Kim, Minjae

Research Overview

At Kim Lab Research Group, we are dedicated to exploring the fascinating world of microorganisms: bacteria, archaea, and viruses. These tiny life forms, collectively known as microbiota, represent the most extensive reservoir of biodiversity on our planet. They play a pivotal role in driving essential biogeochemical cycles that sustain life and can influence or even govern diseases in human, animals, and plants.

Our Focus:

Our research endeavors revolve around the study of microbial communities across diverse environmental samples. Our aim is to pioneer innovative biotechnological solutions that have a positive impact on both the environment and human health. In pursuit of this goal, my research group focuses on critical microbial systems, including but not limited to:

Bioremediation: We investigate methods to mitigate environmental pollutants, such as disinfectants, through microbial processes.
Wastewater Treatment: Our research addresses the improvement of wastewater treatment technologies, contributing to cleaner and safer water resources.
Microbial Nitrogen Cycles: We explore the complex dynamics of microbial nitrogen cycles in soils, crucial for nutrient availability in ecosystems.
OPPPs in Healthcare: We study opportunistic premise plumbing pathogens (OPPPs) in healthcare settings, including UK healthcare hospitals.
Microbial Communities in Floodwaters: We examine microbial communities in floodwaters, with implications for disaster preparedness and response.

Our Approach:

To tackle these intricate research subjects, we adopt an interdisciplinary approach. Our methodology incorporates a range of cutting-edge techniques, including multi-omics approaches (such as metagenomics and proteomics), molecular biology, and engineering. This integrative approach allows us to delve deep into the world of microorganisms and uncover insights that can drive positive change.

Research Projects

Healthcare-associated infections (HAI):

Recent attention in infection control guidelines has focused on the prevention and management of opportunistic premise plumbing pathogens (OPPPs) within healthcare water systems. Emerging research has highlighted the presence of OPPPs like Legionella pneumophila, Pseudomonas aeruginosa, and Mycobacterium avium within plumbing environments. Notably, certain pathogens not initially present in source water have been found to thrive in biofilms forming on outlet devices (such as tap faucets, showers, and drains), leading to outbreaks of antimicrobial resistance (AMR) healthcare-associated infections (HAIs). The primary aim is to assess the prevalence of OPPPs and other opportunistic pathogens within UK healthcare center water systems by using multi-omics techniques. This investigation aims to propose potential engineering solutions (e.g., antimicrobial polymer coating) or hygiene practices (e.g., disinfection) to mitigate these concerns.

Computational methods:

Read processing, Assembly, Binning (reconstructing metagenome-assembled genomes; MAGs), read mapping, annotations, phylogenetic trees, etc.

Software:

Trim Galore, FastQC, Nonpareil, SortMeRNA, Qiime2, IDBA-UD, MetaBAT2, CheckM, MASH, R, GTDBtk, dRep, bowtie2, blast, Bakta, RAxML-NG, IQ-TREE, Samtools, MMseqs2, etc.

Software availability: all tools will be publicly available or will be developed as necessary. We will use multiple conda environments for each tool on the HPC.

Personnel:

Faculty: John Bauer, Jason Unrine, Minjae Kim

Microbial Communities in Floodwaters:

Following last year’s catastrophic flood in Kentucky, my research group is interested in investigating identifying both known and unknown microbial risks in floodwaters by adopting bioinformatics. Integration of next-generation sequencing might revolutionize how microbial risks in floodwaters are assessed. Identification of viable microbial risks on building materials could reshape architecture and urban planning practices. Effective disinfection strategies could enhance post-flood response protocols. This interdisciplinary approach may foster cross-field collaborations and influence global research agendas. Overall, our work could significantly contribute to a more holistic and effective mitigation of climate change's multifaceted impacts.

Computational methods:

Read processing, Assembly, Binning (reconstructing metagenome-assembled genomes; MAGs), read mapping, annotations, phylogenetic trees, etc.

Software:

Trim Galore, FastQC, Nonpareil, SortMeRNA, Qiime2, IDBA-UD, MetaBAT2, CheckM, MASH, R, GTDBtk, dRep, bowtie2, blast, Bakta, RAxML-NG, IQ-TREE, Samtools, MMseqs2, etc.

Software availability: all tools will be publicly available or will be developed as necessary. We will use multiple conda environments for each tool on the HPC.

Personnel:

Faculty: Minjae Kim, Lauren Cagle, William Andrews, Leigh-Anne Krometis, Jason Unrine

Microbial Nitrogen Cycles:

The global nitrogen (N) cycle has been disrupted by fertilizer use and atmospheric deposition, leading to increased research on nitrate (NO₃^-) fate. Nitrate is lost through leaching and denitrification, especially in saturated conditions. Traditionally, soil organic carbon (SOC) was believed to be the sole electron donor for nitrate reduction in saturated soil. However, recent discoveries have shown that iron(II) oxidation is also linked to nitrate reduction, occurring beyond saturated soils. Soils with perched water tables (PWTs), like Fragipans, pose challenges due to unpredictable temporary saturation. Fragipans, low in organic carbon and nitrogen but rich in Fe(III) minerals, may serve as hot spots for NO₃^- reduction via Fe(II) oxidation. Managing Fragipan soils, which cover 10 million ha in the contiguous United States, is a national priority. Understanding NO₃^- fate in Fragipans is essential for improved N fertilizer recommendations.

Computational methods:

Read processing, Assembly, Binning (reconstructing metagenome-assembled genomes; MAGs), read mapping, annotations, phylogenetic trees, metatranscriptomic analysis, etc.

Software:

Trim Galore, FastQC, Nonpareil, SortMeRNA, Qiime2, IDBA-UD, MetaBAT2, CheckM, MASH, R, GTDBtk, dRep, bowtie2, blast, Bakta, RAxML-NG, IQ-TREE, Samtools, MMseqs2, featureCounts, DESeq2, etc.

Software availability: all tools will be publicly available or will be developed as necessary. We will use multiple conda environments for each tool on the HPC.

Personnel:

Faculty: Andrea Erhardt, Christopher Matocha, Minjae Kim, Christopher Shepard