EES Seminar: Integrating Multi-Omics to Understand Microbial Risk, Minjae Kim, University of Kentucky

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The misuse of antibiotics is a well-established driver of resistance, but less attention has been given to the role of disinfectants. In the first part of this seminar, I will present findings showing that exposure to benzalkonium chloride (BAC), a widely used disinfectant, promotes cross-resistance to clinically relevant antibiotics. Using long-term bioreactor experiments, metagenomics, and adaptive evolution assays, we demonstrated that BAC exposure selects for opportunistic pathogens such as Pseudomonas aeruginosa and drives resistance through integrative conjugative elements, efflux pumps, and mutations in polymyxin resistance genes. In the second part, I will highlight research comparing the gut microbiomes of children from Maputo, Mozambique, and Atlanta, USA. Shotgun metagenomic analyses revealed that children in Maputo harbor higher loads of enteric pathogens and antibiotic resistance genes, while Atlanta children showed greater microbial diversity and higher abundances of commensal species. These differences underscore how sanitation, hygiene, and environmental conditions influence early-life microbiome development and long-term health outcomes. Together, these studies illustrate how anthropogenic stressors, from chemical disinfectants to inadequate sanitation, shape microbial community structure, function, and health risk.

Minjae Kim, Ph.D. is an Assistant Professor in Civil Engineering at the University of Kentucky. His research focuses on developing innovative biotechnological solutions to improve environmental and human health, spanning microbial bioremediation, antibiotic resistance, the preterm lung microbiome, floodwater microbial risks, and soil carbon sequestration. He integrates -omics, molecular biology, and engineering approaches to address these global challenges.