Daniel Daehyun Kim (Fed)

Daniel joined the Complex Microbial Systems Group at NIST in 2026 as a NIST-NRC Research Fellow. His research focuses on biosurveillance of environmental pathogens from an ecological perspective, complementing conventional approaches based on direct pathogen detection. He investigates how interactions between pathogens and indigenous microbial communities, along with physicochemical conditions, influence pathogen persistence and distribution. His work aims to develop data-driven frameworks that leverage microbiome information to characterize and anticipate pathogen behavior, with applications spanning natural and built environments.

Before joining NIST, Daniel studied microbial ecology in natural and engineered systems—including subsurface oil reservoirs, coastal marine environments, and wastewater treatment systems—to understand microbial interactions and develop biotechnological approaches for energy and environmental applications. His work focused on identifying microbial guilds capable of reducing low concentrations of nitrous oxide (N₂O), a byproduct of biological nitrogen removal processes. Following his Ph.D., he joined the University of California, Berkeley as a postdoctoral researcher, where he investigated the strain-sharing dynamics of pathogens and antimicrobial resistance (AMR) in communities with limited access to water, sanitation, and hygiene (WASH) infrastructure. His research provided scientific evidence to inform public health strategies aimed at reducing disease transmission and limiting the spread of antibiotic resistance.

Selected Publications  

1. Kim DD, Swarthout JM, Worby CJ, Chieng B, Mboya J, Earl AM, Njenga SM, Pickering AJ. 2025. Contaminated drinking water facilitates Escherichia coli strain-sharing within households in urban informal settlements. Nature Microbiology, 10, 1198–1209
2. Kim DD, Han H, Yun T, Song M, Terada A, Laureni M, Yoon S. 2022. Identification of nosZ-expressing microorganisms consuming trace N₂O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales. ISME Journal, 16(9), 2087-2098.
3. Kim DD*, Wan L*, Cao X, Klisarova D, Gerdzhikov D, Zhou Y, Song C, Yoon S. 2021. Metagenomic insights into co-proliferation of Vibrio spp. and dinoflagellates Prorocentrum during a spring algal bloom in the coastal East China Sea. Water Research, 204, 117625. *equal contributions
4. Kim DD, Park D, Yoon H, Yun T, Song MJ, Yoon S. 2020. Quantification of nosZ genes and transcripts in activated sludge microbiomes with novel group-specific qPCR methods validated with metagenomic analyses. Water Research, 185, 116261.
5. Kim DD, O'Farrell C, Toth CR, Montoya O, Gieg LM, Kwon TH, Yoon S. 2018. Microbial community analyses of produced waters from high-temperature oil reservoirs reveal unexpected similarity between geographically distant oil reservoirs. Microbial biotechnology, 11, 788-96

• NRC Research Associateship Award (2025)
• Featured Research, UC Berkeley College of Engineering News (Link) (2025)
• Featured Research, Hanbitsa (People Who Made Korea Shine) (2025)
• Featured Research, Hanbitsa (People Who Made Korea Shine) (2022)
• Best Paper Award, BrainKorea21 FOUR Center (2021)
• Best Poster Presentation Award, 2021 International Meeting of the Microbiological Society of Korea (2021)
• Outstanding Abstract Award, 2017 ASM Microbe (2017)
• Social Innovation Idea Competition – 1^st Place, BrainKorea21 FOUR Center (2017)
• Value Engineering (VE) Competition for University Students – 2^nd Place, Korea Environment Corporation (2015)