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Ecosystem Health and Microbiomes

Ecosystems are essential to our survival and welfare, yet extensive human activities have drastically impaired their health. As a crucial component of ecosystems, microbes are victims of these adverse effects, but they could also be savers. In the LEAPH Lab, we aim to generate innovative, sustainable solutions to protect and nurture ecosystems, particularly soil and surface water. Our approach is to study the microbiome (i.e., all the microbes in a given environment) as a system. We employ field sampling, metagenomics, metabolomics, machine learning, and experimental manipulation to understand how environmental stresses caused by human activities interact with microbiomes. We further translate this knowledge into practical solutions to enhance ecosystem health and protect the environment.

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Food Safety and Pathogens

Foodborne pathogens pose a heavy burden on human health and the food industry globally. However, generalizable strategies to control foodborne pathogens in the agricultural and food systems remain limited. We tackle this challenge by integrating environmental surveillance, microbial ecology, and population genomics. We use environmental sampling to monitor foodborne pathogens (chiefly Listeria monocytogenes and Salmonella) in diverse environments and use whole genome sequencing and bioinformatics to identify genetic and environmental factors important to their distribution, transmission, and adaptation. We further develop ecological-informed tools for foodborne pathogen control and outbreak investigation.

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Antimicrobial Resistance in the Environment

Antimicrobial resistance (AMR) is a global health threat. While the environment is an important reservoir, it is an overlooked dimension for AMR. To fill the gap, we study AMR in the environment from two angles: the resistome (i.e., all the AMR genes in microbial communities) and the AMR of foodborne pathogens. We employ field sampling, high-throughput sequencing, population genetics tools, data analysis methods, and experimental evolution to understand ecological and evolutionary mechanisms underlying the emergence, persistence, and dissemination of AMR. With the mechanistic knowledge, we inform science-based decisions and environmental actions to mitigate the threats from AMR to public health.