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Plant-Soil Microbiome Interactions
Plant-Soil Microbiome Interactions
Microbiomes (i.e., microbial communities and their genes) in agriculture play important roles from supporting crop production to impacting food safety and spoilage. In efforts to promote 'beneficial' microbial diversity along the food chain, we are investigating factors that shape microbiomes of fresh produce, specific impacts of crop management practices (e.g., using food waste compost and biochar soil amendments), and prospective applications in biocontrol and value-added products.
Genomics in Food Safety
Genomics in Food Safety
Whole genome sequencing initiatives to trace contamination of foodborne pathogens has provided novel opportunities for food safety control. We process big data on the genomic diversity of foodborne pathogens with artificial intelligence (AI) and machine learning (ML) technologies to uncover genetic signatures of foodborne pathogens for applications to enhance molecular surveillance frameworks.
Emerging Antimicrobial Resistance
Emerging Antimicrobial Resistance
Antimicrobial resistance (AMR) in food and agriculture systems is an increasingly important public health threat. We are exploring farm-scale transmission of the genetic elements involved and the potential for co-selection of AMR due to intrinsic soil contaminants, such as heavy metals, to inform strategies to mitigate risks.
Crosscutting Themes
Crosscutting Themes
Additional collaborations focus on microbial interactions in response to various processing technologies and novel antimicrobials used to support food safety and quality.
Field and Lab Highlights
Field and Lab Highlights
Urban farm sampling. Qinyue Zeng (left) and Derek Konsen (right)
Leafy green processing for microbial analysis
Soil data collection. Left to right: Mairui Gao, Autumn Salcedo, Qingyue Zeng, Maya Mulligan
Screening bacteria for antibiotic resistance patterns
Vineyard sampling. James Jeffrey (left) and Erin Harrelson (right)
Grape processing for microbial analysis
Micro-fermentations
Isolated yeasts
Publications
Publications
2025
Timilsina M, Chundru D, Pradhan A, Blaustein RA, Ghanem M. (2025). Benchmarking metagenomic pipelines for the detection of foodborne pathogens in simulated microbial communities. Journal of Food Protection 100583. https://doi.org/10.1016/j.jfp.2025.100583
Gao M, Pradhan AK, Blaustein RA. (2025). Genomic diversity of Cronobacter sakazakii across the food system to consumers at the global scale. International Journal of Food Microbiology 441:111335. https://doi.org/10.1016/j.ijfoodmicro.2025.111335
Blaustein RA, Smith JE, Toro M, Pachepsky YA, Stocker MD. (2025). Water metagenomes reflect physicochemical water quality throughout a model agricultural pond. Frontiers in Microbiology 16:153509. https://doi.org/10.3389/fmicb.2025.1535096
Feng S, Ramachandran P, Blaustein RA, Pradhan A. (2025). Bioinformatics combined with machine learning unravels differences among environmental, seafood, and clinical isolates of Vibrio parahaemolyticus. Frontiers in Microbiology 16:1549260. https://doi.org/10.3389/fmicb.2025.1549260
Proctor DM, Sansom SE, Deming C, Conlan S, Blaustein RA, Atkins TK, NISC Comparative Sequencing Program, Dangana T, Fukuda C, Thotapalli L, Kong HH, Lin MY, Hayden MK, Segre JA. (2025). Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes. Nature. https://doi.org/10.1038/s41586-025-08608-9
Gilbert-Eckman A, Gao M, Blaustein RA, Tikekar R. (2025). Cold atmospheric plasma treatment induces oxidative stress and alters microbial community profile in the leaves of sweet of basil (Ocimum basilicum var. Kiera) plant. Journal of Food Science 90:e70066. https://ift.onlinelibrary.wiley.com/doi/10.1111/1750-3841.70066
2024
Ma P, Jia X, Gao M, Yi Z, Tsai S, He Y, Zhen D, Blaustein RA, Wang Q, Wei C. (2024). Innovative food supply chain through spatial computing technologies: A review. Comprehensive Reviews in Food Science and Food Safety 23:e70055. https://doi.org/10.1111/1541-4337.70055
Zeng Q, Lam K, Salcedo A, Tikekar RV, Micallef SA, Blaustein RA. (2024). Effects of organic soil amendments on antimicrobial-resistant bacteria in urban agricultural environments. Journal of Food Protection 80 (10): 100344. https://doi.org/10.1016/j.jfp.2024.100344
Wu H, Liu Z, Zhang Y, Gao B, Li Y, He X, Sun J, Choe U, Chen P, Blaustein R, Yu L. (2024). Chemical composition of turmeric (Curcuma longa L.) ethanol extract and its antimicrobial activities and free radical scavenging capacities. Foods 13(10):1550. https://doi.org/10.3390/foods13101550
Stocker MD, Smith JE, Pachepsky YA, Blaustein RA. (2024). Fine-scale spatiotemporal variations in bacterial community diversity in agricultural pond water. Science of the Total Environment 915, 170143. https://doi.org/10.1016/j.scitotenv.2024.170143
2023
Blaustein RA, Shen Z, Saheb Kashaf S, Lee-Lin S, Conlan S, ... Notarangelo LD, Kong HH, Segre JA. (2023). Expanded microbiome niches in RAG-deficient patients. Cell Reports Medicine 4, 101205. https://doi.org/10.1016/j.xcrm.2023.101205
2022
Shen J, McFarland AG, Blaustein RA, Rose LJ, Perry-Dow KA, Moghadam AA, Hayden MK, Young VB, Hartmann EM. (2022). An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics. Microbiome 10(1):206. https://doi.org/10.1186/s40168-022-01412-x
Data & Code in Published Research
Data & Code in Published Research
Lab Repository: https://github.com/rablaustein
Other Contributions:
https://github.com/skinmicrobiome/Blaustein_RAG_2023
https://github.com/hartmann-lab/Toothbrush_Microbiome_Project
https://github.com/hartmann-lab/Rhodococcus_pangenome
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