E. Kunselman, Y. Garodia, A.E. Allen, J. Griffith, J.A. Gilbert (2023). Host and water microbiota are differentially linked to potential human pathogen accumulation in oysters. Applied and Environmental Microbiology 89. publication online.
  • S.M. Kodera, A. Sharma, C. Martino, M. Dsouza, M. Grippo, H.L. Lutz, R. Knight, J.A. Gilbert, C. Negri, S.M. Allard (2023). Microbiome response in an urban river system is dominated by seasonality over wastewater treatment upgrades. Environmental Microbiome 18:10. publication online.
  • L. Zhu, S. Chattopadhyay, O.E. Akanbi, S. Lobo, S. Panthi, L. Malayil, H.A. Craddock, S.M. Allard, M. Sharma, K.E. Kniel, E.F. Mongodin, P.C. Chiu, A. Sapkota, A.R. Sapkota (2023). Biochar and zero-valent iron sand filtration simultaneously removes contaminants of emerging concern and Escherichia coli from wastewater effluent. Biochar 5:1. publication online.
  • M.S. Thoemmes, S.M. Allard, J.A. Gilbert (2022). Embracing Healthy Microbiomes, Including Access to Nature and Pets. The Bridge 52:3. publication online.
  • L. Malayil, P. Ramachandran, S. Chattopadhyay, S. Allard, A. Bui, J. Butron, M. Callahan, H. Craddock, R. Murray, C. East, M. Sharma, K. Kniel, S. Micallef, F. Hashem, C. Gerba, S. Ravishankar, S. Parveen, E. May, E. Handy, P. Kulkarni, B. Anderson-Coughlin, S. Craighead, S. Gartley, A. Vanore, R. Duncan, D. Foust, J. Haymaker, W. Betancourt, L. Zhu, E. Mongodin, A. Sapkota, M. Pop, A.R. Sapkota (2022). Variations in bacterial communities and antibiotic resistance genes across diverse recycled and surface water irrigation sources in the Mid-Atlantic and Southwestern United States: A CONSERVE two-year field study. Environmental Science & Technology 56. publication online.
  • M.E. Morgado, C.L. Hudson, S. Chattopadhyay, K. Ta, C. East, N. Purser, S. Allard, M.D. Ferrier, A.R. Sapkota, M. Sharma, R. Rosenberg Goldstein (2022). The effect of a first flush rainwater harvesting and subsurface irrigation system on E. coli and pathogen concentrations in irrigation water, soil, and produce. Science of the Total Environment 843. publication online.
  • M.E. Gerdes, R. Cruz-Cano, S. Solaiman, S. Ammons, S.M. Allard, A.R. Sapkota, S.A. Micallef, R.E. Rosenberg Goldstein (2022). Impact of irrigation water type and sampling frequency on Microbial Water Quality Profiles required for compliance with U.S. Food Safety Modernization Act Produce Safety Rule standards. Environmental Research 205:1. publication online.
  • M. Priyadarshini, G. Navarro, D.J. Reiman, A. Sharma, K. Xu, K. Lednovich, C.R. Manzella, M.W. Khan, M. Salas Garcia, S. Allard, B. Wicksteed, G.E. Chlipala, B. Szynal, B. Penalver Bernabe, P.M. Maki, R.K. Gill, G.H. Perdew, J. Gilbert, Y. Dai, B.T. Layden (2022). Gestational insulin resistance is mediated by the gut microbiome-indoleamine 2,3-dioxygenase axis. Gastroenterology. publication online.
  • C.L. Acheamfour, S. Parveen, F. Hashem, M. Sharma, M.E. Gerdes, E.B. May, K. Rogers, J. Haymaker, R. Duncan, D. Foust, M. Taabodi, E.T. Handy, C. East, R. Bradshaw, S. Kim, S.A. Micallef, M.T. Callahan, S. Allard, B. Anderson-Coughlin, S. Craighead, S. Gartley, A. Vanore, K.E. Kniel, S. Solaiman, A. Bui, R. Murray, H.A. Craddock, P. Kulkarni, R.E. Rosenberg Goldstein, A.R. Sapkota (2021). Levels of Salmonella enterica and Listeria monocytogenes in Alternative Irrigation Water Vary Based on Water Source on the Eastern Shore of Maryland. Microbiology Spectrum 9:2. publication online.
  • C. Marotz, P. Belda-Ferre, F. Ali, P. Das, S. Huang, K. Cantrell, L. Jiang, C. Martino, R.E. Diner, G. Rahman, D. McDonald, G. Armstrong, S. Kodera, S. Donato, G. Ecklu-Mensah, N. Gottel, M.C. Salas Garcia, L.Y. Chiang, R.A. Salido, J.P. Shaffer, K. Sanders, G. Humphrey, G. Ackermann, N. Haimeinen, K.L. Beck, H. Kim, A.P. Carrieri, L. Parida, Y. Vazquez Baeza, F.J. Torriani, R. Knight, J.A. Gilbert, D.A. Sweeney, S.M. Allard (2021). SARS-CoV-2 detection status associates with bacterial community composition in patients and the hospital built environment. Microbiome 9:1. publication online.
  • J. Minich, F. Ali, C. Marotz, P. Belda-Ferre, L. Chiang, J.P. Shaffer, C.S. Carpenter, D. McDonald, J.A. Gilbert, S.M. Allard, E.E. Allen, R. Knight, D.A. Sweeney, A.D. Swafford (2021). Feasibility of using alternative swabs and storage solutions for paired SARS-CoV-2 detection and microbiome analysis in the hospital environment. Microbiome 9:25. publication online.
  • B.L. Anderson-Coughlin, S. Craighead, A. Kelly, S. Gartley, A. Vanore, G. Johnson, C. Jiang, J. Haymaker, C. White, D. Foust, R. Duncan, C. East, E.T. Handy, R. Bradshaw, R. Murray, P. Kulkarni, M.T. Callahan, S. Solaiman, W. Betancourt, C. Gerba, S.M. Allard, S. Parveen, F. Hashem, S.A. Micallef, A. Sapkota, A.R. Sapkota, M. Sharma, K. Kniel (2021). Enteric Viruses and Pepper Mild Mottle Virus Show Significant Correlation in Select Mid-Atlantic Agricultural Waters. Applied and Environmental Microbiology 87:13. publication online.
  • S.M. Allard, M.T. Costa, A.N. Bulseco, L.G.E. Wilkins, C. Hassenrück, V. Helfer, K. Zengler, M. Zimmer, N. Erazo, J. L. Mazza Rodrigues, N. Duke, V.M.M. Melo, I. Vanwonterghem, H. Junca, H.M. Makonde, D.J. Jiménez, T.C.L. Tavares, M. Fusi, D. Daffonchio, R.S. Peixoto, A.S. Rosado, J.A. Gilbert, J. Bowman (2020). Introducing the Mangrove Microbiome Initiative: Identifying microbial research priorities and approaches to better understand, protect, and rehabilitate mangrove ecosystems. mSystems 5. publication online.
  • J. Chopyk, D.J. Nasko, S. Allard, A. Bui, M. Pop, E.F. Mongodin, A.R. Sapkota (2020). Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond. Environmental Microbiome 15:18. publication online.
  • L. Zhu, C. Jiang, S. Panthi, S.M. Allard, A.R. Sapkota, A. Sapkota (2020). Impact of high precipitation and temperature events on distribution of emerging contaminants in surface water in the Mid-Atlantic, United States. Science of the Total Environment 755. publication online.
  • S. Solaiman, S.M. Allard, M.T. Callahan, C. Jiang, E. Handy, C. East, J. Haymaker, A. Bui, H. Craddock, R. Murray, P. Kulkarni, B. Anderson-Coughlin, S. Craighead, S. Gartley, A. Vanore, R. Duncan, D. Foust, M. Taabodi, A. Sapkota, E. May, F. Hashem, S. Parveen, K. Kniel, M. Sharma, A. R. Sapkota, and S.A. Micallef (2020). A longitudinal assessment of Escherichia coli, total coliform, Enterococcus and Aeromonas spp. dynamics in alternative irrigation water sources: A CONSERVE study. Applied Environmental Microbiology 86. publication online.
  • S. Kim, R. Bradshaw, P. Kulkarni, S.M. Allard, P. Chiu, A.R. Sapkota, K.E. Kniel, M.J. Newell, E.T. Handy, C. East, M. Sharma (2020). Zero-valent iron filtration reduces Escherichia coli in surface water and leafy green growing environments. Frontiers in Sustainable Food Systems 4:112. publication online.
  • M. Sharma, E. Handy, C. East, S. Kim, C. Jiang. M.T. Callahan, S.M. Allard, S. Micallef, S. Craighead, B. Anderson, S. Gartley, A. Vanore, K.E. Kniel, J. Haymaker, R. Duncan, C. White, D. Foust, F. Hashem, S. Parveen, E. May, P. Kulkarni, A. Bui, H. Craddock, R.T. Murray, A.R. Sapkota (2020). Prevalence of Salmonella spp. and Listeria monocytogenes in Non-traditional Irrigation Waters in the Mid-Atlantic United States is Affected by Water Type, Season, and Recovery Method. PLOS ONE 15:3. publication online.
  • S. Allard, A. Ottesen, S. Micallef (2020). Rainfall induces temporary shifts in epiphytic bacterial communities of cucumber and tomato fruit. Nature Scientific Reports 10. publication online.
  • J. Chopyk, D. Nasko, S. Allard, M.T. Callahan, A. Bui, A.M. Ferelli, S. Chattopadhyay, E. Mongodin, M. Pop, S. Micallef, A.R. Sapkota (2020). Metagenomic analysis of bacterial and viral assemblages from a freshwater creek and irrigated field reveals temporal and spatial dynamics. Science of the Total Environment 706. publication online.
  • J. Chopyk, D. Nasko, S. Allard, A. Bui, T. Treangen, M. Pop, E. Mongodin, A.R. Sapkota (2019). Comparative metagenomic analysis of microbial taxonomic and functional variations in untreated surface and reclaimed waters used in irrigation applications. Water Research 169. publication online.
  • 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.

    Other Media

  • S. Allard, J.A. Gilbert, B. Penalver Bernabe. Biotechniques. Blog: Overcoming sex bias in clinically relevant microbiome research 22 Dec 2020.
  • S. Allard and J.A. Gilbert. Biotechniques. Blog: Taking stock 8 months in: refocusing our microbiome lab for SARS-CoV-2 research 9 Dec 2020.
  • S. Allard. Biotechniques. Blog: Benefits of online and hybrid conferences for public health, climate impact and inclusivity. 6 Aug 2020.
  • S. Allard. Biotechniques. Blog: Refocusing our microbiome lab for SARS-CoV-2 research. 21 Apr 2020.
  • S. Allard and J.A. Gilbert. Biotechniques. Blog: Navigating the landscape of research-based careers with a PhD. 28 Nov 2019.
  • S. Allard. University of Maryland School of Public Health News. “There Is No Bad Water:” Scholars Learn About Food, Energy, and Water Systems in Israel and the West Bank. 18 Apr 2019.