Research

Our laboratory, the Environmental–Human Microbiome Lab (EHM Lab), investigates the diversity, ecophysiology, and functions of microorganisms at the interface of human health and the environment. We focus on both fundamental discoveries and translational applications of microbiomes across multiple ecosystems. Our research plan is organized into three interconnected themes:

Theme 1. Archaea in the Human Microbiome: Diverse Niches and Novel Functions

Archaea represent an underexplored component of the human microbiome. We study methanogens (Methanobacteriaceae), ammonia-oxidizing archaea (Thaumarchaeota), and potential symbiotic DPANN lineages (e.g., Woesearchaeota) across human body sites such as the skin, respiratory tract, and gastrointestinal system. Using culture-based and culture-independent approaches, we aim to reveal their ecological roles, metabolic interactions, and potential impacts on human health. Particular emphasis is placed on identifying novel archaeal taxa, such as previously unknown members of the Nitrososphaeraceae, and evaluating their contribution to immune modulation and inflammation control.

Theme 2. Culturing the Uncultured: Culture-Based Discovery of Microbiome Function

Most microbial diversity remains uncultured, limiting functional understanding. We combine genome-resolved metagenomics with targeted cultivation to recover novel human- and environment-associated microbes. Transcriptomic signals guide the prioritization of strains for cultivation, and functional traits are validated through laboratory experiments. By expanding the repertoire of cultured microbes, we can reveal key microbial interactions, validate predicted metabolic pathways, and bridge the gap between metagenomic predictions and experimental validation.

Theme 3. Microbial Regulation of Carbon and Nitrogen Cycles: Engineering Microbiomes for Greenhouse Gas Mitigation

Environmental microbes drive critical biogeochemical cycles, including those of carbon, nitrogen, sulfur, and phosphorus. Our lab isolates and characterizes nitrifying microbes (AOA, AOB, comammox, NOB) and metabolically versatile methanotrophs to investigate their ecophysiology under environmentally relevant conditions. We aim to harness these microbes for microbial community engineering—developing strategies to regulate methane and nitrous oxide emissions, mitigate greenhouse gas release, and synthesize value-added bioproducts. This integrative approach links microbial ecology to applied biotechnology, with relevance to agriculture, wastewater treatment, industrial bioprocessing, and climate change mitigation.